diff --git a/HTAN.model.csv b/HTAN.model.csv index cf42c7aa..bae4f647 100644 --- a/HTAN.model.csv +++ b/HTAN.model.csv @@ -7,13 +7,22 @@ Patient,HTAN patient,,"Component, HTAN Participant ID",,FALSE,Individual Organis File,A type of Information Content Entity specific to OS,,,,FALSE,Information Content Entity,,https://w3id.org/biolink/vocab/DataFile, Filename,Name of a file,,,,TRUE,,,,regex search ^.+\/\S*$ File Format,"Format of a file (e.g. txt, csv, fastq, bam, etc.)","hdf5, bedgraph, idx, idat, bam, bai, excel, powerpoint, tif, tiff, OME-TIFF, png, doc, pdf, fasta, fastq, sam, vcf, bcf, maf, bed, chp, cel, sif, tsv, csv, txt, plink, bigwig, wiggle, gct, bgzip, zip, seg, html, mov, hyperlink, svs, md, flagstat, gtf, raw, msf, rmd, bed narrowPeak, bed broadPeak, bed gappedPeak, avi, pzfx, fig, xml, tar, R script, abf, bpm, dat, jpg, locs, Sentrix descriptor file, Python script, sav, gzip, sdf, RData, hic, ab1, 7z, gff3, json, sqlite, svg, sra, recal, tranches, mtx, tagAlign, dup, DICOM, czi, mex, cloupe, am, cell am, mpg, m, mzML,scn, dcc, rcc, pkc, sf, bedpe",,,TRUE,,,, -CDS Sequencing Template,"CDS compatible template file, includes attributes for Genomic Reference, Library Layout, Data Type, Sequencing Platform, Library Selection Method",,"Component, Filename, File Format, HTAN Data File ID, HTAN Parent Biospecimen ID, CDS Genomic Reference, CDS Library Layout, CDS Data Type, CDS Sequencing Platform, CDS Library Selection Method",,TRUE,,,, -CDS Genomic Reference,One or more characters used to identify the published NCBI genetic sequence that is used as a reference against which other sequences are compared.,,,,TRUE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,str -CDS Library Layout,The read strategy or method that was used for sequencing and analysis of a nucleotide library.,"Paired End, Single Read",,,TRUE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources, -CDS Data Type,"Types of data associated with the content. Fill out Other Data Type Specified, if not on the list.","10x Visium Spatial Transcriptomics, Bulk Methylation-seq, Bulk RNA-seq, Bulk WES, Electron Microscopy, ExSeq, HI-C-seq, RPPA, Imaging, Mass Spectrometry, NanoString GeoMx DSP Spatial Transcriptomics, Other Assay, SRRS Imaging, Slide-seq, scATAC-seq, scDNA-seq, scRNA-seq, Accessory Manifest, Other Data Type Specified",,,TRUE,Publication,,https://dataservice.datacommons.cancer.gov/#/resources,list like -CDS Sequencing Platform,The words used to describe the instrument used to carry out a high-throughput sequencing experiment.,"Illumina Next Seq 500, Illumina Next Seq 550, Illumina Next Seq 2500, Illumina NovaSeq 6000, Illumina MiSeq, 454 GS FLX Titanium, AB SOLiD 4, AB SOLiD 2, AB SOLiD 3, Complete Genomics, Illumina HiSeq X Ten, Illumina HiSeq X Five, Illumina Genome Analyzer II, Illumina Genome Analyzer IIx, Illumina HiSeq 2000, Illumina HiSeq 2500, Illumina HiSeq 4000, Illumina MiSeq, Illumina NextSeq, Ion Torrent PGM, Ion Torrent Proton, Ion Torrent S5, PacBio RS, NovaSeq 6000, NovaSeqS4, Ultima Genomics UG100, Oxford Nanopore minION, GridION, PromethION, PacBio Sequel2, Revio, Illumina NextSeq 1000, Illumina NextSeq 2000, Other, unknown, Not Reported",,,TRUE,Device,,https://dataservice.datacommons.cancer.gov/#/resources, -CDS Library Selection Method,The type of systematic actions performed to select or enrich DNA fragments used in analysis by high-throughput sequencing.,"Random, rRNA Depletion, Other",,,TRUE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources, -CDS Other Data Type Specified,Other types of data associated with the content.,,CDS Data Type,,FALSE,Sequencing,,, +CDS Sequencing Template,"CDS compatible template file, includes attributes for Genomic Reference, Library Layout, Data Type, Sequencing Platform, Library Selection Method",,"Component, Filename, File Format, HTAN Data File ID, HTAN Parent Biospecimen ID, CDS library_id, CDS library_strategy, CDS library_source, CDS library_selection, CDS library_layout, CDS platform, CDS instrument_model, CDS design_description, CDS reference_genome_assembly, CDS custom_assembly_fasta_file_for_alignment, CDS bases, CDS number_of_reads, CDS coverage, CDS avg_read_length, CDS sequence_alignment_software",,TRUE,,,, +CDS library_id,Short unique identifier for the sequencing library.,,,,TRUE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,str +CDS library_strategy,Library strategy,"AMPLICON, ATAC-seq, Bisulfite-Seq, ChIA-PET, ChIP-Seq, CLONE, CLONEEND, CTS, DNase-Hypersensitivity, EST, FAIRE-seq, FINISHING, FL-cDNA, Hi-C, MBD-Seq, MeDIP-Seq, miRNA-Seq, MNase-Seq, MRE-Seq, ncRNA-Seq, OTHER, POOLCLONE, RAD-Seq, RIP-Seq, RNA-Seq, SELEX, ssRNA-seq, Synthetic-Long-Read, Targeted-Capture, Tethered Chromatin Conformation Capture, Tn-Seq, WCS, WGA, WGS, WXS",,,TRUE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,str +CDS library_source,The Library Source specifies the type of source material that is being sequenced,"GENOMIC, GENOMIC SINGLE CELL, METAGENOMIC, METATRANSCRIPTOMIC, OTHER, SYNTHETIC, TRANSCRIPTOMIC, TRANSCRIPTOMIC SINGLE CELL, VIRAL RNA",,,TRUE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,str +CDS library_selection,Library Selection Method,"5-methylcytidine antibody, CAGE, cDNA, cDNA_oligo_dT, cDNA_randomPriming, CF-H, CF-M, CF-S, CF-T, ChIP, DNAse, HMPR, Hybrid Selection, Inverse rRNA, MBD2 protein methyl-CpG binding domain, MDA, MF, MNase, MSLL, Oligo-dT, other, Padlock probes capture method, PCR, PolyA, RACE, RANDOM, RANDOM PCR, Reduced Representation, repeat fractionation, Restriction Digest, RT-PCR, size fractionation, unspecified",,,TRUE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,str +CDS library_layout,Paired-end or Single,"Paired-end, Single-end",,,TRUE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,str +CDS platform,Sequencing Platform used for Sequencing,"LS454, ABI_SOLID, BGISEQ, CAPILLARY, COMPLETE_GENOMICS, HELICOS, ILLUMINA, ION_TORRENT, OXFORD_NANOPORE, PACBIO_SMRT",,,TRUE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,str +CDS instrument_model,Instrument model used for sequencing,"454 GS, 454 GS 20, 454 GS FLX, 454 GS FLX+, 454 GS FLX Titanium, 454 GS Junior, HiSeq X Five, HiSeq X Ten, Illumina Genome Analyzer, Illumina Genome Analyzer II, Illumina Genome Analyzer IIx, Illumina HiScanSQ, Illumina HiSeq 1000, Illumina HiSeq 1500, Illumina HiSeq 2000, Illumina HiSeq 2500, Illumina HiSeq 3000, Illumina HiSeq 4000, Illumina iSeq 100, Illumina NovaSeq 6000, Illumina MiniSeq, Illumina MiSeq, NextSeq 500, NextSeq 550, Helicos HeliScope, AB 5500 Genetic Analyzer, AB 5500xl Genetic Analyzer, AB 5500x-Wl Genetic Analyzer, AB SOLiD 3 Plus System, AB SOLiD 4 System, AB SOLiD 4hq System, AB SOLiD PI System, AB SOLiD System, AB SOLiD System 2.0, AB SOLiD System 3.0, Complete Genomics, PacBio RS, PacBio RS II, PacBio Sequel, PacBio Sequel II, Ion Torrent PGM, Ion Torrent Proton, Ion Torrent S5 XL, Ion Torrent S5, AB 310 Genetic Analyzer, AB 3130 Genetic Analyzer, AB 3130xL Genetic Analyzer, AB 3500 Genetic Analyzer, AB 3500xL Genetic Analyzer, AB 3730 Genetic Analyzer, AB 3730xL Genetic Analyzer, GridION, MinION, PromethION, BGISEQ-500, DNBSEQ-G400, DNBSEQ-T7, DNBSEQ-G50, MGISEQ-2000RS",,,TRUE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,str +CDS design_description,Free-form description of the methods used to create the sequencing library; a brief 'materials and methods' section.,,,,FALSE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,str +CDS reference_genome_assembly,This is only if you are submitting a bam file aligned against a NCBI assembly.,,,,FALSE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,str +CDS custom_assembly_fasta_file_for_alignment,Please provide the name of the custom assembly fasta file used during alignment,,,,FALSE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,str +CDS bases,Count of unique basecalls present in the data. Please count each base only once if using secondary alignments.,,,,FALSE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,int +CDS number_of_reads,Count of the number of reads in the data. Please count each read only once if using secondary alignments.,,,,FALSE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,int +CDS coverage,Depth of coverage on assembly used. Found by (Unique Aligned Basecalls)/(Reference Length),,,,FALSE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,int +CDS avg_read_length,Found by (Bases)/(Reads),,,,FALSE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,int +CDS sequence_alignment_software,The name of the software program used to align nucleotide sequencing data.,,,,FALSE,Sequencing,,https://dataservice.datacommons.cancer.gov/#/resources,str Checksum,MD5 checksum of the BAM file,,,,TRUE,Information Content Entity,,, HTAN Data File ID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),,,,TRUE,File,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\d*|0000))_([0-9]\d*|0000)$ warning HTAN Participant ID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),,,,TRUE,Patient,,https://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing,regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\d*|0000))$ warning @@ -928,8 +937,9 @@ Other Data Type Specified,Other types of data associated with the content.,,,,FA Supporting Link,Relevant external links associated with the content (e.g external datasets used for validation). Please note: Supporting Links and Supporting Link Descriptions are provided by authors and are not verified by the NIH NCI or the HTAN DCC. This information and any linked data should only be shared by an authorized individual(s) in accordance with the terms of the HTAN data sharing agreements and policies and/or any other applicable agreement(s). Validated as URL,,,,FALSE,Publication,,,url warning Supporting Link Description,Description of relevant external links associated with the publication (e.g An external mouse dataset used for validation). Please note: Supporting Links and Supporting Link Descriptions are provided by authors and are not verified by the NIH NCI or the HTAN DCC. This information and any linked data should only be shared by an authorized individual(s) in accordance with the terms of the HTAN data sharing agreements and policies and-or any other applicable agreement(s).,,,,FALSE,Publication,,, Tool,Were any software or computational tools generated for this content,"Yes, No",,,TRUE,Publication,,, +Accessory Data Type,Accesory specific data type,,,,FALSE,,,, Accessory,An empty parent attribute for accessory ,,,,FALSE,,,, -Accessory Manifest,Accessory specific attributes,,"Component,Dataset Name,Accessory Synapse ID,Accessory Description,Data Type,HTAN Center ID,HTAN Parent Biospecimen ID,Accessory-associated HTAN Parent Data File ID",,FALSE,Accessory,,, +Accessory Manifest,Accessory specific attributes,,"Component,Dataset Name,Accessory Synapse ID,Accessory Description, Accessory Data Type,HTAN Center ID,HTAN Parent Biospecimen ID,Accessory-associated HTAN Parent Data File ID",,FALSE,Accessory,,, Dataset Name,Name of a dataset (e.g. a Synapse folder),,,,TRUE,Accessory,,, Accessory Synapse ID,Synapse ID of folder containing accessory files,,,,TRUE,Accessory,,,regex match syn\d+ Accessory Description,Free text field containing description of accessory file(s),,,,TRUE,Accessory,,, @@ -1051,4 +1061,4 @@ Days to Vital Status Reference,Number of days between the date used for index an Precancer Case,Yes/No indicator to designate the participant for whom precancerous lesion(s) was identified (premalignancy only).,"Yes - Precancer Case, No, Not Reported, unknown",,,TRUE,Patient,,, Yes - Precancer Case,Indicates that the participant is a precancer case,,"Precancerous Condition Type, Days to Precancer Case Designation, WHO Precursor Lesion Code",,FALSE,Patient,,, Days to Precancer Case Designation,Number of days between the date used for index and the reference date for designation of precancer status.,,,,FALSE,Patient,,,int -WHO Precursor Lesion Code,"World Health Organization Classification of Tumour cytopathology-based coding system, includes 'precursor lesion' designations for precancers. ICD-O-3 morphology axis format eg 1234/1",,,,FALSE,Patient,,,regex match ^\d{4}\/[0-3]$ +WHO Precursor Lesion Code,"World Health Organization Classification of Tumour cytopathology-based coding system, includes 'precursor lesion' designations for precancers. ICD-O-3 morphology axis format eg 1234/1",,,,FALSE,Patient,,,regex match ^\d{4}\/[0-3]$ \ No newline at end of file diff --git a/HTAN.model.jsonld b/HTAN.model.jsonld index 0bdbb642..e92e381c 100644 --- a/HTAN.model.jsonld +++ b/HTAN.model.jsonld @@ -2908,19 +2908,49 @@ "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:CDSGenomicReference" + "@id": "bts:CDSlibraryId" }, { - "@id": "bts:CDSLibraryLayout" + "@id": "bts:CDSlibraryStrategy" }, { - "@id": "bts:CDSDataType" + "@id": "bts:CDSlibrarySource" }, { - "@id": "bts:CDSSequencingPlatform" + "@id": "bts:CDSlibrarySelection" }, { - "@id": "bts:CDSLibrarySelectionMethod" + "@id": "bts:CDSlibraryLayout" + }, + { + "@id": "bts:CDSplatform" + }, + { + "@id": "bts:CDSinstrumentModel" + }, + { + "@id": "bts:CDSdesignDescription" + }, + { + "@id": "bts:CDSreferenceGenomeAssembly" + }, + { + "@id": "bts:CDScustomAssemblyFastaFileForAlignment" + }, + { + "@id": "bts:CDSbases" + }, + { + "@id": "bts:CDSnumberOfReads" + }, + { + "@id": "bts:CDScoverage" + }, + { + "@id": "bts:CDSavgReadLength" + }, + { + "@id": "bts:CDSsequenceAlignmentSoftware" } ], "sms:validationRules": [] @@ -2962,10 +2992,10 @@ "sms:validationRules": [] }, { - "@id": "bts:CDSGenomicReference", + "@id": "bts:CDSlibraryId", "@type": "rdfs:Class", - "rdfs:comment": "One or more characters used to identify the published NCBI genetic sequence that is used as a reference against which other sequences are compared.", - "rdfs:label": "CDSGenomicReference", + "rdfs:comment": "Short unique identifier for the sequencing library.", + "rdfs:label": "CDSlibraryId", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -2974,17 +3004,17 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "CDS Genomic Reference", + "sms:displayName": "CDS library_id", "sms:required": "sms:true", "sms:validationRules": [ "str" ] }, { - "@id": "bts:CDSLibraryLayout", + "@id": "bts:CDSlibraryStrategy", "@type": "rdfs:Class", - "rdfs:comment": "The read strategy or method that was used for sequencing and analysis of a nucleotide library.", - "rdfs:label": "CDSLibraryLayout", + "rdfs:comment": "Library strategy", + "rdfs:label": "CDSlibraryStrategy", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -2995,24 +3025,125 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:PairedEnd" + "@id": "bts:AMPLICON" }, { - "@id": "bts:SingleRead" + "@id": "bts:ATAC-seq" + }, + { + "@id": "bts:Bisulfite-Seq" + }, + { + "@id": "bts:ChIA-PET" + }, + { + "@id": "bts:ChIP-Seq" + }, + { + "@id": "bts:CLONE" + }, + { + "@id": "bts:CLONEEND" + }, + { + "@id": "bts:CTS" + }, + { + "@id": "bts:DNase-Hypersensitivity" + }, + { + "@id": "bts:EST" + }, + { + "@id": "bts:FAIRE-seq" + }, + { + "@id": "bts:FINISHING" + }, + { + "@id": "bts:FL-cDNA" + }, + { + "@id": "bts:Hi-C" + }, + { + "@id": "bts:MBD-Seq" + }, + { + "@id": "bts:MeDIP-Seq" + }, + { + "@id": "bts:MiRNA-Seq" + }, + { + "@id": "bts:MNase-Seq" + }, + { + "@id": "bts:MRE-Seq" + }, + { + "@id": "bts:NcRNA-Seq" + }, + { + "@id": "bts:OTHER" + }, + { + "@id": "bts:POOLCLONE" + }, + { + "@id": "bts:RAD-Seq" + }, + { + "@id": "bts:RIP-Seq" + }, + { + "@id": "bts:RNA-Seq" + }, + { + "@id": "bts:SELEX" + }, + { + "@id": "bts:SsRNA-seq" + }, + { + "@id": "bts:Synthetic-Long-Read" + }, + { + "@id": "bts:Targeted-Capture" + }, + { + "@id": "bts:TetheredChromatinConformationCapture" + }, + { + "@id": "bts:Tn-Seq" + }, + { + "@id": "bts:WCS" + }, + { + "@id": "bts:WGA" + }, + { + "@id": "bts:WGS" + }, + { + "@id": "bts:WXS" } ], - "sms:displayName": "CDS Library Layout", + "sms:displayName": "CDS library_strategy", "sms:required": "sms:true", - "sms:validationRules": [] + "sms:validationRules": [ + "str" + ] }, { - "@id": "bts:CDSDataType", + "@id": "bts:CDSlibrarySource", "@type": "rdfs:Class", - "rdfs:comment": "Types of data associated with the content. Fill out Other Data Type Specified, if not on the list.", - "rdfs:label": "CDSDataType", + "rdfs:comment": "The Library Source specifies the type of source material that is being sequenced", + "rdfs:label": "CDSlibrarySource", "rdfs:subClassOf": [ { - "@id": "bts:Publication" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -3020,77 +3151,167 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:10xVisiumSpatialTranscriptomics" + "@id": "bts:GENOMIC" }, { - "@id": "bts:BulkMethylation-seq" + "@id": "bts:GENOMICSINGLECELL" }, { - "@id": "bts:BulkRNA-seq" + "@id": "bts:METAGENOMIC" }, { - "@id": "bts:BulkWES" + "@id": "bts:METATRANSCRIPTOMIC" }, { - "@id": "bts:ElectronMicroscopy" + "@id": "bts:OTHER" }, { - "@id": "bts:ExSeq" + "@id": "bts:SYNTHETIC" }, { - "@id": "bts:HI-C-seq" + "@id": "bts:TRANSCRIPTOMIC" }, { - "@id": "bts:RPPA" + "@id": "bts:TRANSCRIPTOMICSINGLECELL" }, { - "@id": "bts:Imaging" + "@id": "bts:VIRALRNA" + } + ], + "sms:displayName": "CDS library_source", + "sms:required": "sms:true", + "sms:validationRules": [ + "str" + ] + }, + { + "@id": "bts:CDSlibrarySelection", + "@type": "rdfs:Class", + "rdfs:comment": "Library Selection Method", + "rdfs:label": "CDSlibrarySelection", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:5-methylcytidineantibody" }, { - "@id": "bts:MassSpectrometry" + "@id": "bts:CAGE" }, { - "@id": "bts:NanoStringGeoMxDSPSpatialTranscriptomics" + "@id": "bts:CDNA" }, { - "@id": "bts:OtherAssay" + "@id": "bts:CDNAOligoDT" }, { - "@id": "bts:SRRSImaging" + "@id": "bts:CDNARandomPriming" }, { - "@id": "bts:Slide-seq" + "@id": "bts:CF-H" }, { - "@id": "bts:ScATAC-seq" + "@id": "bts:CF-M" }, { - "@id": "bts:ScDNA-seq" + "@id": "bts:CF-S" }, { - "@id": "bts:ScRNA-seq" + "@id": "bts:CF-T" }, { - "@id": "bts:AccessoryManifest" + "@id": "bts:ChIP" }, { - "@id": "bts:OtherDataTypeSpecified" + "@id": "bts:DNAse" + }, + { + "@id": "bts:HMPR" + }, + { + "@id": "bts:HybridSelection" + }, + { + "@id": "bts:InverserRNA" + }, + { + "@id": "bts:MBD2proteinmethyl-CpGbindingdomain" + }, + { + "@id": "bts:MDA" + }, + { + "@id": "bts:MF" + }, + { + "@id": "bts:MNase" + }, + { + "@id": "bts:MSLL" + }, + { + "@id": "bts:Oligo-dT" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:Padlockprobescapturemethod" + }, + { + "@id": "bts:PCR" + }, + { + "@id": "bts:PolyA" + }, + { + "@id": "bts:RACE" + }, + { + "@id": "bts:RANDOM" + }, + { + "@id": "bts:RANDOMPCR" + }, + { + "@id": "bts:ReducedRepresentation" + }, + { + "@id": "bts:Repeatfractionation" + }, + { + "@id": "bts:RestrictionDigest" + }, + { + "@id": "bts:RT-PCR" + }, + { + "@id": "bts:Sizefractionation" + }, + { + "@id": "bts:Unspecified" } ], - "sms:displayName": "CDS Data Type", + "sms:displayName": "CDS library_selection", "sms:required": "sms:true", "sms:validationRules": [ - "list like" + "str" ] }, { - "@id": "bts:CDSSequencingPlatform", + "@id": "bts:CDSlibraryLayout", "@type": "rdfs:Class", - "rdfs:comment": "The words used to describe the instrument used to carry out a high-throughput sequencing experiment.", - "rdfs:label": "CDSSequencingPlatform", + "rdfs:comment": "Paired-end or Single", + "rdfs:label": "CDSlibraryLayout", "rdfs:subClassOf": [ { - "@id": "bts:Device" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -3098,40 +3319,109 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:IlluminaNextSeq500" + "@id": "bts:Paired-end" }, { - "@id": "bts:IlluminaNextSeq550" + "@id": "bts:Single-end" + } + ], + "sms:displayName": "CDS library_layout", + "sms:required": "sms:true", + "sms:validationRules": [ + "str" + ] + }, + { + "@id": "bts:CDSplatform", + "@type": "rdfs:Class", + "rdfs:comment": "Sequencing Platform used for Sequencing", + "rdfs:label": "CDSplatform", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:LS454" }, { - "@id": "bts:IlluminaNextSeq2500" + "@id": "bts:ABISOLID" }, { - "@id": "bts:IlluminaNovaSeq6000" + "@id": "bts:BGISEQ" }, { - "@id": "bts:IlluminaMiSeq" + "@id": "bts:CAPILLARY" }, { - "@id": "bts:454GSFLXTitanium" + "@id": "bts:COMPLETEGENOMICS" }, { - "@id": "bts:ABSOLiD4" + "@id": "bts:HELICOS" }, { - "@id": "bts:ABSOLiD2" + "@id": "bts:ILLUMINA" }, { - "@id": "bts:ABSOLiD3" + "@id": "bts:IONTORRENT" }, { - "@id": "bts:CompleteGenomics" + "@id": "bts:OXFORDNANOPORE" }, { - "@id": "bts:IlluminaHiSeqXTen" + "@id": "bts:PACBIOSMRT" + } + ], + "sms:displayName": "CDS platform", + "sms:required": "sms:true", + "sms:validationRules": [ + "str" + ] + }, + { + "@id": "bts:CDSinstrumentModel", + "@type": "rdfs:Class", + "rdfs:comment": "Instrument model used for sequencing", + "rdfs:label": "CDSinstrumentModel", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:454GS" }, { - "@id": "bts:IlluminaHiSeqXFive" + "@id": "bts:454GS20" + }, + { + "@id": "bts:454GSFLX" + }, + { + "@id": "bts:454GSFLX+" + }, + { + "@id": "bts:454GSFLXTitanium" + }, + { + "@id": "bts:454GSJunior" + }, + { + "@id": "bts:HiSeqXFive" + }, + { + "@id": "bts:HiSeqXTen" + }, + { + "@id": "bts:IlluminaGenomeAnalyzer" }, { "@id": "bts:IlluminaGenomeAnalyzerII" @@ -3139,17 +3429,92 @@ { "@id": "bts:IlluminaGenomeAnalyzerIIx" }, + { + "@id": "bts:IlluminaHiScanSQ" + }, + { + "@id": "bts:IlluminaHiSeq1000" + }, + { + "@id": "bts:IlluminaHiSeq1500" + }, { "@id": "bts:IlluminaHiSeq2000" }, { "@id": "bts:IlluminaHiSeq2500" }, + { + "@id": "bts:IlluminaHiSeq3000" + }, { "@id": "bts:IlluminaHiSeq4000" }, { - "@id": "bts:IlluminaNextSeq" + "@id": "bts:IlluminaiSeq100" + }, + { + "@id": "bts:IlluminaNovaSeq6000" + }, + { + "@id": "bts:IlluminaMiniSeq" + }, + { + "@id": "bts:IlluminaMiSeq" + }, + { + "@id": "bts:NextSeq500" + }, + { + "@id": "bts:NextSeq550" + }, + { + "@id": "bts:HelicosHeliScope" + }, + { + "@id": "bts:AB5500GeneticAnalyzer" + }, + { + "@id": "bts:AB5500xlGeneticAnalyzer" + }, + { + "@id": "bts:AB5500x-WlGeneticAnalyzer" + }, + { + "@id": "bts:ABSOLiD3PlusSystem" + }, + { + "@id": "bts:ABSOLiD4System" + }, + { + "@id": "bts:ABSOLiD4hqSystem" + }, + { + "@id": "bts:ABSOLiDPISystem" + }, + { + "@id": "bts:ABSOLiDSystem" + }, + { + "@id": "bts:ABSOLiDSystem2.0" + }, + { + "@id": "bts:ABSOLiDSystem3.0" + }, + { + "@id": "bts:CompleteGenomics" + }, + { + "@id": "bts:PacBioRS" + }, + { + "@id": "bts:PacBioRSII" + }, + { + "@id": "bts:PacBioSequel" + }, + { + "@id": "bts:PacBioSequelII" }, { "@id": "bts:IonTorrentPGM" @@ -3157,61 +3522,69 @@ { "@id": "bts:IonTorrentProton" }, + { + "@id": "bts:IonTorrentS5XL" + }, { "@id": "bts:IonTorrentS5" }, { - "@id": "bts:PacBioRS" + "@id": "bts:AB310GeneticAnalyzer" }, { - "@id": "bts:NovaSeq6000" + "@id": "bts:AB3130GeneticAnalyzer" }, { - "@id": "bts:NovaSeqS4" + "@id": "bts:AB3130xLGeneticAnalyzer" }, { - "@id": "bts:UltimaGenomicsUG100" + "@id": "bts:AB3500GeneticAnalyzer" }, { - "@id": "bts:OxfordNanoporeminION" + "@id": "bts:AB3500xLGeneticAnalyzer" }, { - "@id": "bts:GridION" + "@id": "bts:AB3730GeneticAnalyzer" }, { - "@id": "bts:PromethION" + "@id": "bts:AB3730xLGeneticAnalyzer" }, { - "@id": "bts:PacBioSequel2" + "@id": "bts:GridION" }, { - "@id": "bts:Revio" + "@id": "bts:MinION" }, { - "@id": "bts:IlluminaNextSeq1000" + "@id": "bts:PromethION" }, { - "@id": "bts:IlluminaNextSeq2000" + "@id": "bts:BGISEQ-500" }, { - "@id": "bts:Other" + "@id": "bts:DNBSEQ-G400" }, { - "@id": "bts:Unknown" + "@id": "bts:DNBSEQ-T7" }, { - "@id": "bts:NotReported" + "@id": "bts:DNBSEQ-G50" + }, + { + "@id": "bts:MGISEQ-2000RS" } ], - "sms:displayName": "CDS Sequencing Platform", + "sms:displayName": "CDS instrument_model", "sms:required": "sms:true", - "sms:validationRules": [] + "sms:validationRules": [ + "str" + ] }, { - "@id": "bts:CDSLibrarySelectionMethod", + "@id": "bts:CDSdesignDescription", "@type": "rdfs:Class", - "rdfs:comment": "The type of systematic actions performed to select or enrich DNA fragments used in analysis by high-throughput sequencing.", - "rdfs:label": "CDSLibrarySelectionMethod", + "rdfs:comment": "Free-form description of the methods used to create the sequencing library; a brief 'materials and methods' section.", + "rdfs:label": "CDSdesignDescription", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -3220,1160 +3593,1260 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "CDS design_description", + "sms:required": "sms:false", + "sms:validationRules": [ + "str" + ] + }, + { + "@id": "bts:CDSreferenceGenomeAssembly", + "@type": "rdfs:Class", + "rdfs:comment": "This is only if you are submitting a bam file aligned against a NCBI assembly.", + "rdfs:label": "CDSreferenceGenomeAssembly", + "rdfs:subClassOf": [ { - "@id": "bts:Random" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "CDS reference_genome_assembly", + "sms:required": "sms:false", + "sms:validationRules": [ + "str" + ] + }, + { + "@id": "bts:CDScustomAssemblyFastaFileForAlignment", + "@type": "rdfs:Class", + "rdfs:comment": "Please provide the name of the custom assembly fasta file used during alignment", + "rdfs:label": "CDScustomAssemblyFastaFileForAlignment", + "rdfs:subClassOf": [ { - "@id": "bts:RRNADepletion" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "CDS custom_assembly_fasta_file_for_alignment", + "sms:required": "sms:false", + "sms:validationRules": [ + "str" + ] + }, + { + "@id": "bts:CDSbases", + "@type": "rdfs:Class", + "rdfs:comment": "Count of unique basecalls present in the data. Please count each base only once if using secondary alignments.", + "rdfs:label": "CDSbases", + "rdfs:subClassOf": [ { - "@id": "bts:Other" + "@id": "bts:Sequencing" } ], - "sms:displayName": "CDS Library Selection Method", - "sms:required": "sms:true", - "sms:validationRules": [] + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "CDS bases", + "sms:required": "sms:false", + "sms:validationRules": [ + "int" + ] }, { - "@id": "bts:PairedEnd", + "@id": "bts:CDSnumberOfReads", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "PairedEnd", + "rdfs:comment": "Count of the number of reads in the data. Please count each read only once if using secondary alignments.", + "rdfs:label": "CDSnumberOfReads", "rdfs:subClassOf": [ { - "@id": "bts:CDSLibraryLayout" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "CDS number_of_reads", + "sms:required": "sms:false", + "sms:validationRules": [ + "int" + ] + }, + { + "@id": "bts:CDScoverage", + "@type": "rdfs:Class", + "rdfs:comment": "Depth of coverage on assembly used. Found by (Unique Aligned Basecalls)/(Reference Length)", + "rdfs:label": "CDScoverage", + "rdfs:subClassOf": [ { - "@id": "bts:LibraryLayout" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Paired End", + "sms:displayName": "CDS coverage", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "int" + ] }, { - "@id": "bts:SingleRead", + "@id": "bts:CDSavgReadLength", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "SingleRead", + "rdfs:comment": "Found by (Bases)/(Reads)", + "rdfs:label": "CDSavgReadLength", "rdfs:subClassOf": [ { - "@id": "bts:CDSLibraryLayout" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "CDS avg_read_length", + "sms:required": "sms:false", + "sms:validationRules": [ + "int" + ] + }, + { + "@id": "bts:CDSsequenceAlignmentSoftware", + "@type": "rdfs:Class", + "rdfs:comment": "The name of the software program used to align nucleotide sequencing data.", + "rdfs:label": "CDSsequenceAlignmentSoftware", + "rdfs:subClassOf": [ { - "@id": "bts:LibraryLayout" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Single Read", + "sms:displayName": "CDS sequence_alignment_software", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "str" + ] }, { - "@id": "bts:10xVisiumSpatialTranscriptomics", + "@id": "bts:AMPLICON", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "10xVisiumSpatialTranscriptomics", + "rdfs:label": "AMPLICON", "rdfs:subClassOf": [ { - "@id": "bts:CDSDataType" - }, - { - "@id": "bts:DataType" + "@id": "bts:CDSlibraryStrategy" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "10x Visium Spatial Transcriptomics", + "sms:displayName": "AMPLICON", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BulkMethylation-seq", + "@id": "bts:ATAC-seq", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "BulkMethylation-seq", + "rdfs:label": "ATAC-seq", "rdfs:subClassOf": [ { - "@id": "bts:CDSDataType" - }, - { - "@id": "bts:DataType" + "@id": "bts:CDSlibraryStrategy" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk Methylation-seq", + "sms:displayName": "ATAC-seq", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BulkRNA-seq", + "@id": "bts:Bisulfite-Seq", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "BulkRNA-seq", + "rdfs:label": "Bisulfite-Seq", "rdfs:subClassOf": [ { - "@id": "bts:CDSDataType" - }, - { - "@id": "bts:DataType" + "@id": "bts:CDSlibraryStrategy" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk RNA-seq", + "sms:displayName": "Bisulfite-Seq", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BulkWES", + "@id": "bts:ChIA-PET", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "BulkWES", + "rdfs:label": "ChIA-PET", "rdfs:subClassOf": [ { - "@id": "bts:CDSDataType" - }, - { - "@id": "bts:DataType" + "@id": "bts:CDSlibraryStrategy" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk WES", + "sms:displayName": "ChIA-PET", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ElectronMicroscopy", + "@id": "bts:ChIP-Seq", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "ElectronMicroscopy", + "rdfs:label": "ChIP-Seq", "rdfs:subClassOf": [ { - "@id": "bts:CDSDataType" - }, - { - "@id": "bts:DataType" + "@id": "bts:CDSlibraryStrategy" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Electron Microscopy", + "sms:displayName": "ChIP-Seq", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ExSeq", + "@id": "bts:CLONE", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "ExSeq", + "rdfs:label": "CLONE", "rdfs:subClassOf": [ { - "@id": "bts:CDSDataType" - }, - { - "@id": "bts:DataType" - }, - { - "@id": "bts:ImagingAssayType" + "@id": "bts:CDSlibraryStrategy" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "ExSeq", + "sms:displayName": "CLONE", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HI-C-seq", + "@id": "bts:CLONEEND", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "HI-C-seq", + "rdfs:label": "CLONEEND", "rdfs:subClassOf": [ { - "@id": "bts:CDSDataType" - }, - { - "@id": "bts:DataType" + "@id": "bts:CDSlibraryStrategy" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HI-C-seq", + "sms:displayName": "CLONEEND", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RPPA", + "@id": "bts:CTS", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "RPPA", + "rdfs:label": "CTS", "rdfs:subClassOf": [ { - "@id": "bts:CDSDataType" - }, - { - "@id": "bts:DataType" + "@id": "bts:CDSlibraryStrategy" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "RPPA", + "sms:displayName": "CTS", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Imaging", + "@id": "bts:DNase-Hypersensitivity", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Imaging", + "rdfs:label": "DNase-Hypersensitivity", "rdfs:subClassOf": [ { - "@id": "bts:CDSDataType" - }, - { - "@id": "bts:DataType" + "@id": "bts:CDSlibraryStrategy" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Imaging", + "sms:displayName": "DNase-Hypersensitivity", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MassSpectrometry", + "@id": "bts:EST", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "MassSpectrometry", + "rdfs:label": "EST", "rdfs:subClassOf": [ { - "@id": "bts:CDSDataType" - }, - { - "@id": "bts:DataType" + "@id": "bts:CDSlibraryStrategy" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Mass Spectrometry", + "sms:displayName": "EST", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NanoStringGeoMxDSPSpatialTranscriptomics", + "@id": "bts:FAIRE-seq", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "NanoStringGeoMxDSPSpatialTranscriptomics", + "rdfs:label": "FAIRE-seq", "rdfs:subClassOf": [ { - "@id": "bts:CDSDataType" - }, - { - "@id": "bts:DataType" + "@id": "bts:CDSlibraryStrategy" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "NanoString GeoMx DSP Spatial Transcriptomics", + "sms:displayName": "FAIRE-seq", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:OtherAssay", + "@id": "bts:FINISHING", "@type": "rdfs:Class", - "rdfs:comment": "Metadata applying to any assay without standard descriptors. Can be used as a placeholder for minimal amount of metadata until the assay descriptors are standardized", - "rdfs:label": "OtherAssay", + "rdfs:comment": "TBD", + "rdfs:label": "FINISHING", "rdfs:subClassOf": [ { - "@id": "bts:Assay" - }, - { - "@id": "bts:CDSDataType" - }, - { - "@id": "bts:DataType" + "@id": "bts:CDSlibraryStrategy" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Other Assay", + "sms:displayName": "FINISHING", "sms:required": "sms:false", - "sms:requiresComponent": [ + "sms:validationRules": [] + }, + { + "@id": "bts:FL-cDNA", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "FL-cDNA", + "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:CDSlibraryStrategy" } ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:HTANDataFileID" - }, + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "FL-cDNA", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Hi-C", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Hi-C", + "rdfs:subClassOf": [ { - "@id": "bts:AssayType" + "@id": "bts:CDSlibraryStrategy" } ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Hi-C", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SRRSImaging", + "@id": "bts:MBD-Seq", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "SRRSImaging", + "rdfs:label": "MBD-Seq", "rdfs:subClassOf": [ { - "@id": "bts:CDSDataType" - }, - { - "@id": "bts:DataType" + "@id": "bts:CDSlibraryStrategy" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SRRS Imaging", + "sms:displayName": "MBD-Seq", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Slide-seq", + "@id": "bts:MeDIP-Seq", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Slide-seq", + "rdfs:label": "MeDIP-Seq", "rdfs:subClassOf": [ { - "@id": "bts:CDSDataType" - }, - { - "@id": "bts:DataType" + "@id": "bts:CDSlibraryStrategy" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - 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Parent could be another biospecimen or a research participant.", + "rdfs:label": "HTANParentID", + "rdfs:subClassOf": [ + { + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "HTAN Parent ID", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:HTANParentDataFileID", + "@type": "rdfs:Class", + "rdfs:comment": "HTAN Data File Identifier indicating the file(s) from which these files were derived", + "rdfs:label": "HTANParentDataFileID", + "rdfs:subClassOf": [ + { + "@id": "bts:File" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "HTAN Parent Data File ID", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:ClinicalDataTier2", + "@type": "rdfs:Class", + "rdfs:comment": "Tier 2 Cancer Data", + "rdfs:label": "ClinicalDataTier2", + "rdfs:subClassOf": [ + { + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Clinical Data Tier 2", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:HTANParticipantID" + }, + { + "@id": "bts:TimepointLabel" + }, + { + "@id": "bts:StartDaysfromIndex" + }, + { + "@id": "bts:StopDaysfromIndex" + }, + { + "@id": "bts:SentinelLymphNodeCount" + }, + { + "@id": "bts:SentinelNodePositiveAssessmentCount" + }, + { + "@id": "bts:TumorExtranodalExtensionIndicator" + }, + { + "@id": "bts:SatelliteMetastasisPresentIndicator" + }, + { + "@id": "bts:OtherBiopsyResectionSite" + }, + { + "@id": "bts:ExtentofTumorResection" + }, + { + "@id": "bts:PriorSitesofRadiation" + }, + { + "@id": "bts:Immunosuppression" + }, + { + "@id": "bts:ConcomitantMedicationReceivedType" + }, + { + "@id": "bts:FamilyMemberVitalStatusIndicator" + }, + { + "@id": "bts:COVID19OccurrenceIndicator" + }, + { + "@id": "bts:COVID19CurrentStatus" + }, + { + "@id": "bts:COVID19PositiveLabTestIndicator" + }, + { + "@id": "bts:COVID19AntibodyTesting" + }, + { + "@id": "bts:COVID19ComplicationsSeverity" + }, + { + "@id": "bts:COVID19CancerTreatmentFollowup" + }, + { + "@id": "bts:Ecigvapeuse" + }, + { + "@id": "bts:Ecigvape30dayusenum" + }, + { + "@id": "bts:Ecigvapetimesperday" + }, + { + "@id": "bts:Typeofsmokeexposurecumulativeyears" + }, + { + "@id": "bts:Chewingtobaccodailyusecount" + }, + { + "@id": "bts:Secondhandsmokeexposureyears" + }, + { + "@id": "bts:KnownGeneticPredispositionMutation" + }, + { + "@id": "bts:HereditaryCancerPredispositionSyndrome" + }, + { + "@id": "bts:CancerAssociatedGeneMutations" + }, + { + "@id": "bts:MutationalSignatures" + }, + { + "@id": "bts:MismatchRepairSystemStatus" + }, + { + "@id": "bts:LabTestsforMMRStatus" + }, + { + "@id": "bts:ModeofCancerDetection" + }, + { + "@id": "bts:EducationLevel" + }, + { + "@id": "bts:CountryofBirth" + }, + { + "@id": "bts:MedicallyUnderservedArea" + }, + { + "@id": "bts:RuralvsUrban" + }, + { + "@id": "bts:CancerIncidence" + }, + { + "@id": "bts:CancerIncidenceLocation" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:TimepointLabel", + "@type": "rdfs:Class", + "rdfs:comment": "Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.", + "rdfs:label": "TimepointLabel", + "rdfs:subClassOf": [ + { + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Timepoint Label", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:StartDaysfromIndex", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'", + "rdfs:label": "StartDaysfromIndex", + "rdfs:subClassOf": [ + { + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Start Days from Index", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:StopDaysfromIndex", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'", + "rdfs:label": "StopDaysfromIndex", + "rdfs:subClassOf": [ + { + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Stop Days from Index", + "sms:required": "sms:false", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:SentinelLymphNodeCount", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric count of sentinel lymph nodes.", + "rdfs:label": "SentinelLymphNodeCount", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Sentinel Lymph Node Count", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SentinelNodePositiveAssessmentCount", + "@type": "rdfs:Class", + "rdfs:comment": "The number or amount of metastatic 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{ + "@id": "bts:YES" + }, + { + "@id": "bts:Nosourcedocumentation" + }, + { + "@id": "bts:Notapplicable" + }, + { + "@id": "bts:Notsampledordissected" + }, + { + "@id": "bts:Present" + }, + { + "@id": "bts:Present-extensive" + }, + { + "@id": "bts:Present-minimal" + }, + { + "@id": "bts:UNKNOWN" + }, + { + "@id": "bts:Unspecified" + } + ], + "sms:displayName": "Tumor Extranodal Extension Indicator", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SatelliteMetastasisPresentIndicator", + "@type": "rdfs:Class", + "rdfs:comment": "A yes/no indicator to ask if intransit metastases or satellite lesions are present.", + "rdfs:label": "SatelliteMetastasisPresentIndicator", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Satellite Metastasis 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"bts:GenitourinaryNOS" + }, + { + "@id": "bts:Groin" + }, + { + "@id": "bts:Gum" + }, + { + "@id": "bts:Hand" + }, + { + "@id": "bts:HardPalate" + }, + { + "@id": "bts:HeadFaceOrNeckNos" + }, + { + "@id": "bts:HeadandNeck" + }, + { + "@id": "bts:Heart" + }, + { + "@id": "bts:Hepatic" + }, + { + "@id": "bts:HepaticDuct" + }, + { + "@id": "bts:HepaticVein" + }, + { + "@id": "bts:Hilar" + }, + { + "@id": "bts:Hip" + }, + { + "@id": "bts:Hippocampus" + }, + { + "@id": "bts:Humerus" + }, + { + "@id": "bts:Hypopharynx" + }, + { + "@id": "bts:IleocecalValve" + }, + { + "@id": "bts:Ileum" + }, + { + "@id": "bts:Ilium" + }, + { + "@id": "bts:IndexFinger" + }, + { + "@id": "bts:Ischium" + }, + { + "@id": "bts:IsletCells" + }, + { + "@id": "bts:Jaw" + }, + { + "@id": "bts:Jejunum" + }, + { + "@id": "bts:Joint" + }, + { + "@id": "bts:Kidney" + }, + { + "@id": "bts:Knee" + }, + { + "@id": "bts:LacrimalGland" + }, + { + "@id": "bts:LargeBowel" + }, + { + "@id": "bts:Laryngopharynx" + }, + { + "@id": "bts:Larynx" + }, + { + "@id": "bts:Leg" + }, + { + "@id": "bts:Leptomeninges" + }, + { + "@id": "bts:Ligament" + }, + { + "@id": "bts:Lip" + }, + { + "@id": "bts:Liver" + }, + { + "@id": "bts:LumbarSpine" + }, + { + "@id": "bts:Lung" + }, + { + "@id": "bts:LymphNode" + }, + { + "@id": "bts:LymphNode(s)Axilla" + }, + { + "@id": "bts:LymphNode(s)Cervical" + }, + { + "@id": "bts:LymphNode(s)Distant" + }, + { + "@id": "bts:LymphNode(s)Epitrochlear" + }, + { + "@id": "bts:LymphNode(s)Femoral" + }, + { + "@id": "bts:LymphNode(s)Hilar" + }, + { + "@id": "bts:LymphNode(s)Iliac-Common" + }, + { + "@id": "bts:LymphNode(s)Iliac-External" + }, + { + "@id": "bts:LymphNode(s)Inguinal" + }, + { + "@id": "bts:LymphNode(s)InternalMammary" + }, + { + "@id": "bts:LymphNode(s)Mammary" + }, + { + "@id": "bts:LymphNode(s)Mediastinal" + }, + { + "@id": "bts:LymphNode(s)Mesenteric" + }, + { + "@id": "bts:LymphNode(s)Occipital" + }, + { + "@id": "bts:LymphNode(s)Paraaortic" + }, + { + "@id": "bts:LymphNode(s)Parotid" + }, + { + "@id": "bts:LymphNode(s)Pelvic" + }, + { + "@id": "bts:LymphNode(s)Popliteal" + }, + { + "@id": "bts:LymphNode(s)Regional" + }, + { + "@id": "bts:LymphNode(s)Retroperitoneal" + }, + { + "@id": "bts:LymphNode(s)Scalene" + }, + { + "@id": "bts:LymphNode(s)Splenic" + }, + { + "@id": "bts:LymphNode(s)Subclavicular" + }, + { + "@id": "bts:LymphNode(s)Submandibular" + }, + { + "@id": "bts:LymphNode(s)Supraclavicular" + }, + { + "@id": "bts:Mandible" + }, + { + "@id": "bts:Mantle" + }, + { + "@id": "bts:Maxilla" + }, + { + "@id": "bts:MediastinalSoftTissue" + }, + { + "@id": "bts:Mediastinum" + }, + { + "@id": "bts:Mesentery" + }, + { + "@id": "bts:Mesothelium" + }, + { + "@id": "bts:MiddleFinger" + }, + { + "@id": "bts:Mitochondria" + }, + { + "@id": "bts:Muscle" + }, + { + "@id": "bts:Nails" + }, + { + "@id": "bts:NasalCavity" + }, + { + "@id": "bts:NasalSoftTissue" + }, + { + "@id": "bts:Nasopharynx" + }, + { + "@id": "bts:Neck" + }, + { + "@id": "bts:Nerve" + }, + { + "@id": "bts:Nerve(s)Cranial" + }, + { + "@id": "bts:OccipitalCortex" + }, + { + "@id": "bts:OcularOrbits" + }, + { + "@id": "bts:Omentum" + }, + { + "@id": "bts:OralCavity" + }, + { + "@id": "bts:OralCavityMucosaOnly" + }, + { + "@id": "bts:Oropharynx" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:Ovary" + }, + { + "@id": "bts:Palate" + }, + { + "@id": "bts:Pancreas" + }, + { + "@id": "bts:Parametrium" + }, + { + "@id": "bts:ParaspinalGanglion" + }, + { + "@id": "bts:Parathyroid" + }, + { + "@id": "bts:ParotidGland" + }, + { + "@id": "bts:Patella" + }, + { + "@id": "bts:Pelvis" + }, + { + "@id": "bts:Penis" + }, + { + "@id": "bts:Pericardium" + }, + { + "@id": "bts:PeriorbitalSoftTissue" + }, + { + "@id": "bts:PeritonealCavity" + }, + { + "@id": "bts:Peritoneum" + }, + { + "@id": "bts:Pharynx" + }, + { + "@id": "bts:Pineal" + }, + { + "@id": "bts:PinealGland" + }, + { + "@id": "bts:PituitaryGland" + }, + { + "@id": "bts:Placenta" + }, + { + "@id": "bts:Pleura" + }, + { + "@id": "bts:PoplitealFossa" + }, + { + "@id": "bts:Pouch" + }, + { + "@id": "bts:PrimaryTumorField" + }, + { + "@id": "bts:Primarytumorsite" + }, + { + "@id": "bts:Prostate" + }, + { + "@id": "bts:ProstateBed" + }, + { + "@id": "bts:ProstateSeminalVesiclesandLymphNodes" + }, + { + "@id": "bts:Pylorus" + }, + { + "@id": "bts:RectosigmoidJunction" + }, + { + "@id": "bts:Rectum" + }, + { + "@id": "bts:RegionalSite" + }, + { + "@id": "bts:Retina" + }, + { + "@id": "bts:Retro-OrbitalRegion" + }, + { + "@id": "bts:Retroperitoneum" + }, + { + "@id": "bts:Rib" + }, + { + "@id": "bts:RingFinger" + }, + { + "@id": "bts:RoundLigament" + }, + { + "@id": "bts:Sacrum" + }, + { + "@id": "bts:SalivaryGland" + }, + { + "@id": "bts:Scalp" + }, + { + "@id": "bts:Scapula" + }, + { + "@id": "bts:SciaticNerve" + }, + { + "@id": "bts:Scrotum" + }, + { + "@id": "bts:SeminalVesicle" + }, + { + "@id": "bts:Shoulder" + }, + { + "@id": "bts:SigmoidColon" + }, + { + "@id": "bts:Sinus" + }, + { + "@id": "bts:Sinus(es)Maxillary" + }, + { + "@id": "bts:SkeletalMuscle" + }, + { + "@id": "bts:Skin" + }, + { + "@id": "bts:Skinlowerextremitylocal" + }, + { + "@id": "bts:Skintotal" + }, + { + "@id": "bts:Skintrunklocal" + }, + { + "@id": "bts:Skinupperextremitylocal" + }, + { + "@id": "bts:Skull" + }, + { + "@id": "bts:SmallBowel" + }, + { + "@id": "bts:SmallBowelMucosaOnly" + }, + { + "@id": "bts:SmallFinger" + }, + { + "@id": "bts:SoftTissue" + }, + { + "@id": "bts:SpinalColumn" + }, + { + "@id": "bts:SpinalCord" + }, + { + "@id": "bts:Spine" + }, + { + "@id": "bts:Spleen" + }, + { + "@id": "bts:SplenicFlexure" + }, + { + "@id": "bts:Sternum" + }, + { + "@id": "bts:Stomach" + }, + { + "@id": "bts:StomachMucosaOnly" + }, + { + "@id": "bts:SubcutaneousTissue" + }, + { + "@id": "bts:Synovium" + }, + { + "@id": "bts:TemporalCortex" + }, + { + "@id": "bts:Tendon" + }, + { + "@id": "bts:Testis" + }, + { + "@id": "bts:Thigh" + }, + { + "@id": "bts:ThoracicSpine" + }, + { + "@id": "bts:Thorax" + }, + { + "@id": "bts:Throat" + }, + { + "@id": "bts:Thumb" + }, + { + "@id": "bts:Thymus" + }, + { + "@id": "bts:Thyroid" + }, + { + "@id": "bts:Tibia" + }, + { + "@id": "bts:Tongue" + }, + { + "@id": "bts:Tonsil" + }, + { + "@id": "bts:Tonsil(Pharyngeal)" + }, + { + "@id": "bts:Trachea/MajorBronchi" + }, + { + "@id": "bts:TransverseColon" + }, + { + "@id": "bts:Trunk" + }, + { + "@id": "bts:UmbilicalCord" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:Ureter" + }, + { + "@id": "bts:Urethra" + }, + { + "@id": "bts:UrinaryTract" + }, + { + "@id": "bts:Uterus" + }, + { + "@id": "bts:Uvula" + }, + { + "@id": "bts:Vagina" + }, + { + "@id": "bts:VasDeferens" + }, + { + "@id": "bts:Vein" + }, + { + "@id": "bts:Venous" + }, { - "@id": "bts:VitalStatus" + "@id": "bts:Vertebra" }, { - "@id": "bts:PrematureAtBirth" + "@id": "bts:Vulva" }, { - "@id": "bts:RelationshipGender" + "@id": "bts:WhiteBloodCells" }, { - "@id": "bts:RelativewithCancerHistory" + "@id": "bts:Wrist" }, { - "@id": "bts:AlcoholHistory" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Prior Sites of Radiation", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Immunosuppression", + "@type": "rdfs:Class", + "rdfs:comment": "The indicator that describes whether or not immunosuppressive therapy was administered.", + "rdfs:label": "Immunosuppression", + "rdfs:subClassOf": [ + { + "@id": "bts:Therapy" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" }, { - "@id": "bts:AsbestosExposure" + "@id": "bts:No" }, { - "@id": "bts:CoalDustExposure" + "@id": "bts:Unknown" }, { - "@id": "bts:EnvironmentalTobaccoSmokeExposure" + "@id": "bts:NotApplicable" }, { - "@id": "bts:RadonExposure" + "@id": "bts:NotDone" + } + ], + "sms:displayName": "Immunosuppression", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ConcomitantMedicationReceivedType", + "@type": "rdfs:Class", + "rdfs:comment": "An enumerated list of the type of concomitant medication received by the patient.", + "rdfs:label": "ConcomitantMedicationReceivedType", + "rdfs:subClassOf": [ + { + "@id": "bts:Therapy" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Anticoagulantagents" }, { - "@id": "bts:RespirableCrystallineSilicaExposure" + "@id": "bts:Anticonvulsant" }, { - "@id": "bts:SmokingFrequency" + "@id": "bts:Antifungal" }, { - "@id": "bts:SecondhandSmokeasChild" + "@id": "bts:Antiplateletagents" }, { - "@id": "bts:HepatitisSustainedVirologicalResponse" + "@id": "bts:Antidepressants-ModerateCYP2D6inhibitors" }, { - "@id": "bts:HAARTTreatmentIndicator" + "@id": "bts:Antidepressants-StrongCYP2D6inhibitors" }, { - "@id": "bts:ProgressionorRecurrence" + "@id": "bts:Antidepressants-weakCYP2D2inhibitorsornon-inhibitors" }, { - "@id": "bts:RiskFactorTreatment" + "@id": "bts:Anxiolyticsorsedatives" }, { - "@id": "bts:TreatmentorTherapy" + "@id": "bts:Aspirin" }, { - "@id": "bts:ChemoConcurrenttoRadiation" + "@id": "bts:Bisphosphonatesfortreatment/preventionofboneloss" }, { - "@id": "bts:SatelliteMetastasisPresentIndicator" + "@id": "bts:Corticosteroid" }, { - "@id": "bts:Immunosuppression" + "@id": "bts:COX-2inhibitor" }, { - "@id": "bts:FamilyMemberVitalStatusIndicator" + "@id": "bts:Decadron" }, { - "@id": "bts:COVID19OccurrenceIndicator" + "@id": "bts:Diabetes-Insulin" }, { - "@id": "bts:COVID19PositiveLabTestIndicator" + "@id": "bts:Diabetes-Metformincontainingagents" }, { - "@id": "bts:COVID19CancerTreatmentFollowup" + "@id": "bts:Growthfactor" }, { - "@id": "bts:KnownGeneticPredispositionMutation" + "@id": "bts:Intravaginalestrogenpreparations" }, { - "@id": "bts:MismatchRepairMutation" + "@id": "bts:Lipid-loweringdrugs" }, { - "@id": "bts:VariantOrigin" + "@id": "bts:Non-prescriptionsupplementsformemory" }, { - "@id": "bts:INPCHistologicGroup" + "@id": "bts:Non-prescriptionsupplementsforreliefofhotflashes" }, { - "@id": "bts:MicropapillaryFeatures" + "@id": "bts:Non-steroidalanti-inflammatoryagents" }, { - "@id": "bts:NonNodalTumorDeposits" + "@id": "bts:Opioids" }, { - "@id": "bts:PregnantatDiagnosis" + "@id": "bts:Other" }, { - "@id": "bts:PriorMalignancy" + "@id": "bts:Prescriptionmedicationsformemory" }, { - "@id": "bts:PriorTreatment" + "@id": "bts:Prescriptionmedicationsforreliefofhotflashes" }, { - "@id": "bts:AnaplasiaPresent" + "@id": "bts:Prophylacticantiplatelettherapy" }, { - "@id": "bts:LymphaticInvasionPresent" + "@id": "bts:Tricyclicantidepressants" }, { - "@id": "bts:PerineuralInvasionPresent" + "@id": "bts:NotApplicable" }, { - "@id": "bts:SynchronousMalignancy" + "@id": "bts:Unknown" }, { - "@id": "bts:TumorConfinedtoOrganofOrigin" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Concomitant Medication Received Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:FamilyMemberVitalStatusIndicator", + "@type": "rdfs:Class", + "rdfs:comment": "The response indicates whether the family member of the patient with a history of cancer is alive. (Extension to GDC attributes in Family History Tier 1)", + "rdfs:label": "FamilyMemberVitalStatusIndicator", + "rdfs:subClassOf": [ + { + "@id": "bts:FamilyHistory" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:VitalStatusAlive" }, { - "@id": "bts:TumorFocality" + "@id": "bts:VitalStatusDead" }, { - "@id": "bts:VascularInvasionPresent" + "@id": "bts:Unknown" }, { - "@id": "bts:ImmediateFamilyHistoryEndometrialCancer" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Family Member Vital Status Indicator", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:COVID19OccurrenceIndicator", + "@type": "rdfs:Class", + "rdfs:comment": "The indicator that describes whether or not a COVID-19 infectious disorder occurred.", + "rdfs:label": "COVID19OccurrenceIndicator", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" }, { - "@id": "bts:ImmediateFamilyHistoryOvarianCancer" + "@id": "bts:No" }, { - "@id": "bts:ColorectalCancerKRASIndicator" + "@id": "bts:Unknown" }, { - "@id": "bts:ColonPolypOccurenceIndicator" + "@id": "bts:NotApplicable" }, { - "@id": "bts:FamilyHistoryColorectalPolyp" + "@id": "bts:NotDone" + } + ], + "sms:displayName": "COVID19 Occurrence Indicator", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:COVID19CurrentStatus", + "@type": "rdfs:Class", + "rdfs:comment": "The patient's current COVID-19 status of sign or symptom events or interventions", + "rdfs:label": "COVID19CurrentStatus", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Patientcurrentlyhassymptoms" }, { - "@id": "bts:ColorectalPolypNewIndicator" + "@id": "bts:Patienthadsymptomsbutnowisfullyrecovered" }, { - "@id": "bts:HormoneTherapyBreastCancerPreventionIndicator" + "@id": "bts:PatientneverhadanysymptomsofCOVID-19" }, { - "@id": "bts:MultifocalBreastCarcinomaPresentIndicator" + "@id": "bts:StatusunknownduetogeneralCOVID-19relatedtravelrestrictions" }, { - "@id": "bts:MulticentricBreastCarcinomaPresentIndicator" + "@id": "bts:Statusunknownduetolackofdisease/tumorassessmentduetoCOVID-19diagnosis" }, { - "@id": "bts:GliomaSpecificRadiationField" + "@id": "bts:Statusunknownduetootherreasons" + } + ], + "sms:displayName": "COVID19 Current Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:COVID19PositiveLabTestIndicator", + "@type": "rdfs:Class", + "rdfs:comment": "The indicator that describes whether or not there was a COVID-19 positive test result.", + "rdfs:label": "COVID19PositiveLabTestIndicator", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" }, { - "@id": "bts:SupraTentorialEpendymomaMolecularSubgroup" + "@id": "bts:No" }, { - "@id": "bts:NCIALLRiskGroup" + "@id": "bts:Unknown" }, { - "@id": "bts:ProstateCancerLocalExtent" + "@id": "bts:NotApplicable" }, { - "@id": "bts:CutaneousMelanomaSurgicalMargins" + "@id": "bts:NotDone" + } + ], + "sms:displayName": "COVID19 Positive Lab Test Indicator", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:COVID19AntibodyTesting", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that demonstrates the test results of immunoglobulin M (IgM) and immunoglobulin G (IgG) antibodies to the SARS-CoV-2 virus in subject serum samples.", + "rdfs:label": "COVID19AntibodyTesting", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:SARS-CoV-2IgMantibodypositive" }, { - "@id": "bts:HistoryofBlisteringSunburn" + "@id": "bts:SARS-CoV-2IgGantibodypositive" }, { - "@id": "bts:ImmediateFamilyHistoryMelanoma" + "@id": "bts:SARS-CoV-2IgG/IgMantibodypositive" }, { - "@id": "bts:CutaneousMelanomaUlceration" + "@id": "bts:SARS-CoV-2IgMantibodynegative" }, { - 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"@id": "bts:AJCCClinicalM" + "@id": "bts:Rwanda" }, { - "@id": "bts:AJCCPathologicM" + "@id": "bts:SaintHelenaAscensionandTristandaCunha" }, { - "@id": "bts:SarcomaSubtype" + "@id": "bts:SaintKittsandNevis" }, { - "@id": "bts:CauseofDeath" + "@id": "bts:SaintLucia" }, { - "@id": "bts:ViralHepatitisSerologies" + "@id": "bts:SaintPierreandMiquelon" }, { - "@id": "bts:AJCCStagingSystemEdition" + "@id": "bts:SaintVincentandtheGrenadines" }, { - "@id": "bts:DiabetesTreatmentType" + "@id": "bts:Samoa" }, { - "@id": "bts:TreatmentFrequency" + "@id": "bts:SanMarino" }, { - "@id": "bts:TumorGrade" + "@id": "bts:SaoTomeandPrincipe" }, { - "@id": "bts:PancreasPrecancerHistopathologicGrade" + "@id": "bts:SaudiArabia" }, { - "@id": "bts:IRSGroup" + "@id": "bts:Senegal" }, { - "@id": "bts:KarnofskyPerformanceStatus" + "@id": "bts:Serbia" }, { - "@id": "bts:TreatmentOutcome" + "@id": "bts:Seychelles" }, { - "@id": "bts:ECOGPerformanceStatus" + "@id": "bts:SierraLeone" }, { - "@id": "bts:ExtentofTumorResection" + "@id": "bts:Singapore" }, { - "@id": "bts:TestResult" + "@id": "bts:Slovakia" }, { - "@id": "bts:LungAdjacentHistologyType" + "@id": "bts:Slovenia" }, { - "@id": "bts:LungCancerParticipantProcedureHistory" + "@id": "bts:SolomonIslands" }, { - "@id": "bts:HistoneVariant" + "@id": "bts:Somalia" }, { - "@id": "bts:PreservationMethod" + "@id": "bts:SouthAfrica" }, { - "@id": "bts:MolecularAnalysisMethod" + "@id": "bts:SouthKorea" }, { - "@id": "bts:LocationExtentExtraprostaticExtension" + "@id": "bts:SouthSudan" }, { - "@id": "bts:MelanomaBiopsyResectionSites" + "@id": "bts:Spain" }, { - "@id": "bts:HPVPositiveType" + "@id": "bts:SriLanka" }, { - "@id": "bts:LymphNodeInvolvedSite" + "@id": "bts:StateofPalestine" }, { - "@id": "bts:AdditionalTopography" + "@id": "bts:Sudan" }, { - "@id": "bts:ClinicalBiospecimenType" + "@id": "bts:Suriname" }, { - "@id": "bts:VariantType" + "@id": "bts:Svalbard&JanMayenIslands" }, { - "@id": "bts:MethodofDiagnosis" + "@id": "bts:Sweden" }, { - "@id": "bts:AJCCClinicalN" + "@id": "bts:Switzerland" }, { - "@id": "bts:AJCCPathologicN" + "@id": "bts:Syria" }, { - "@id": "bts:Chromosome" + "@id": "bts:Taiwan" }, { - "@id": "bts:LocationNaturePositiveMargins" + "@id": "bts:Tajikistan" }, { - "@id": "bts:ConcomitantMedicationReceivedType" + "@id": "bts:Tanzania" }, { - "@id": "bts:Antigen" + "@id": "bts:Thailand" }, { - "@id": "bts:CurrentLungCancerSymptoms" + "@id": "bts:Timor-Leste" }, { - "@id": "bts:DiseaseResponse" + "@id": "bts:Togo" }, { - "@id": "bts:AJCCClinicalStage" + "@id": "bts:Tokelau" }, { - "@id": "bts:AJCCPathologicStage" + "@id": "bts:Tonga" }, { - "@id": "bts:MetastasisatDiagnosisSite" + "@id": "bts:TrinidadandTobago" }, { - "@id": "bts:CDSSequencingPlatform" + "@id": "bts:Tunisia" }, { - "@id": "bts:SequencingPlatform" + "@id": "bts:Turkey" }, { - "@id": "bts:AJCCClinicalT" + "@id": "bts:Turkmenistan" }, { - "@id": "bts:AJCCPathologicT" + "@id": "bts:Tuvalu" }, { - "@id": "bts:HereditaryCancerPredispositionSyndrome" + "@id": "bts:Uganda" }, { - "@id": "bts:CancerAssociatedGeneMutations" + "@id": "bts:Ukraine" }, { - "@id": "bts:MutationalSignatures" + "@id": "bts:UnitedArabEmirates" }, { - "@id": "bts:LungCancerHarboringGenomicAberrations" + "@id": "bts:UnitedKingdom" }, { - "@id": "bts:LaboratoryTest" + "@id": "bts:UnitedStates" }, { - "@id": "bts:RelationshipPrimaryDiagnosis" + "@id": "bts:Uruguay" }, { - "@id": "bts:TreatmentType" + "@id": "bts:Uzbekistan" }, { - "@id": "bts:LungTopography" + "@id": "bts:Vanuatu" }, { - "@id": "bts:RiskFactor" + "@id": "bts:Venezuela" }, { - "@id": "bts:RelationshipType" + "@id": "bts:Vietnam" }, { - "@id": "bts:Comorbidity" + "@id": "bts:VirginIslandsBritish" }, { - "@id": "bts:PriorSitesofRadiation" + "@id": "bts:VirginIslandsU.S." }, { - "@id": "bts:TopographyCode" + "@id": "bts:WallisandFutuna" }, { - "@id": "bts:ProgressionorRecurrenceAnatomicSite" + "@id": "bts:WesternSahara" }, { - "@id": "bts:TreatmentAnatomicSite" + "@id": "bts:Yemen" }, { - "@id": "bts:SiteofResectionorBiopsy" + "@id": "bts:Zambia" }, { - "@id": "bts:TissueorOrganofOrigin" + "@id": "bts:Zimbabwe" }, { - "@id": "bts:PrimaryDiagnosis" + "@id": "bts:Unknown" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Not Reported", + "sms:displayName": "Country of Birth", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Random", + "@id": "bts:MedicallyUnderservedArea", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Random", + "rdfs:comment": "Areas or populations designated by HRSA as having too few primary care providers, high infant mortality, high poverty or a high elderly population: Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/ - enter the zip code in the main text field and use the associated county on the right side of the result field. Go to data.hrsa.gov website and select \"Query Data\". Pick the Medically Underserved Areas/Populations (MUA/P) data source in the step 1 menu and select \"View Data\". Enter the name of the county (_______ county) in the first \"Service Area\" column, adding the state in the 5th column may help direct you to the data. If the designation type in the third column is \"medically underserved area\" enter \"Yes\" as the value. If the county generates a \"No data available in table\" enter \"No\" as the value. A value of \"Unknown\" indicates that sufficient data was not available to look up the value. If value is yes, complete the Medically_underserved_score data element.", + "rdfs:label": "MedicallyUnderservedArea", "rdfs:subClassOf": [ { - "@id": "bts:CDSLibrarySelectionMethod" - }, - { - "@id": "bts:ReverseTranscriptionPrimer" - }, - { - "@id": "bts:LibrarySelectionMethod" + "@id": "bts:ClinicalTier2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Random", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:RRNADepletion", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "RRNADepletion", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ + { + "@id": "bts:MedicallyUnderservedArea-Yes" + }, { - "@id": "bts:CDSLibrarySelectionMethod" + "@id": "bts:MedicallyUnderservedArea-No" }, { - "@id": "bts:LibrarySelectionMethod" + "@id": "bts:MedicallyUnderservedArea-Unknown" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "rRNA Depletion", + "sms:displayName": "Medically Underserved Area", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CDSOtherDataTypeSpecified", + "@id": "bts:RuralvsUrban", "@type": "rdfs:Class", - "rdfs:comment": "Other types of data associated with the content.", - "rdfs:label": "CDSOtherDataTypeSpecified", + "rdfs:comment": "Density of population in the county of residence, based on census data (updated last on 4/28/20). Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the associated county on the right side of the result field. Go to https://www2.census.gov/programs-surveys/acs/data/covid_19/Data_Profiles_for_HHS/050-County_By_State/. Select the dp02_XX.csv file where XX = the two letter abbreviation for the appropriate state. On row 166 find the total population for the appropriate county. If the total population is <2,500 enter a value of \"Rural Population\"; if 2,500 - 50,000 enter a value of \"Urban Cluster\"; or if >50,000 enter \"Urban Population\"", + "rdfs:label": "RuralvsUrban", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ClinicalTier2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "CDS Other Data Type Specified", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "schema:rangeIncludes": [ + { + "@id": "bts:UrbanPopulation(population>50000)" + }, + { + "@id": "bts:UrbanCluster(population2500-50000)" + }, { - "@id": "bts:CDSDataType" + "@id": "bts:RuralPopulation(population<2500)" } ], + "sms:displayName": "Rural vs Urban", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Checksum", + "@id": "bts:CancerIncidence", "@type": "rdfs:Class", - "rdfs:comment": "MD5 checksum of the BAM file", - "rdfs:label": "Checksum", + "rdfs:comment": "Incidence of specific cancer type in a defined area (a number between 0 and 100). The rate of incident cases per population of 100,000 persons of a specific type of cancer as designated in the \"primary_diagnosis\" data element in the county where the patient resides, using the most recent 2013-2017 NCI Cancer Atlas derived data. Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the asociated county on the right side of the result field. On the https://gis.cancer.gov/canceratlas/tableview/ website, choose \"Incidence\" from the Topic dropdown menu, state of interest from the Area menu, \"All Races\" from the Race menu, and the cancer type (\"Both Sexes\" when possible) from the Statistic menu. Find the county of interest and enter the numeric Age-Adjusted Rate per 100,000 as the value.", + "rdfs:label": "CancerIncidence", "rdfs:subClassOf": [ { - "@id": "bts:InformationContentEntity" + "@id": "bts:ClinicalTier2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Checksum", - "sms:required": "sms:true", + "sms:displayName": "Cancer Incidence", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HTANBiospecimenID", + "@id": "bts:CancerIncidenceLocation", "@type": "rdfs:Class", - "rdfs:comment": "HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz)", - "rdfs:label": "HTANBiospecimenID", + "rdfs:comment": "The county and state in which the patient lives and to which the cancer_incidence data correlates. Record as \"County, State\" as they appear in the incidence box from which the cancer_incidence data is obtained in the https://gis.cancer.gov/canceratlas/tableview/ website", + "rdfs:label": "CancerIncidenceLocation", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ClinicalTier2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HTAN Biospecimen ID", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\\d*|0000))_([0-9]\\d*|0000)$ warning" - ] + "sms:displayName": "Cancer Incidence Location", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:Biospecimen", + "@id": "bts:SRRSClinicalDataTier2", "@type": "rdfs:Class", - "rdfs:comment": "HTAN biological entity; this can be tissue, blood, analyte and subsamples of those", - "rdfs:label": "Biospecimen", + "rdfs:comment": "Cancer related clinical data specific to SRRS", + "rdfs:label": "SRRSClinicalDataTier2", "rdfs:subClassOf": [ { - "@id": "bts:Biosample" + "@id": "bts:Patient" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Biospecimen", + "sms:displayName": "SRRS Clinical Data Tier 2", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Patient" - } - ], "sms:requiresDependency": [ { "@id": "bts:Component" }, { - "@id": "bts:HTANBiospecimenID" - }, - { - "@id": "bts:SourceHTANBiospecimenID" - }, - { - "@id": "bts:HTANParentID" + "@id": "bts:HTANParticipantID" }, { "@id": "bts:TimepointLabel" }, { - "@id": "bts:CollectionDaysfromIndex" - }, - { - "@id": "bts:AdjacentBiospecimenIDs" - }, - { - "@id": "bts:BiospecimenType" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:AcquisitionMethodType" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:FixativeType" + "@id": "bts:EducationLevel" }, { - "@id": "bts:StorageMethod" + "@id": "bts:CountryofBirth" }, { - "@id": "bts:ProcessingDaysfromIndex" + "@id": "bts:MedicallyUnderservedArea" }, { - "@id": "bts:ProtocolLink" + "@id": "bts:RuralvsUrban" }, { - "@id": "bts:SiteDataSource" + "@id": "bts:CancerIncidence" }, { - "@id": "bts:CollectionMedia" + "@id": "bts:CancerIncidenceLocation" }, { - "@id": "bts:MountingMedium" + "@id": "bts:Ethnicity" }, { - "@id": "bts:ProcessingLocation" + "@id": "bts:Gender" }, { - "@id": "bts:HistologyAssessmentBy" + "@id": "bts:Race" }, { - "@id": "bts:HistologyAssessmentMedium" + "@id": "bts:VitalStatus" }, { - "@id": "bts:PreinvasiveMorphology" + "@id": "bts:AgeatDiagnosis" }, { - "@id": "bts:TumorInfiltratingLymphocytes" + "@id": "bts:DaystoLastFollowup" }, { - "@id": "bts:DegreeofDysplasia" + "@id": "bts:DaystoLastKnownDiseaseStatus" }, { - "@id": "bts:DysplasiaFraction" + "@id": "bts:DaystoRecurrence" }, { - "@id": "bts:NumberProliferatingCells" + "@id": "bts:LastKnownDiseaseStatus" }, { - "@id": "bts:PercentEosinophilInfiltration" + "@id": "bts:Morphology" }, { - "@id": "bts:PercentGranulocyteInfiltration" + "@id": "bts:PrimaryDiagnosis" }, { - "@id": "bts:PercentInflamInfiltration" + "@id": "bts:ProgressionorRecurrence" }, { - "@id": "bts:PercentLymphocyteInfiltration" + "@id": "bts:SiteofResectionorBiopsy" }, { - "@id": "bts:PercentMonocyteInfiltration" + "@id": "bts:TissueorOrganofOrigin" }, { - "@id": "bts:PercentNecrosis" + "@id": "bts:NCIAtlasCancerSite" }, { - "@id": "bts:PercentNeutrophilInfiltration" + "@id": "bts:TumorGrade" }, { - "@id": "bts:PercentNormalCells" + "@id": "bts:PackYearsSmoked" }, { - "@id": "bts:PercentStromalCells" + "@id": "bts:YearsSmoked" }, { - "@id": "bts:PercentTumorCells" + "@id": "bts:DaystoFollowUp" }, { - "@id": "bts:PercentTumorNuclei" + "@id": "bts:GeneSymbol" }, { - "@id": "bts:FiducialMarker" + "@id": "bts:MolecularAnalysisMethod" }, { - "@id": "bts:SlicingMethod" + "@id": "bts:TestResult" }, { - "@id": "bts:LysisBuffer" + "@id": "bts:TreatmentType" }, { - "@id": "bts:MethodofNucleicAcidIsolation" + "@id": "bts:TumorLargestDimensionDiameter" } ], "sms:validationRules": [] }, { - "@id": "bts:HTANParentID", + "@id": "bts:Ethnicity", "@type": "rdfs:Class", - "rdfs:comment": "HTAN ID of parent from which the biospecimen was obtained. Parent could be another biospecimen or a research participant.", - "rdfs:label": "HTANParentID", + "rdfs:comment": "An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.", + "rdfs:label": "Ethnicity", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Demographics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HTAN Parent ID", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:HTANParentDataFileID", - "@type": "rdfs:Class", - "rdfs:comment": "HTAN Data File Identifier indicating the file(s) from which these files were derived", - "rdfs:label": "HTANParentDataFileID", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:File" + "@id": "bts:Hispanicorlatino" + }, + { + "@id": "bts:Nothispanicorlatino" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + }, + { + "@id": "bts:Notallowedtocollect" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "HTAN Parent Data File ID", + "sms:displayName": "Ethnicity", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ClinicalDataTier2", + "@id": "bts:Gender", "@type": "rdfs:Class", - "rdfs:comment": "Tier 2 Cancer Data", - "rdfs:label": "ClinicalDataTier2", + "rdfs:comment": "Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc.]", + "rdfs:label": "Gender", "rdfs:subClassOf": [ { - "@id": "bts:Patient" + "@id": "bts:Demographics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Clinical Data Tier 2", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:HTANParticipantID" - }, - { - "@id": "bts:TimepointLabel" - }, - { - "@id": "bts:StartDaysfromIndex" - }, - { - "@id": "bts:StopDaysfromIndex" - }, - { - "@id": "bts:SentinelLymphNodeCount" - }, - { - "@id": "bts:SentinelNodePositiveAssessmentCount" - }, - { - "@id": "bts:TumorExtranodalExtensionIndicator" - }, - { - "@id": "bts:SatelliteMetastasisPresentIndicator" - }, - { - "@id": "bts:OtherBiopsyResectionSite" - }, - { - "@id": "bts:ExtentofTumorResection" - }, - { - "@id": "bts:PriorSitesofRadiation" - }, - { - "@id": "bts:Immunosuppression" - }, - { - "@id": "bts:ConcomitantMedicationReceivedType" - }, - { - "@id": "bts:FamilyMemberVitalStatusIndicator" - }, - { - "@id": "bts:COVID19OccurrenceIndicator" - }, - { - "@id": "bts:COVID19CurrentStatus" - }, - { - "@id": "bts:COVID19PositiveLabTestIndicator" - }, - { - "@id": "bts:COVID19AntibodyTesting" - }, - { - "@id": "bts:COVID19ComplicationsSeverity" - }, - { - "@id": "bts:COVID19CancerTreatmentFollowup" - }, - { - "@id": "bts:Ecigvapeuse" - }, - { - "@id": "bts:Ecigvape30dayusenum" - }, - { - "@id": "bts:Ecigvapetimesperday" - }, - { - "@id": "bts:Typeofsmokeexposurecumulativeyears" - }, + "schema:rangeIncludes": [ { - "@id": "bts:Chewingtobaccodailyusecount" + "@id": "bts:Female" }, { - "@id": "bts:Secondhandsmokeexposureyears" + "@id": "bts:Male" }, { - "@id": "bts:KnownGeneticPredispositionMutation" + "@id": "bts:Unknown" }, { - "@id": "bts:HereditaryCancerPredispositionSyndrome" + "@id": "bts:Unspecified" }, { - "@id": "bts:CancerAssociatedGeneMutations" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Gender", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Race", + "@type": "rdfs:Class", + "rdfs:comment": "An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation withina a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution.", + "rdfs:label": "Race", + "rdfs:subClassOf": [ { - "@id": "bts:MutationalSignatures" - }, + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:MismatchRepairSystemStatus" + "@id": "bts:White" }, { - "@id": "bts:LabTestsforMMRStatus" + "@id": "bts:Americanindianoralaskanative" }, { - "@id": "bts:ModeofCancerDetection" + "@id": "bts:Blackorafricanamerican" }, { - "@id": "bts:EducationLevel" + "@id": "bts:Asian" }, { - "@id": "bts:CountryofBirth" + "@id": "bts:Nativehawaiianorotherpacificislander" }, { - "@id": "bts:MedicallyUnderservedArea" + "@id": "bts:Other" }, { - "@id": "bts:RuralvsUrban" + "@id": "bts:Unknown" }, { - "@id": "bts:CancerIncidence" + "@id": "bts:NotReported" }, { - "@id": "bts:CancerIncidenceLocation" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:TimepointLabel", - "@type": "rdfs:Class", - "rdfs:comment": "Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.", - "rdfs:label": "TimepointLabel", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" + "@id": "bts:Notallowedtocollect" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Timepoint Label", + "sms:displayName": "Race", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:StartDaysfromIndex", + "@id": "bts:VitalStatus", "@type": "rdfs:Class", - "rdfs:comment": "Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'", - "rdfs:label": "StartDaysfromIndex", + "rdfs:comment": "The survival state of the person registered on the protocol.", + "rdfs:label": "VitalStatus", "rdfs:subClassOf": [ { - "@id": "bts:Patient" + "@id": "bts:Demographics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Start Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:StopDaysfromIndex", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'", - "rdfs:label": "StopDaysfromIndex", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Stop Days from Index", - "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:SentinelLymphNodeCount", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric count of sentinel lymph nodes.", - "rdfs:label": "SentinelLymphNodeCount", - "rdfs:subClassOf": [ + "@id": "bts:Alive" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Sentinel Lymph Node Count", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SentinelNodePositiveAssessmentCount", - "@type": "rdfs:Class", - "rdfs:comment": "The number or amount of metastatic neoplasms related to the confirmed presence of disease or specific microorganisms during examination of the first rounded mass of lymphatic tissue to which cancer is likely to spread from the primary tumor.", - "rdfs:label": "SentinelNodePositiveAssessmentCount", - "rdfs:subClassOf": [ + "@id": "bts:Dead" + }, { - "@id": "bts:Diagnosis" + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Sentinel Node Positive Assessment Count", - "sms:required": "sms:false", + "sms:displayName": "Vital Status", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TumorExtranodalExtensionIndicator", + "@id": "bts:AgeatDiagnosis", "@type": "rdfs:Class", - "rdfs:comment": "The indicator to determine extranodal involvement or extent of the disease.", - "rdfs:label": "TumorExtranodalExtensionIndicator", + "rdfs:comment": "Age at the time of diagnosis expressed in number of days since birth.", + "rdfs:label": "AgeatDiagnosis", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Absent" - }, - { - "@id": "bts:Indeterminate" - }, - { - "@id": "bts:NO" - }, - { - "@id": "bts:YES" - }, - { - "@id": "bts:Nosourcedocumentation" - }, - { - "@id": "bts:Notapplicable" - }, - { - "@id": "bts:Notsampledordissected" - }, - { - "@id": "bts:Present" - }, - { - "@id": "bts:Present-extensive" - }, - { - "@id": "bts:Present-minimal" - }, - { - "@id": "bts:UNKNOWN" - }, - { - "@id": "bts:Unspecified" + "@id": "bts:Diagnosis" } ], - "sms:displayName": "Tumor Extranodal Extension Indicator", - "sms:required": "sms:false", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Age at Diagnosis", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SatelliteMetastasisPresentIndicator", + "@id": "bts:DaystoLastFollowup", "@type": "rdfs:Class", - "rdfs:comment": "A yes/no indicator to ask if intransit metastases or satellite lesions are present.", - "rdfs:label": "SatelliteMetastasisPresentIndicator", + "rdfs:comment": "Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoLastFollowup", "rdfs:subClassOf": [ { "@id": "bts:Diagnosis" @@ -6494,43 +10408,55 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, + "sms:displayName": "Days to Last Follow up", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:DaystoLastKnownDiseaseStatus", + "@type": "rdfs:Class", + "rdfs:comment": "Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoLastKnownDiseaseStatus", + "rdfs:subClassOf": [ { - "@id": "bts:Unknown" + "@id": "bts:Diagnosis" } ], - "sms:displayName": "Satellite Metastasis Present Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Days to Last Known Disease Status", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:OtherBiopsyResectionSite", + "@id": "bts:DaystoRecurrence", "@type": "rdfs:Class", - "rdfs:comment": "A description of the location on or within the human body where the surgical biopsy/resection procedure was performed (Not covered under HTAN Clinical Data Tier 1)", - "rdfs:label": "OtherBiopsyResectionSite", + "rdfs:comment": "Number of days between the date used for index and the date the patient's disease recurred. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoRecurrence", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Other Biopsy Resection Site", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "Days to Recurrence", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:ExtentofTumorResection", + "@id": "bts:LastKnownDiseaseStatus", "@type": "rdfs:Class", - "rdfs:comment": "The degree to which the lesion has been cut out, or resected.", - "rdfs:label": "ExtentofTumorResection", + "rdfs:comment": "Text term that describes the last known state or condition of an individual's neoplasm.", + "rdfs:label": "LastKnownDiseaseStatus", "rdfs:subClassOf": [ { "@id": "bts:Diagnosis" @@ -6541,2053 +10467,1596 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:GrossTotalResection" - }, - { - "@id": "bts:OpenBiopsy" - }, - { - "@id": "bts:SubtotalResection" - }, - { - "@id": "bts:ExtensiveSubtotal" - }, - { - "@id": "bts:Minor" - }, - { - "@id": "bts:Optimaldebulking" - }, - { - "@id": "bts:Other" + "@id": "bts:Distantmetrecurrence/progression" }, { - "@id": "bts:Partialdebulking" + "@id": "bts:Loco-regionalrecurrence/progression" }, { - "@id": "bts:Segmental" + "@id": "bts:Biochemicalevidenceofdiseasewithoutstructuralcorrelate" }, { - "@id": "bts:Suboptimal" + "@id": "bts:Tumorfree" }, { - "@id": "bts:Suboptimaldebulking" + "@id": "bts:Unknowntumorstatus" }, { - "@id": "bts:NTR" + "@id": "bts:Withtumor" }, { - "@id": "bts:Unknown" + "@id": "bts:NotReported" }, { - "@id": "bts:NotReported" + "@id": "bts:NotAllowedToCollect" }, { "@id": "bts:NotApplicable" } ], - "sms:displayName": "Extent of Tumor Resection", - "sms:required": "sms:false", + "sms:displayName": "Last Known Disease Status", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PriorSitesofRadiation", + "@id": "bts:Morphology", "@type": "rdfs:Class", - "rdfs:comment": "The anatomic location to which radiation treatment was administered to a patient prior to enrollment on a protocol.", - "rdfs:label": "PriorSitesofRadiation", + "rdfs:comment": "The third edition of the International Classification of Diseases for Oncology, published in 2000 used principally in tumor and cancer registries for coding the site (topography) and the histology (morphology) of neoplasms. The study of the structure of the cells and their arrangement to constitute tissues and, finally, the association among these to form organs. In pathology, the microscopic process of identifying normal and abnormal morphologic characteristics in tissues, by employing various cytochemical and immunocytochemical stains. A system of numbered categories for representation of data.", + "rdfs:label": "Morphology", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Abdomentotal" - }, - { - "@id": "bts:AbdominalWall" - }, - { - "@id": "bts:Acetabulum" - }, - { - "@id": "bts:Adenoid" - }, - { - "@id": "bts:Adipose" - }, - { - "@id": "bts:Adrenal" - }, - { - "@id": "bts:AlveolarRidge" - }, - { - "@id": "bts:AmnioticFluid" - }, - { - "@id": "bts:AmpullaofVater" - }, - { - "@id": "bts:AnalSphincter" - }, - { - "@id": "bts:Ankle" - }, - { - "@id": "bts:Anorectum" - }, - { - "@id": "bts:AntecubitalFossa" - }, - { - "@id": "bts:Antrum" - }, - { - "@id": "bts:Anus" - }, - { - "@id": "bts:Aorta" - }, - { - "@id": "bts:AorticBody" - }, - { - "@id": "bts:Appendix" - }, - { - "@id": "bts:AqueousFluid" - }, - { - "@id": "bts:Arm" - }, - { - "@id": "bts:Artery" - }, - { - "@id": "bts:AscendingColon" - }, - { - "@id": "bts:AscendingColonHepaticFlexure" - }, - { - "@id": "bts:Ascites" - }, - { - "@id": "bts:AuditoryCanal" - }, - { - "@id": "bts:AutonomicNervousSystem" - }, - { - "@id": "bts:Axilla" - }, - { - "@id": "bts:Back" - }, - { - "@id": "bts:BileDuct" - }, - { - "@id": "bts:Bladder" - }, - { - "@id": "bts:Blood" - }, - { - "@id": "bts:BloodVessel" - }, - { - "@id": "bts:Bodytotal" - }, - { - "@id": "bts:Bone" - }, - { - "@id": "bts:BoneMarrow" - }, - { - "@id": "bts:Bonenon-spine" - }, - { - "@id": "bts:Bowel" - }, - { - "@id": "bts:Brain" - }, + "sms:displayName": "Morphology", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:PrimaryDiagnosis", + "@type": "rdfs:Class", + "rdfs:comment": "Text term used to describe the patient's histologic diagnosis, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", + "rdfs:label": "PrimaryDiagnosis", + "rdfs:subClassOf": [ { - "@id": "bts:BrainStem" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Breast" + "@id": "bts:Acinarcellcarcinoma" }, { - "@id": "bts:BroadLigament" + "@id": "bts:Acutebasophilicleukaemia" }, { - "@id": "bts:Bronchiole" + "@id": "bts:AcuteleukemiaBurkitttype" }, { - "@id": "bts:Bronchus" + "@id": "bts:AcuteleukemiaNOS" }, { - "@id": "bts:Brow" + "@id": "bts:Acutelymphaticleukemia" }, { - "@id": "bts:BuccalCavity" + "@id": "bts:Acutelymphoblasticleukemia-lymphomaNOS" }, { - "@id": "bts:BuccalMucosa" + "@id": "bts:AcutelymphoblasticleukemiamatureB-celltype" }, { - "@id": "bts:Buttock" + "@id": "bts:AcutelymphoblasticleukemiaNOS" }, { - "@id": "bts:Calf" + "@id": "bts:Acutelymphoblasticleukemiaprecursorcelltype" }, { - "@id": "bts:Capillary" + "@id": "bts:Acutelymphocyticleukemia" }, { - "@id": "bts:Cardia" + "@id": "bts:Acutelymphoidleukemia" }, { - "@id": "bts:Carina" + "@id": "bts:Acutemyeloidleukemiaminimaldifferentiation" }, { - "@id": "bts:CarotidArtery" + "@id": "bts:AcutemyeloidleukemiaMLL" }, { - "@id": "bts:CarotidBody" + "@id": "bts:AcutemyeloidleukemiaNOS" }, { - "@id": "bts:Cartilage" + "@id": "bts:Acutemyelomonocyticleukemia" }, { - "@id": "bts:Cecum" + "@id": "bts:AcutepromyelocyticleukemiaNOS" }, { - "@id": "bts:Cell-Line" + "@id": "bts:Adenocarcinoidtumor" }, { - "@id": "bts:CentralNervousSystem" + "@id": "bts:Adenocarcinomacombinedwithothertypesofcarcinoma" }, { - "@id": "bts:Cerebellum" + "@id": "bts:AdenocarcinomainapolypNOS" }, { - "@id": "bts:CerebralCortex" + "@id": "bts:Adenocarcinomainadenomatouspolyp" }, { - "@id": "bts:CerebrospinalFluid" + "@id": "bts:Adenocarcinomainpolypoidadenoma" }, { - "@id": "bts:Cerebrum" + "@id": "bts:AdenocarcinomainsituinapolypNOS" }, { - "@id": "bts:CervicalSpine" + "@id": "bts:Adenocarcinomainsituinadenomatouspolyp" }, { - "@id": "bts:Cervix" + "@id": "bts:Adenocarcinomainsituintubularadenoma" }, { - "@id": "bts:Chest" + "@id": "bts:Adenocarcinomainsitumucinous" }, { - "@id": "bts:ChestWall" + "@id": "bts:Adenocarcinomainsitunon-mucinous" }, { - "@id": "bts:Chin" + "@id": "bts:AdenocarcinomainsituNOS" }, { - "@id": "bts:Clavicle" + "@id": "bts:Adenocarcinomaintubularadenoma" }, { - "@id": "bts:Clitoris" + "@id": "bts:Adenocarcinomainvillousadenoma" }, { - "@id": "bts:Colon" + "@id": "bts:Adenocarcinomaofanalducts" }, { - "@id": "bts:ColonMucosaOnly" + "@id": "bts:Adenocarcinomaofanalglands" }, { - "@id": "bts:CommonDuct" + "@id": "bts:Adenocarcinomadiffusetype" }, { - "@id": "bts:Conjunctiva" + "@id": "bts:Adenocarcinomaendocervicaltype" }, { - "@id": "bts:ConnectiveTissue" + "@id": "bts:Adenocarcinomaintestinaltype" }, { - "@id": "bts:Dermal" + "@id": "bts:AdenocarcinomametastaticNOS" }, { - "@id": "bts:DescendingColon" + "@id": "bts:AdenocarcinomaNOS" }, { - "@id": "bts:Diaphragm" + "@id": "bts:Adenocarcinomapancreatobiliarytype" }, { - "@id": "bts:DistantSite" + "@id": "bts:Adultrhabdomyoma" }, { - "@id": "bts:Duodenum" + "@id": "bts:AdultT-celllymphoma" }, { - "@id": "bts:Ear" + "@id": "bts:AdultT-celllymphoma/leukemia" }, { - "@id": "bts:EarCanal" + "@id": "bts:Astrocytomaanaplastic" }, { - "@id": "bts:EarPinna(External)" + "@id": "bts:Astrocytomalowgrade" }, { - "@id": "bts:Elbow" + "@id": "bts:AstrocytomaNOS" }, { - "@id": "bts:EndocrineGland" + "@id": "bts:BcelllymphomaNOS" }, { - "@id": "bts:Epididymis" + "@id": "bts:Blymphoblasticleukemia/lymphomawithhyperdiploidy" }, { - "@id": "bts:EpiduralSpace" + "@id": "bts:Blymphoblasticleukemia/lymphomawithhypodiploidy(HypodiploidALL)" }, { - "@id": "bts:Epitrochlear" + "@id": "bts:Blymphoblasticleukemia/lymphomaNOS" }, { - "@id": "bts:EsophagogastricJunction" + "@id": "bts:B-ALL" }, { - "@id": "bts:Esophagus" + "@id": "bts:B-celllymphocyticleukemia/smalllymphocyticlymphoma" }, { - "@id": "bts:EsophagusMucosaOnly" + "@id": "bts:Basalcelladenocarcinoma" }, { - "@id": "bts:Eye" + "@id": "bts:Basalcelladenoma" }, { - "@id": "bts:FallopianTube" + "@id": "bts:BasalcellcarcinomaNOS" }, { - "@id": "bts:FemoralArtery" + "@id": "bts:Basalcellepithelioma" }, { - "@id": "bts:FemoralVein" + "@id": "bts:Basalcelltumor" }, { - "@id": "bts:Femur" + "@id": "bts:Basophiladenocarcinoma" }, { - "@id": "bts:Fibroblasts" + "@id": "bts:Basophiladenoma" }, { - "@id": "bts:Fibula" + "@id": "bts:Basophilcarcinoma" }, { - "@id": "bts:Finger" + "@id": "bts:Bileductadenocarcinoma" }, { - "@id": "bts:FloorofMouth" + "@id": "bts:Bileductadenoma" }, { - "@id": "bts:Fluid" + "@id": "bts:Bileductcarcinoma" }, { - "@id": "bts:Foot" + "@id": "bts:Bileductcystadenocarcinoma" }, { - "@id": "bts:Forearm" + "@id": "bts:Bileductcystadenoma" }, { - "@id": "bts:Forehead" + "@id": "bts:Bronchialadenomacarcinoid" }, { - "@id": "bts:Foreskin" + "@id": "bts:Bronchialadenomacylindroid" }, { - "@id": "bts:FrontalCortex" + "@id": "bts:BronchialadenomaNOS" }, { - "@id": "bts:FrontalLobe" + "@id": "bts:Bronchial-associatedlymphoidtissuelymphoma" }, { - "@id": "bts:FundusofStomach" + "@id": "bts:Bronchio-alveolarcarcinomamixedmucinousandnon-mucinous" }, { - "@id": "bts:Gallbladder" + "@id": "bts:Bronchio-alveolarcarcinomamucinous" }, { - "@id": "bts:Ganglia" + "@id": "bts:Bronchiolaradenocarcinoma" }, { - "@id": "bts:GastroesophagealJunction" + "@id": "bts:Bronchiolarcarcinoma" }, { - "@id": "bts:GastrointestinalTract" + "@id": "bts:Bronchiolo-alveolaradenocarcinomaNOS" }, { - "@id": "bts:GastrointestinalIntestine" + "@id": "bts:Bronchiolo-alveolarcarcinomaClaracell" }, { - "@id": "bts:GenitourinaryNOS" + "@id": "bts:Bronchiolo-alveolarcarcinomaClaracellandgobletcelltype" }, { - "@id": "bts:Groin" + "@id": "bts:Bronchiolo-alveolarcarcinomagobletcelltype" }, { - "@id": "bts:Gum" + "@id": "bts:Bronchiolo-alveolarcarcinomaindeterminatetype" }, { - "@id": "bts:Hand" + "@id": "bts:Bronchiolo-alveolarcarcinomanon-mucinous" }, { - "@id": "bts:HardPalate" + "@id": "bts:Bronchiolo-alveolarcarcinomaNOS" }, { - "@id": "bts:HeadFaceOrNeckNos" + "@id": "bts:Burkittcellleukemia" }, { - "@id": "bts:HeadandNeck" + "@id": "bts:BurkittlymphomaNOS(Includesallvariants)" }, { - "@id": "bts:Heart" + "@id": "bts:Burkitttumor" }, { - "@id": "bts:Hepatic" + "@id": "bts:Burkitt-likelymphoma" }, { - 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"@id": "bts:Non-prescriptionsupplementsformemory" + "@id": "bts:Melanocytomaeyeball" }, { - "@id": "bts:Non-prescriptionsupplementsforreliefofhotflashes" + "@id": "bts:MelanocytomaNOS" }, { - "@id": "bts:Non-steroidalanti-inflammatoryagents" + "@id": "bts:Melanomainsitu" }, { - "@id": "bts:Opioids" + "@id": "bts:Melanomamalignantofsoftparts" }, { - "@id": "bts:Other" + "@id": "bts:MelanomaNOS" }, { - "@id": "bts:Prescriptionmedicationsformemory" + "@id": "bts:Melanoticmedulloblastoma" }, { - "@id": "bts:Prescriptionmedicationsforreliefofhotflashes" + "@id": "bts:MelanoticMPNST" }, { - "@id": "bts:Prophylacticantiplatelettherapy" + "@id": "bts:Melanoticneuroectodermaltumor" }, { - "@id": "bts:Tricyclicantidepressants" + "@id": "bts:Melanoticneurofibroma" }, { - "@id": "bts:NotApplicable" + "@id": "bts:Melanoticprogonoma" }, { - "@id": "bts:Unknown" + "@id": "bts:MelanoticpsammomatousMPNST" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Concomitant Medication Received Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FamilyMemberVitalStatusIndicator", - "@type": "rdfs:Class", - "rdfs:comment": "The response indicates whether the family member of the patient with a history of cancer is alive. (Extension to GDC attributes in Family History Tier 1)", - "rdfs:label": "FamilyMemberVitalStatusIndicator", - "rdfs:subClassOf": [ - { - "@id": "bts:FamilyHistory" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:VitalStatusAlive" + "@id": "bts:Melanoticschwannoma" }, { - "@id": "bts:VitalStatusDead" + "@id": "bts:Meningealmelanocytoma" }, { - "@id": "bts:Unknown" + "@id": "bts:Meningealmelanoma" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Family Member Vital Status Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:COVID19OccurrenceIndicator", - "@type": "rdfs:Class", - "rdfs:comment": "The indicator that describes whether or not a COVID-19 infectious disorder occurred.", - "rdfs:label": "COVID19OccurrenceIndicator", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" + "@id": "bts:Meningiomaanaplastic" }, { - "@id": "bts:No" + "@id": "bts:Meningiomamalignant" }, { - "@id": "bts:Unknown" + "@id": "bts:MeningiomaNOS" }, { - "@id": "bts:NotApplicable" + "@id": "bts:MicropapillarycarcinomaNOS" }, { - "@id": "bts:NotDone" - } - ], - "sms:displayName": "COVID19 Occurrence Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:COVID19CurrentStatus", - "@type": "rdfs:Class", - "rdfs:comment": "The patient's current COVID-19 status of sign or symptom events or interventions", - "rdfs:label": "COVID19CurrentStatus", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Patientcurrentlyhassymptoms" + "@id": "bts:Mixedadenocarcinomaandepidermoidcarcinoma" }, { - "@id": "bts:Patienthadsymptomsbutnowisfullyrecovered" + "@id": "bts:Mixedadenocarcinomaandsquamouscellcarcinoma" }, { - "@id": "bts:PatientneverhadanysymptomsofCOVID-19" + "@id": "bts:Mixedmedullary-follicularcarcinoma" }, { - "@id": "bts:StatusunknownduetogeneralCOVID-19relatedtravelrestrictions" + "@id": "bts:Mixedmedullary-papillarycarcinoma" }, { - "@id": "bts:Statusunknownduetolackofdisease/tumorassessmentduetoCOVID-19diagnosis" + "@id": "bts:Mixedpancreaticendocrineandexocrinetumormalignant" }, { - "@id": "bts:Statusunknownduetootherreasons" - } - ], - "sms:displayName": "COVID19 Current Status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:COVID19PositiveLabTestIndicator", - "@type": "rdfs:Class", - "rdfs:comment": "The indicator that describes whether or not there was a COVID-19 positive test result.", - "rdfs:label": "COVID19PositiveLabTestIndicator", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" + "@id": "bts:Mixedpinealtumor" }, { - "@id": "bts:No" + "@id": "bts:Mixedsmallcellcarcinoma" }, { - "@id": "bts:Unknown" + "@id": "bts:Mixedsquamouscellandglandularpapilloma" }, { - "@id": "bts:NotApplicable" + "@id": "bts:MixedtumormalignantNOS" }, { - "@id": "bts:NotDone" - } - ], - "sms:displayName": "COVID19 Positive Lab Test Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:COVID19AntibodyTesting", - "@type": "rdfs:Class", - "rdfs:comment": "Text term that demonstrates the test results of immunoglobulin M (IgM) and immunoglobulin G (IgG) antibodies to the SARS-CoV-2 virus in subject serum samples.", - "rdfs:label": "COVID19AntibodyTesting", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:SARS-CoV-2IgMantibodypositive" + "@id": "bts:MixedtumorNOS" }, { - "@id": "bts:SARS-CoV-2IgGantibodypositive" + "@id": "bts:MonocyticleukemiaNOS" }, { - "@id": "bts:SARS-CoV-2IgG/IgMantibodypositive" + "@id": "bts:Mucosal-associatedlymphoidtissuelymphoma" }, { - "@id": "bts:SARS-CoV-2IgMantibodynegative" + "@id": "bts:Mucousadenocarcinoma" }, { - 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}, - { - "@id": "bts:Ecigvape30dayusenum", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days e-cigarettes or vaping device was used in the last 30 days", - "rdfs:label": "Ecigvape30dayusenum", - "rdfs:subClassOf": [ + "@id": "bts:NevusNOS" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Ecig vape 30 day use num", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Ecigvapetimesperday", - "@type": "rdfs:Class", - "rdfs:comment": "e-cig frequency of use (times per day—one “time” consists of around 15 puffs or lasts around 10 minutes)", - "rdfs:label": "Ecigvapetimesperday", - "rdfs:subClassOf": [ + "@id": "bts:Non-HodgkinlymphomaNOS" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Ecig vape times per day", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Typeofsmokeexposurecumulativeyears", - "@type": "rdfs:Class", - "rdfs:comment": "The number of cumulative years of the patient's specific type of smoke exposure", - "rdfs:label": "Typeofsmokeexposurecumulativeyears", - "rdfs:subClassOf": [ + "@id": "bts:Non-invasivelowgradeserouscarcinoma" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Type of smoke exposure cumulative years", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Chewingtobaccodailyusecount", - "@type": "rdfs:Class", - "rdfs:comment": "The quantity of daily use of tobacco, in the form of a plug, usually flavored, for chewing rather than smoking.", - "rdfs:label": "Chewingtobaccodailyusecount", - "rdfs:subClassOf": [ + "@id": "bts:Non-lymphocyticleukemiaNOS" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Chewing tobacco daily use count", - "sms:required": "sms:false", - "sms:validationRules": [] - 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"@id": "bts:Hereditaryretinoblastoma" + "@id": "bts:Papillaryrenalcellcarcinoma" }, { - "@id": "bts:Juvenilepolyposissyndrome" + "@id": "bts:Papillaryserousadenocarcinoma" }, { - "@id": "bts:Li-Fraumenisyndrome" + "@id": "bts:Papillaryserouscystadenocarcinoma" }, { - "@id": "bts:Lynchsyndrome" + "@id": "bts:PapillaryserouscystadenomaNOS" }, { - "@id": "bts:Melanoma–astrocytomasyndrome" + "@id": "bts:Papillarysquamouscellcarcinoma" }, { - "@id": "bts:MultipleendocrineneoplasiatypeI" + "@id": "bts:Papillarysquamouscellcarcinomainsitu" }, { - "@id": "bts:MultipleendocrineneoplasiatypeII" + "@id": "bts:Papillarytransitionalcellcarcinoma" }, { - "@id": "bts:MUTYH-associatedpolyposis" + "@id": "bts:Papillarytumorofthepinealregion" }, { - "@id": "bts:Nevoidbasalcellcarcinomasyndrome" + "@id": "bts:Papillaryurothelialcarcinoma" }, { - "@id": "bts:NotApplicable" + "@id": "bts:Papillomaofbladder" }, { - "@id": "bts:NotReported" + "@id": "bts:PapillomaNOS" }, { - "@id": "bts:Peutz–Jegherssyndrome" + "@id": "bts:Papillomatosisglandular" }, { - "@id": "bts:Cowdensyndrome" + "@id": "bts:PapillomatosisNOS" }, { - "@id": "bts:RhabdoidtumorpredispositionsyndrometypeI" + "@id": "bts:Papillotubularadenocarcinoma" }, { - "@id": "bts:RhabdoidtumorpredispositionsyndrometypeII" + "@id": "bts:Papillotubularadenoma" }, { - "@id": "bts:Rubinstein-Taybisyndrome" + "@id": "bts:Paragangliomabenign" }, { - "@id": "bts:SDHassociatedrenalcancer" + "@id": "bts:Paragangliomamalignant" }, { - "@id": "bts:Serratedpolyposissyndrome" + "@id": "bts:ParagangliomaNOS" }, { - "@id": "bts:Tuberoussclerosiscomplex" + "@id": "bts:PeripheralT-celllymphomalargecell" }, { - "@id": "bts:Turcotsyndrome" + "@id": "bts:PeripheralT-celllymphomaNOS" }, { - "@id": "bts:Tyrosinemia" + "@id": "bts:Pigmentedadenoma" }, { - "@id": "bts:Unknown" + "@id": "bts:Pigmentedbasalcellcarcinoma" }, { - "@id": "bts:VonHippel-LindauSyndrome" - } - ], - "sms:displayName": "Hereditary Cancer Predisposition Syndrome", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CancerAssociatedGeneMutations", - "@type": "rdfs:Class", - "rdfs:comment": "Type of inherited germline or other gene mutations that confers heightened susceptibility to cancer identified in patient history", - "rdfs:label": "CancerAssociatedGeneMutations", - "rdfs:subClassOf": [ + "@id": "bts:PigmentednevusNOS" + }, { - "@id": "bts:FamilyHistory" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:PituitaryadenomaNOS" + }, { - "@id": "bts:APCmutation" + "@id": "bts:PituitarycarcinomaNOS" }, { - "@id": "bts:ALKmutation" + "@id": "bts:Pleomorphicadenoma" }, { - "@id": "bts:ARFmutation" + "@id": "bts:Pleomorphiccarcinoma" }, { - "@id": "bts:ATMmutation" + "@id": "bts:Pleomorphiclipoma" }, { - "@id": "bts:ATRXmutation" + "@id": "bts:Pleomorphicliposarcoma" }, { - "@id": "bts:ACVR1mutation" + "@id": "bts:Pleomorphiclobularcarcinoma" }, { - "@id": "bts:BAP1mutation" + "@id": "bts:Pleomorphiclobularcarcinomainsitu" }, { - "@id": "bts:BMPR1Amutation" + "@id": "bts:PrecancerousmelanosisNOS" }, { - "@id": "bts:BLMmutation" + "@id": "bts:PrecursorB-celllymphoblasticleukemia" }, { - "@id": "bts:BRCA1mutation" + "@id": "bts:PrecursorB-celllymphoblasticlymphoma" }, { - "@id": "bts:BRCA1and2mutation" + "@id": "bts:PrecursorcelllymphoblasticleukemiaNOS" }, { - "@id": "bts:BRCA2mutation" + "@id": "bts:PrecursorT-celllymphoblasticleukemia" }, { - "@id": "bts:BRAFmutation" + "@id": "bts:PrecursorT-celllymphoblasticlymphoma" }, { - "@id": "bts:CDH1mutation" + "@id": "bts:Preleukemia" }, { - "@id": "bts:CDKN2Amutation" + "@id": "bts:Preleukemicsyndrome" }, { - "@id": "bts:CDKN2Aandp14ARFmutation" + "@id": "bts:Primaryamyloidosis" }, { - "@id": "bts:CHKmutation" + "@id": "bts:Pro-BALL" }, { - "@id": "bts:ETV6mutation" + "@id": "bts:Pro-TALL" }, { - "@id": "bts:EGFRmutation" + "@id": "bts:ProstaticintraepithelialneoplasiagradeIII" }, { - "@id": "bts:FHmutation" + "@id": "bts:Pulmonaryadenomatosis" }, { - "@id": "bts:FLCNmutation" + "@id": "bts:Pulmonaryarteryintimalsarcoma" }, { - "@id": "bts:GREM1mutation" + "@id": "bts:Pulmonaryblastoma" }, { - "@id": "bts:HOXB13mutation" + "@id": "bts:Renalcarcinomacollectingducttype" }, { - "@id": "bts:H3K27Mmutation" + "@id": "bts:Renalcelladenocarcinoma" }, { - "@id": "bts:H3G34R/Vmutation" + "@id": "bts:Renalcellcarcinomachromophobetype" }, { - "@id": "bts:IKZF1mutation" + "@id": "bts:RenalcellcarcinomaNOS" }, { - "@id": "bts:KITmutation" + "@id": "bts:Renalcellcarcinomasarcomatoid" }, { - "@id": "bts:KRASmutation" + "@id": "bts:Renalcellcarcinomaspindlecell" }, { - "@id": "bts:MAXmutation" + "@id": "bts:Renalcellcarcinomaunclassified" }, { - "@id": "bts:MEN1mutation" + "@id": "bts:Renalmedullarycarcinoma" }, { - "@id": "bts:METmutation" + "@id": "bts:Rhabdoidmeningioma" }, { - "@id": "bts:MLH1mutation" + "@id": "bts:Rhabdoidsarcoma" }, { - "@id": "bts:MSH2mutation" + "@id": "bts:RhabdoidtumorNOS" }, { - "@id": "bts:MSH6mutation" + "@id": "bts:RhabdomyomaNOS" }, { - "@id": "bts:MUTYHmutation" + "@id": "bts:Rhabdomyosarcomawithganglionicdifferentiation" }, { - "@id": "bts:NF1mutation" + "@id": "bts:RhabdomyosarcomaNOS" }, { - "@id": "bts:NF2mutation" + "@id": "bts:Rhabdosarcoma" }, { - "@id": "bts:NotApplicable" + "@id": "bts:Rodentulcer" }, { - "@id": "bts:NotReported" + "@id": "bts:SarcomaNOS" }, { - "@id": "bts:P14ARFmutation" + "@id": "bts:Sclerosinghemangioma" }, { - "@id": "bts:PALB2mutation" + "@id": "bts:Sclerosinghepaticcarcinoma" }, { - "@id": "bts:PAX5mutation" + "@id": "bts:Secondarycarcinoma" }, { - "@id": "bts:PDGFRAmutation" + "@id": "bts:Secretorycarcinomaofbreast" }, { - "@id": "bts:PHOX2Bmutation" + "@id": "bts:SerouscystadenocarcinomaNOS" }, { - "@id": "bts:PMS2mutation" + "@id": "bts:Seroussurfacepapillarycarcinoma" }, { - "@id": "bts:PolDmutation" + "@id": "bts:High-gradeserouscarcinoma" }, { - "@id": "bts:PolEmutation" + "@id": "bts:Skinappendagecarcinoma" }, { - "@id": "bts:POT1mutation" + "@id": "bts:SmallcellcarcinomaNOS" }, { - "@id": "bts:PRKAR1Amutation" + "@id": "bts:Smallcellneuroendocrinecarcinoma" }, { - "@id": "bts:PTCHmutation" + "@id": "bts:Smallcellosteosarcoma" }, { - "@id": "bts:PTENmutation" + "@id": "bts:Smallcellsarcoma" }, { - "@id": "bts:ROS1mutation" + "@id": "bts:Smallcongenitalnevus" }, { - "@id": "bts:RB1mutation" + "@id": "bts:SpindlecellcarcinomaNOS" }, { - "@id": "bts:RETmutation" + "@id": "bts:SpindlecellmelanomaNOS" }, { - "@id": "bts:SDHAF2mutation" + "@id": "bts:SplenicB-celllymphoma/leukemiaunclassifiable" }, { - "@id": "bts:SDHBmutation" + "@id": "bts:SplenicdiffuseredpulpsmallB-celllymphoma" }, { - "@id": "bts:SDHCmutation" + "@id": "bts:Spleniclymphomawithvillouslymphocytes" }, { - "@id": "bts:SDHDmutation" + "@id": "bts:SplenicmarginalzoneB-celllymphoma" }, { - "@id": "bts:SETD2mutation" + "@id": "bts:SplenicmarginalzonelymphomaNOS" }, { - "@id": "bts:SMAD4mutation" + "@id": "bts:SquamouscellcarcinomainsituNOS" }, { - "@id": "bts:SMARCA4mutation" + "@id": "bts:Squamouscellcarcinomaadenoid" }, { - "@id": "bts:SMARCB1mutation" + "@id": "bts:Squamouscellcarcinomaclearcelltype" }, { - "@id": "bts:STK11mutation" + "@id": "bts:SquamouscellcarcinomaNOS" }, { - 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Note: Include only outputs of tests that were completed clinically for the participant and only include data from a diagnostic array that was completed prior to research sequencing was done.", - "rdfs:label": "MutationalSignatures", - "rdfs:subClassOf": [ + "@id": "bts:TeratomaNOS" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Therapyrelatedmyeloidneoplasm" + }, { - "@id": "bts:UVlightinducedmutations" + "@id": "bts:Transitionalcarcinoma" }, { - "@id": "bts:AlkylatingAgents(Temozolomide)inducedmutations" + "@id": "bts:Transitionalcellcarcinoma" }, { - "@id": "bts:Tobaccouseassociatedmutations" + "@id": "bts:Transitionalcellcarcinomainsitu" }, { - "@id": "bts:Ageofcancerdiagnosis" + "@id": "bts:Tubularadenocarcinoma" }, { - "@id": "bts:Transcriptionalstrandbias" + "@id": "bts:TubularadenomaNOS" }, { - "@id": "bts:Microsatelliteinstability(additionsanddeletions)" + "@id": "bts:Tubularandroblastomawithlipidstorage" }, { - "@id": "bts:MethylatedCpGsequencesmutagenesis(deaminationof5-methyl-cytosine)" + "@id": "bts:TubularandroblastomaNOS" }, { - "@id": "bts:ActivationInducedDeaminases(AID)associatedmutations" + "@id": "bts:Tubularcarcinoid" }, { - "@id": "bts:APOBECenzymesassociatedmutations" + "@id": "bts:Tubularcarcinoma" }, { - "@id": "bts:Alteredactivityoftheerror-pronepolymerasePOLε(POLE)" + "@id": "bts:Tubulo-papillaryadenoma" }, { - "@id": "bts:Localizedsubstitutionhypermutation(kataegis)" + "@id": "bts:Tubulocysticrenalcellcarcinoma" }, { - "@id": "bts:DNAMMRDeficiency" + "@id": "bts:Tubulolobularcarcinoma" }, { - "@id": "bts:Iggenehypermutation" + "@id": "bts:Tubulopapillaryadenocarcinoma" }, { - "@id": "bts:Signature1A" + "@id": "bts:TubulovillousadenomaNOS" }, { - "@id": "bts:Signature1B" + "@id": "bts:Tumorcellsbenign" }, { - "@id": "bts:Signature2" + "@id": "bts:Tumorcellsmalignant" }, { - "@id": "bts:Signature3" + "@id": "bts:TumorcellsNOS" }, { - "@id": "bts:Signature4" + "@id": "bts:Tumorcellsuncertainwhetherbenignormalignant" }, { - "@id": "bts:Signature5" + "@id": "bts:Tumorembolus" }, { - "@id": "bts:Signature6" + "@id": "bts:Tumorbenign" }, { - "@id": "bts:Signature7" + "@id": "bts:TumormalignantNOS" }, { - "@id": "bts:Signature8" + "@id": "bts:Tumormetastatic" }, { - "@id": "bts:Signature9" + "@id": "bts:TumorNOS" }, { - "@id": "bts:Signature10" + "@id": "bts:Tumorsecondary" }, { - "@id": "bts:Signature11" + "@id": "bts:Tumorletbenign" }, { - "@id": "bts:Signature12" + "@id": "bts:Typicalcarcinoid" }, { - "@id": "bts:Signature13" + "@id": "bts:Unclassifiedtumorbenign" }, { - "@id": "bts:Signature14" + "@id": "bts:Unclassifiedtumorborderlinemalignancy" }, { - "@id": "bts:Signature15" + "@id": "bts:Unclassifiedtumormalignant" }, { - "@id": "bts:Signature16" + "@id": "bts:Unclassifiedtumormalignantuncertainwhetherprimaryormetastatic" }, { - "@id": "bts:Signature17" + "@id": "bts:Unclassifiedtumoruncertainwhetherbenignormalignant" }, { - "@id": "bts:Signature18" + "@id": "bts:Undifferentiatedepithelioidsarcoma" }, { - "@id": "bts:Signature19" + "@id": "bts:Undifferentiatedhigh-gradepleomorphicsarcoma" }, { - "@id": "bts:Signature20" + "@id": "bts:Undifferentiatedleukaemia" }, { - "@id": "bts:Signature21" + "@id": "bts:Undifferentiatedpleomorphicsarcoma" }, { - "@id": "bts:Other" + "@id": "bts:Undifferentiatedroundcellsarcoma" }, { - "@id": "bts:Datanotavailable" + "@id": "bts:Undifferentiatedsarcoma" }, { - "@id": "bts:NotApplicable" + "@id": "bts:Undifferentiatedspindlecellsarcoma" }, { - "@id": "bts:NotReported" + "@id": "bts:Undifferentiateduterinesarcoma" }, { "@id": "bts:Unknown" } ], - "sms:displayName": "Mutational Signatures", - "sms:required": "sms:false", + "sms:displayName": "Primary Diagnosis", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MismatchRepairSystemStatus", + "@id": "bts:ProgressionorRecurrence", "@type": "rdfs:Class", - "rdfs:comment": "The text that best describes the condition or state of MMR (mismatch repair system) in the patient", - "rdfs:label": "MismatchRepairSystemStatus", + "rdfs:comment": "Yes/No/unknown indicator to identify whether a patient has had a new tumor event after initial treatment.", + "rdfs:label": "ProgressionorRecurrence", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -8595,33 +12064,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:MismatchrepairdeficiencyMMRD" - }, - { - "@id": "bts:MismatchrepairproficiencyMMPP" + "@id": "bts:Yes-ProgressionorRecurrence" }, { - "@id": "bts:MicrosatelliteinstabilityhighMSIH" + "@id": "bts:No" }, { - "@id": "bts:MicrosatellitestableMSS" + "@id": "bts:Unknown" }, { - "@id": "bts:Unknownorother" + "@id": "bts:NotReported" } ], - "sms:displayName": "Mismatch Repair System Status", - "sms:required": "sms:false", + "sms:displayName": "Progression or Recurrence", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LabTestsforMMRStatus", + "@id": "bts:SiteofResectionorBiopsy", "@type": "rdfs:Class", - "rdfs:comment": "Laboratory tests used to evaluate the status of mismatch repair pathways", - "rdfs:label": "LabTestsforMMRStatus", + "rdfs:comment": "The text term used to describe the anatomic site of the resection or biopsy of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", + "rdfs:label": "SiteofResectionorBiopsy", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -8629,1054 +12095,1017 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:IHCstainingformismatchrepairproteins" + "@id": "bts:AbdomenNOS" }, { - "@id": "bts:PCRtoevaluatemicrosatelliteinstability" + "@id": "bts:Abdominalesophagus" }, { - "@id": "bts:MLH1 promotermethylationanalysis" + "@id": "bts:AccessorysinusNOS" }, { - "@id": "bts:BRAF sequencing" + "@id": "bts:Acousticnerve" }, { - "@id": "bts:Other" + "@id": "bts:AdrenalglandNOS" }, { - "@id": "bts:NotApplicable" + "@id": "bts:AmpullaofVater" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Lab Tests for MMR Status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ModeofCancerDetection", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the mode of cancer detection, like standard of care screening or random detection", - "rdfs:label": "ModeofCancerDetection", - "rdfs:subClassOf": [ + "@id": "bts:Analcanal" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Anterior2/3oftongueNOS" + }, { - "@id": "bts:StandardofCareScreening" + "@id": "bts:Anteriorfloorofmouth" }, { - "@id": "bts:ClinicalExaminationofunrelatedcancersymptoms" + "@id": "bts:Anteriormediastinum" }, { - "@id": "bts:Incidentaloma" + "@id": "bts:Anteriorsurfaceofepiglottis" }, { - "@id": "bts:IntervalCancer" + "@id": "bts:Anteriorwallofbladder" }, { - "@id": "bts:Datanotavailable" - } - ], - "sms:displayName": "Mode of Cancer Detection", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:EducationLevel", - "@type": "rdfs:Class", - "rdfs:comment": "Highest level of education that the patient completed (direct patient-derived information)", - "rdfs:label": "EducationLevel", - "rdfs:subClassOf": [ + "@id": "bts:Anteriorwallofnasopharynx" + }, { - "@id": "bts:ClinicalTier2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:AnusNOS" + }, { - "@id": "bts:Bachelor'sdegree" + "@id": "bts:Aorticbodyandotherparaganglia" }, { - "@id": "bts:Doctoraldegreeorprofessionaldegree" + "@id": "bts:Appendix" }, { - "@id": "bts:Gradeschool" + "@id": "bts:Ascendingcolon" }, { - "@id": "bts:Graduateorprofessionaldegree" + "@id": "bts:AutonomicnervoussystemNOS" }, { - "@id": "bts:Highschoolgraduate(includingequivalency)" + "@id": "bts:Axillarytailofbreast" }, { - "@id": "bts:Master'sdegree" + "@id": "bts:BaseoftongueNOS" }, { - "@id": "bts:Noformaleducation" + "@id": "bts:Bladderneck" }, { - "@id": "bts:Nothighschoolgraduate" + "@id": "bts:BladderNOS" }, { - "@id": "bts:Somecollegeorassociatedegree" + "@id": "bts:Blood" }, { - "@id": "bts:Datanotavailable" - } - ], - "sms:displayName": "Education Level", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CountryofBirth", - "@type": "rdfs:Class", - "rdfs:comment": "Country where the patient was born.", - "rdfs:label": "CountryofBirth", - "rdfs:subClassOf": [ + "@id": "bts:Bodyofpancreas" + }, { - "@id": "bts:ClinicalTier2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Bodyofpenis" + }, { - "@id": "bts:Afghanistan" + "@id": "bts:Bodyofstomach" }, { - "@id": "bts:Albania" + "@id": "bts:Bonemarrow" }, { - "@id": "bts:Algeria" + "@id": "bts:BoneoflimbNOS" }, { - "@id": "bts:Andorra" + "@id": "bts:BoneNOS" }, { - "@id": "bts:Angola" + "@id": "bts:Bonesofskullandfaceandassociatedjoints" }, { - "@id": "bts:Anguilla" + "@id": "bts:Borderoftongue" }, { - "@id": "bts:AntiguaandBarbuda" + "@id": "bts:Brainstem" }, { - "@id": "bts:Argentina" + "@id": "bts:BrainNOS" }, { - "@id": "bts:Armenia" + "@id": "bts:Branchialcleft" }, { - "@id": "bts:Aruba" + "@id": "bts:BreastNOS" }, { - "@id": "bts:Australia" + "@id": "bts:Broadligament" }, { - "@id": "bts:Austria" + "@id": "bts:CardiaNOS" }, { - "@id": "bts:Azerbaijan" + "@id": "bts:Carotidbody" }, { - "@id": "bts:Bahamas" + "@id": "bts:Caudaequina" }, { - "@id": "bts:Bahrain" + "@id": "bts:Cecum" }, { - "@id": "bts:Bangladesh" + "@id": "bts:Centralportionofbreast" }, { - "@id": "bts:Barbados" + "@id": "bts:CerebellumNOS" }, { - "@id": "bts:Belarus" + "@id": "bts:Cerebralmeninges" }, { - "@id": "bts:Belgium" + "@id": "bts:Cerebrum" }, { - "@id": "bts:Belize" + "@id": "bts:Cervicalesophagus" }, { - "@id": "bts:Benin" + "@id": "bts:Cervixuteri" }, { - "@id": "bts:Bermuda" + "@id": "bts:Choroid" }, { - "@id": "bts:Bhutan" + "@id": "bts:Ciliarybody" }, { - "@id": "bts:Bolivia" + "@id": "bts:Cloacogeniczone" }, { - "@id": "bts:BosniaandHerzegovina" + "@id": "bts:ColonNOS" }, { - "@id": "bts:Botswana" + "@id": "bts:Commissureoflip" }, { - "@id": "bts:Brazil" + "@id": "bts:Conjunctiva" }, { - "@id": "bts:Brunei" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofabdomen" }, { - "@id": "bts:Bulgaria" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofheadfaceandneck" }, { - "@id": "bts:BurkinaFaso" + "@id": "bts:Connectivesubcutaneousandothersofttissuesoflowerlimbandhip" }, { - "@id": "bts:Burundi" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofpelvis" }, { - "@id": "bts:Cambodia" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofthorax" }, { - "@id": "bts:Cameroon" + "@id": "bts:ConnectivesubcutaneousandothersofttissuesoftrunkNOS" }, { - "@id": "bts:Canada" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofupperlimbandshoulder" }, { - "@id": "bts:CapeVerde" + "@id": "bts:ConnectivesubcutaneousandothersofttissuesNOS" }, { - "@id": "bts:CaymanIslands" + "@id": "bts:CorneaNOS" }, { - "@id": "bts:CentralAfricanRepublic" + "@id": "bts:Corpusuteri" }, { - "@id": "bts:Chad" + "@id": "bts:Cortexofadrenalgland" }, { - "@id": "bts:Chile" + "@id": "bts:CranialnerveNOS" }, { - "@id": "bts:China" + "@id": "bts:Craniopharyngealduct" }, { - "@id": "bts:Colombia" + "@id": "bts:Descendedtestis" }, { - "@id": "bts:Comoros" + "@id": "bts:Descendingcolon" }, { - "@id": "bts:Congo" + "@id": "bts:Domeofbladder" }, { - "@id": "bts:CookIslands" + "@id": "bts:DorsalsurfaceoftongueNOS" }, { - "@id": "bts:CostaRica" + "@id": "bts:Duodenum" }, { - "@id": "bts:Coted'Ivoire" + "@id": "bts:Endocervix" }, { - "@id": "bts:Croatia" + "@id": "bts:EndocrineglandNOS" }, { - "@id": "bts:Cuba" + "@id": "bts:Endometrium" }, { - "@id": "bts:Curacao" + "@id": "bts:Epididymis" }, { - "@id": "bts:Cyprus" + "@id": "bts:EsophagusNOS" }, { - "@id": "bts:CzechRepublic(Czechia)" + "@id": "bts:Ethmoidsinus" }, { - "@id": "bts:DemocraticRepublicoftheCongo" + "@id": "bts:Exocervix" }, { - "@id": "bts:Denmark" + "@id": "bts:Externalear" }, { - "@id": "bts:Djibouti" + "@id": "bts:ExternallipNOS" }, { - "@id": "bts:Dominica" + "@id": "bts:Externallowerlip" }, { - "@id": "bts:DominicanRepublic" + "@id": "bts:Externalupperlip" }, { - "@id": "bts:Ecuador" + "@id": "bts:Extrahepaticbileduct" }, { - "@id": "bts:Egypt" + "@id": "bts:EyeNOS" }, { - "@id": "bts:ElSalvador" + "@id": "bts:Eyelid" }, { - "@id": "bts:EquatorialGuinea" + "@id": "bts:Fallopiantube" }, { - "@id": "bts:Eritrea" + "@id": "bts:FemalegenitaltractNOS" }, { - "@id": "bts:Estonia" + "@id": "bts:FloorofmouthNOS" }, { - "@id": "bts:Eswatini" + "@id": "bts:Frontallobe" }, { - "@id": "bts:Ethiopia" + "@id": "bts:Frontalsinus" }, { - "@id": "bts:FalklandIslands(Malvinas)" + "@id": "bts:Fundusofstomach" }, { - "@id": "bts:FaroeIslands" + "@id": "bts:Fundusuteri" }, { - "@id": "bts:FederatedStatesofMicronesia" + "@id": "bts:Gallbladder" }, { - "@id": "bts:Fiji" + "@id": "bts:Gastricantrum" }, { - "@id": "bts:Finland" + "@id": "bts:GastrointestinaltractNOS" }, { - "@id": "bts:France" + "@id": "bts:Glanspenis" }, { - "@id": "bts:FrenchGuiana" + "@id": "bts:Glottis" }, { - "@id": "bts:FrenchPolynesia" + "@id": "bts:GreatercurvatureofstomachNOS" }, { - "@id": "bts:Gabon" + "@id": "bts:GumNOS" }, { - "@id": "bts:Gambia" + "@id": "bts:Hardpalate" }, { - "@id": "bts:Georgia" + "@id": "bts:Headofpancreas" }, { - "@id": "bts:Germany" + "@id": "bts:HeadfaceorneckNOS" }, { - "@id": "bts:Ghana" + "@id": "bts:Heart" }, { - "@id": "bts:Gibraltar" + "@id": "bts:HematopoieticsystemNOS" }, { - "@id": "bts:Greece" + "@id": "bts:Hepaticflexureofcolon" }, { - "@id": "bts:Greenland" + "@id": "bts:Hypopharyngealaspectofaryepiglotticfold" }, { - "@id": "bts:Grenada" + "@id": "bts:HypopharynxNOS" }, { - "@id": "bts:Guadeloupe" + "@id": "bts:Ileum" }, { - "@id": "bts:Guam" + "@id": "bts:Ill-definedsiteswithinrespiratorysystem" }, { - "@id": "bts:Guatemala" + "@id": "bts:IntestinaltractNOS" }, { - "@id": "bts:Guernsey" + "@id": "bts:Intra-abdominallymphnodes" }, { - "@id": "bts:Guinea" + "@id": "bts:Intrahepaticbileduct" }, { - "@id": "bts:Guinea-Bissau" + "@id": "bts:Intrathoraciclymphnodes" }, { - "@id": "bts:Guyana" + "@id": "bts:IsletsofLangerhans" }, { - "@id": "bts:Haiti" + "@id": "bts:Isthmusuteri" }, { - "@id": "bts:HolySee" + "@id": "bts:Jejunum" }, { - "@id": "bts:Honduras" + "@id": "bts:KidneyNOS" + }, + { + "@id": "bts:Labiummajus" + }, + { + "@id": "bts:Labiumminus" + }, + { + "@id": "bts:Lacrimalgland" + }, + { + "@id": "bts:Laryngealcartilage" + }, + { + "@id": "bts:LarynxNOS" + }, + { + "@id": "bts:Lateralfloorofmouth" + }, + { + "@id": "bts:Lateralwallofbladder" + }, + { + "@id": "bts:Lateralwallofnasopharynx" + }, + { + "@id": "bts:Lateralwalloforopharynx" + }, + { + "@id": "bts:LessercurvatureofstomachNOS" + }, + { + "@id": "bts:Lingualtonsil" + }, + { + "@id": "bts:LipNOS" + }, + { + "@id": "bts:Liver" + }, + { + "@id": "bts:Longbonesoflowerlimbandassociatedjoints" + }, + { + "@id": "bts:Longbonesofupperlimbscapulaandassociatedjoints" + }, + { + "@id": "bts:Lowergum" + }, + { + "@id": "bts:LowerlimbNOS" + }, + { + "@id": "bts:Lowerlobelung" + }, + { + "@id": "bts:Lowerthirdofesophagus" + }, + { + "@id": "bts:Lower-innerquadrantofbreast" + }, + { + "@id": "bts:Lower-outerquadrantofbreast" + }, + { + "@id": "bts:LungNOS" + }, + { + "@id": "bts:LymphnodeNOS" + }, + { + "@id": "bts:Lymphnodesofaxillaorarm" + }, + { + "@id": "bts:Lymphnodesofheadfaceandneck" + }, + { + "@id": "bts:Lymphnodesofinguinalregionorleg" + }, + { + "@id": "bts:Lymphnodesofmultipleregions" + }, + { + "@id": "bts:Mainbronchus" + }, + { + "@id": "bts:MajorsalivaryglandNOS" + }, + { + "@id": "bts:MalegenitalorgansNOS" }, { - "@id": "bts:HongKong" + "@id": "bts:Mandible" }, { - "@id": "bts:Hungary" + "@id": "bts:Maxillarysinus" }, { - "@id": "bts:Iceland" + "@id": "bts:Meckeldiverticulum" }, { - "@id": "bts:India" + "@id": "bts:MediastinumNOS" }, { - "@id": "bts:Indonesia" + "@id": "bts:Medullaofadrenalgland" }, { - "@id": "bts:Iran" + "@id": "bts:MeningesNOS" }, { - "@id": "bts:Iraq" + "@id": "bts:Middleear" }, { - "@id": "bts:Ireland" + "@id": "bts:Middlelobelung" }, { - "@id": "bts:IsleofMan" + "@id": "bts:Middlethirdofesophagus" }, { - "@id": "bts:Israel" + "@id": "bts:MouthNOS" }, { - "@id": "bts:Italy" + "@id": "bts:MucosaoflipNOS" }, { - "@id": "bts:Jamaica" + "@id": "bts:Mucosaoflowerlip" }, { - "@id": "bts:Japan" + "@id": "bts:Mucosaofupperlip" }, { - "@id": "bts:Jersey" + "@id": "bts:Myometrium" }, { - "@id": "bts:Jordan" + "@id": "bts:Nasalcavity" }, { - "@id": "bts:Kazakhstan" + "@id": "bts:NasopharynxNOS" }, { - "@id": "bts:Kenya" + "@id": "bts:NervoussystemNOS" }, { - "@id": "bts:Kiribati" + "@id": "bts:Nipple" }, { - "@id": "bts:Kosovo" + "@id": "bts:Occipitallobe" }, { - "@id": "bts:Kuwait" + "@id": "bts:Olfactorynerve" }, { - "@id": "bts:Kyrgyzstan" + "@id": "bts:Opticnerve" }, { - "@id": "bts:Laos" + "@id": "bts:OrbitNOS" }, { - "@id": "bts:Latvia" + "@id": "bts:OropharynxNOS" }, { - "@id": "bts:Lebanon" + "@id": "bts:Otherill-definedsites" }, { - "@id": "bts:Lesotho" + "@id": "bts:Otherspecifiedpartsoffemalegenitalorgans" }, { - "@id": "bts:Liberia" + "@id": "bts:Otherspecifiedpartsofmalegenitalorgans" }, { - "@id": "bts:Libya" + "@id": "bts:Otherspecifiedpartsofpancreas" }, { - "@id": "bts:Liechtenstein" + "@id": "bts:Ovary" }, { - "@id": "bts:Lithuania" + "@id": "bts:Overlappinglesionofaccessorysinuses" }, { - "@id": "bts:Luxembourg" + "@id": "bts:Overlappinglesionofbladder" }, { - "@id": "bts:Macau" + "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilage" }, { - "@id": "bts:Madagascar" + "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilageoflimbs" }, { - "@id": "bts:Malawi" + "@id": "bts:Overlappinglesionofbrain" }, { - "@id": "bts:Malaysia" + "@id": "bts:Overlappinglesionofbrainandcentralnervoussystem" }, { - "@id": "bts:Maldives" + "@id": "bts:Overlappinglesionofbreast" }, { - "@id": "bts:Mali" + "@id": "bts:Overlappinglesionofcervixuteri" }, { - "@id": "bts:Malta" + "@id": "bts:Overlappinglesionofcolon" }, { - "@id": "bts:MarshallIslands" + "@id": "bts:Overlappinglesionofconnectivesubcutaneousandothersofttissues" }, { - "@id": "bts:Martinique" + "@id": "bts:Overlappinglesionofcorpusuteri" }, { - "@id": "bts:Mauritania" + "@id": "bts:Overlappinglesionofdigestivesystem" }, { - "@id": "bts:Mauritius" + "@id": "bts:Overlappinglesionofendocrineglandsandrelatedstructures" }, { - "@id": "bts:Mayotte" + "@id": "bts:Overlappinglesionofesophagus" }, { - "@id": "bts:Mexico" + "@id": "bts:Overlappinglesionofeyeandadnexa" }, { - "@id": "bts:Moldova" + "@id": "bts:Overlappinglesionoffemalegenitalorgans" }, { - "@id": "bts:Monaco" + "@id": "bts:Overlappinglesionoffloorofmouth" }, { - "@id": "bts:Mongolia" + "@id": "bts:Overlappinglesionofheartmediastinumandpleura" }, { - "@id": "bts:Montenegro" + "@id": "bts:Overlappinglesionofhypopharynx" }, { - "@id": "bts:Montserrat" + "@id": "bts:Overlappinglesionofill-definedsites" }, { - "@id": "bts:Morocco" + "@id": "bts:Overlappinglesionoflarynx" }, { - "@id": "bts:Mozambique" + "@id": "bts:Overlappinglesionoflip" }, { - "@id": "bts:Myanmar" + "@id": "bts:Overlappinglesionofliporalcavityandpharynx" }, { - "@id": "bts:Namibia" + "@id": "bts:Overlappinglesionoflung" }, { - "@id": "bts:Nauru" + "@id": "bts:Overlappinglesionofmajorsalivaryglands" }, { - "@id": "bts:Nepal" + "@id": "bts:Overlappinglesionofmalegenitalorgans" }, { - "@id": "bts:Netherlands" + "@id": "bts:Overlappinglesionofnasopharynx" }, { - "@id": "bts:NewCaledonia" + "@id": "bts:Overlappinglesionofotherandunspecifiedpartsofmouth" }, { - "@id": "bts:NewZealand" + "@id": "bts:Overlappinglesionofpalate" }, { - "@id": "bts:Nicaragua" + "@id": "bts:Overlappinglesionofpancreas" }, { - "@id": "bts:Niger" + "@id": "bts:Overlappinglesionofpenis" }, { - "@id": "bts:Nigeria" + "@id": "bts:Overlappinglesionofperipheralnervesandautonomicnervoussystem" }, { - "@id": "bts:Niue" + "@id": "bts:Overlappinglesionofrectumanusandanalcanal" }, { - "@id": "bts:NorthKorea" + "@id": "bts:Overlappinglesionofrespiratorysystemandintrathoracicorgans" }, { - "@id": "bts:NorthMacedonia" + "@id": "bts:Overlappinglesionofretroperitoneumandperitoneum" }, { - "@id": "bts:NorthernMarianaIslands" + "@id": "bts:Overlappinglesionofskin" }, { - "@id": "bts:Norway" + "@id": "bts:Overlappinglesionofsmallintestine" }, { - "@id": "bts:Oman" + "@id": "bts:Overlappinglesionofstomach" }, { - "@id": "bts:Pakistan" + "@id": "bts:Overlappinglesionoftongue" }, { - "@id": "bts:Palau" + "@id": "bts:Overlappinglesionoftonsil" }, { - "@id": "bts:Panama" + "@id": "bts:Overlappinglesionofurinaryorgans" }, { - "@id": "bts:PapuaNewGuinea" + "@id": "bts:Overlappinglesionofvulva" }, { - "@id": "bts:Paraguay" + "@id": "bts:Overlappinglesionsoforopharynx" }, { - "@id": "bts:Peru" + "@id": "bts:PalateNOS" }, { - "@id": "bts:Philippines" + "@id": "bts:PancreasNOS" }, { - "@id": "bts:Poland" + "@id": "bts:Pancreaticduct" }, { - "@id": "bts:Portugal" + "@id": "bts:Parametrium" }, { - "@id": "bts:PuertoRico" + "@id": "bts:Paraspinal" }, { - "@id": "bts:Qatar" + "@id": "bts:Parathyroidgland" }, { - "@id": "bts:Reunion" + "@id": "bts:Paraurethralgland" }, { - "@id": "bts:Romania" + "@id": "bts:Parietallobe" }, { - "@id": "bts:Russia" + "@id": "bts:Parotidgland" }, { - "@id": "bts:Rwanda" + "@id": "bts:Pelvicbonessacrumcoccyxandassociatedjoints" }, { - "@id": "bts:SaintHelenaAscensionandTristandaCunha" + "@id": "bts:Pelviclymphnodes" }, { - "@id": "bts:SaintKittsandNevis" + "@id": "bts:PelvisNOS" }, { - "@id": "bts:SaintLucia" + "@id": "bts:PenisNOS" }, { - "@id": "bts:SaintPierreandMiquelon" + "@id": "bts:Peripheralnervesandautonomicnervoussystemofabdomen" }, { - "@id": "bts:SaintVincentandtheGrenadines" + "@id": "bts:Peripheralnervesandautonomicnervoussystemofheadfaceandneck" }, { - "@id": "bts:Samoa" + "@id": "bts:Peripheralnervesandautonomicnervoussystemoflowerlimbandhip" }, { - "@id": "bts:SanMarino" + "@id": "bts:Peripheralnervesandautonomicnervoussystemofpelvis" }, { - "@id": "bts:SaoTomeandPrincipe" + "@id": "bts:Peripheralnervesandautonomicnervoussystemofthorax" }, { - "@id": "bts:SaudiArabia" + "@id": "bts:PeripheralnervesandautonomicnervoussystemoftrunkNOS" }, { - "@id": "bts:Senegal" + "@id": "bts:Peripheralnervesandautonomicnervoussystemofupperlimbandshoulder" }, { - "@id": "bts:Serbia" + "@id": "bts:PeritoneumNOS" }, { - "@id": "bts:Seychelles" + "@id": "bts:PharynxNOS" }, { - "@id": "bts:SierraLeone" + "@id": "bts:Pinealgland" }, { - "@id": "bts:Singapore" + "@id": "bts:Pituitarygland" }, { - "@id": "bts:Slovakia" + "@id": "bts:Placenta" }, { - "@id": "bts:Slovenia" + "@id": "bts:PleuraNOS" }, { - "@id": "bts:SolomonIslands" + "@id": "bts:Postcricoidregion" }, { - "@id": "bts:Somalia" + "@id": "bts:Posteriormediastinum" }, { - "@id": "bts:SouthAfrica" + "@id": "bts:Posteriorwallofbladder" }, { - "@id": "bts:SouthKorea" + "@id": "bts:Posteriorwallofhypopharynx" }, { - "@id": "bts:SouthSudan" + "@id": "bts:Posteriorwallofnasopharynx" }, { - "@id": "bts:Spain" + "@id": "bts:Posteriorwalloforopharynx" }, { - "@id": "bts:SriLanka" + "@id": "bts:Prepuce" }, { - "@id": "bts:StateofPalestine" + "@id": "bts:Prostategland" }, { - "@id": "bts:Sudan" + "@id": "bts:Pylorus" }, { - "@id": "bts:Suriname" + "@id": "bts:Pyriformsinus" }, { - "@id": "bts:Svalbard&JanMayenIslands" + "@id": "bts:Rectosigmoidjunction" }, { - "@id": "bts:Sweden" + "@id": "bts:RectumNOS" }, { - "@id": "bts:Switzerland" + "@id": "bts:Renalpelvis" }, { - "@id": "bts:Syria" + "@id": "bts:ReticuloendothelialsystemNOS" }, { - "@id": "bts:Taiwan" + "@id": "bts:Retina" }, { - "@id": "bts:Tajikistan" + "@id": "bts:Retromolararea" }, { - "@id": "bts:Tanzania" + "@id": "bts:Retroperitoneum" }, { - "@id": "bts:Thailand" + "@id": "bts:Ribsternumclavicleandassociatedjoints" }, { - "@id": "bts:Timor-Leste" + "@id": "bts:Roundligament" }, { - "@id": "bts:Togo" + "@id": "bts:ScrotumNOS" }, { - "@id": "bts:Tokelau" + "@id": "bts:Shortbonesoflowerlimbandassociatedjoints" }, { - "@id": "bts:Tonga" + "@id": "bts:Shortbonesofupperlimbandassociatedjoints" }, { - "@id": "bts:TrinidadandTobago" + "@id": "bts:Sigmoidcolon" }, { - "@id": "bts:Tunisia" + "@id": "bts:SkinoflipNOS" }, { - "@id": "bts:Turkey" + "@id": "bts:Skinoflowerlimbandhip" }, { - "@id": "bts:Turkmenistan" + "@id": "bts:Skinofotherandunspecifiedpartsofface" }, { - "@id": "bts:Tuvalu" + "@id": "bts:Skinofscalpandneck" }, { - "@id": "bts:Uganda" + "@id": "bts:Skinoftrunk" }, { - "@id": "bts:Ukraine" + "@id": "bts:Skinofupperlimbandshoulder" }, { - "@id": "bts:UnitedArabEmirates" + "@id": "bts:SkinNOS" }, { - "@id": "bts:UnitedKingdom" + "@id": "bts:SmallintestineNOS" }, { - "@id": "bts:UnitedStates" + "@id": "bts:SoftpalateNOS" }, { - "@id": "bts:Uruguay" + "@id": "bts:Specifiedpartsofperitoneum" }, { - "@id": "bts:Uzbekistan" + "@id": "bts:Spermaticcord" }, { - "@id": "bts:Vanuatu" + "@id": "bts:Sphenoidsinus" }, { - "@id": "bts:Venezuela" + "@id": "bts:Spinalcord" }, { - "@id": "bts:Vietnam" + "@id": "bts:Spinalmeninges" }, { - "@id": "bts:VirginIslandsBritish" + "@id": "bts:Spleen" }, { - "@id": "bts:VirginIslandsU.S." + "@id": "bts:Splenicflexureofcolon" }, { - "@id": "bts:WallisandFutuna" + "@id": "bts:StomachNOS" }, { - "@id": "bts:WesternSahara" + "@id": "bts:Subglottis" }, { - "@id": "bts:Yemen" + "@id": "bts:Sublingualgland" }, { - "@id": "bts:Zambia" + "@id": "bts:Submandibulargland" }, { - "@id": "bts:Zimbabwe" + "@id": "bts:Superiorwallofnasopharynx" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Country of Birth", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MedicallyUnderservedArea", - "@type": "rdfs:Class", - "rdfs:comment": "Areas or populations designated by HRSA as having too few primary care providers, high infant mortality, high poverty or a high elderly population: Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/ - enter the zip code in the main text field and use the associated county on the right side of the result field. Go to data.hrsa.gov website and select \"Query Data\". Pick the Medically Underserved Areas/Populations (MUA/P) data source in the step 1 menu and select \"View Data\". Enter the name of the county (_______ county) in the first \"Service Area\" column, adding the state in the 5th column may help direct you to the data. If the designation type in the third column is \"medically underserved area\" enter \"Yes\" as the value. If the county generates a \"No data available in table\" enter \"No\" as the value. A value of \"Unknown\" indicates that sufficient data was not available to look up the value. If value is yes, complete the Medically_underserved_score data element.", - "rdfs:label": "MedicallyUnderservedArea", - "rdfs:subClassOf": [ - { - "@id": "bts:ClinicalTier2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Supraglottis" + }, { - "@id": "bts:MedicallyUnderservedArea-Yes" + "@id": "bts:Tailofpancreas" }, { - "@id": "bts:MedicallyUnderservedArea-No" + "@id": "bts:Temporallobe" }, { - "@id": "bts:MedicallyUnderservedArea-Unknown" - } - ], - "sms:displayName": "Medically Underserved Area", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:RuralvsUrban", - "@type": "rdfs:Class", - "rdfs:comment": "Density of population in the county of residence, based on census data (updated last on 4/28/20). Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the associated county on the right side of the result field. Go to https://www2.census.gov/programs-surveys/acs/data/covid_19/Data_Profiles_for_HHS/050-County_By_State/. Select the dp02_XX.csv file where XX = the two letter abbreviation for the appropriate state. On row 166 find the total population for the appropriate county. If the total population is <2,500 enter a value of \"Rural Population\"; if 2,500 - 50,000 enter a value of \"Urban Cluster\"; or if >50,000 enter \"Urban Population\"", - "rdfs:label": "RuralvsUrban", - "rdfs:subClassOf": [ + "@id": "bts:TestisNOS" + }, { - "@id": "bts:ClinicalTier2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Thoracicesophagus" + }, { - "@id": "bts:UrbanPopulation(population>50000)" + "@id": "bts:ThoraxNOS" }, { - "@id": "bts:UrbanCluster(population2500-50000)" + "@id": "bts:Thymus" }, { - "@id": "bts:RuralPopulation(population<2500)" - } - ], - "sms:displayName": "Rural vs Urban", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CancerIncidence", - "@type": "rdfs:Class", - "rdfs:comment": "Incidence of specific cancer type in a defined area (a number between 0 and 100). The rate of incident cases per population of 100,000 persons of a specific type of cancer as designated in the \"primary_diagnosis\" data element in the county where the patient resides, using the most recent 2013-2017 NCI Cancer Atlas derived data. Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the asociated county on the right side of the result field. On the https://gis.cancer.gov/canceratlas/tableview/ website, choose \"Incidence\" from the Topic dropdown menu, state of interest from the Area menu, \"All Races\" from the Race menu, and the cancer type (\"Both Sexes\" when possible) from the Statistic menu. Find the county of interest and enter the numeric Age-Adjusted Rate per 100,000 as the value.", - "rdfs:label": "CancerIncidence", - "rdfs:subClassOf": [ + "@id": "bts:Thyroidgland" + }, { - "@id": "bts:ClinicalTier2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Cancer Incidence", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CancerIncidenceLocation", - "@type": "rdfs:Class", - "rdfs:comment": "The county and state in which the patient lives and to which the cancer_incidence data correlates. Record as \"County, State\" as they appear in the incidence box from which the cancer_incidence data is obtained in the https://gis.cancer.gov/canceratlas/tableview/ website", - "rdfs:label": "CancerIncidenceLocation", - "rdfs:subClassOf": [ + "@id": "bts:TongueNOS" + }, { - "@id": "bts:ClinicalTier2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Cancer Incidence Location", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SRRSClinicalDataTier2", - "@type": "rdfs:Class", - "rdfs:comment": "Cancer related clinical data specific to SRRS", - "rdfs:label": "SRRSClinicalDataTier2", - "rdfs:subClassOf": [ + "@id": "bts:TonsilNOS" + }, { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "SRRS Clinical Data Tier 2", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "@id": "bts:Tonsillarfossa" + }, { - "@id": "bts:Component" + "@id": "bts:Tonsillarpillar" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:Trachea" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:Transversecolon" }, { - "@id": "bts:StartDaysfromIndex" + "@id": "bts:Trigoneofbladder" }, { - "@id": "bts:StopDaysfromIndex" + "@id": "bts:Undescendedtestis" }, { - "@id": "bts:EducationLevel" + "@id": "bts:Unknownprimarysite" }, { - "@id": "bts:CountryofBirth" + "@id": "bts:Uppergum" }, { - "@id": "bts:MedicallyUnderservedArea" + "@id": "bts:UpperlimbNOS" }, { - "@id": "bts:RuralvsUrban" + "@id": "bts:Upperlobelung" }, { - "@id": "bts:CancerIncidence" + "@id": "bts:UpperrespiratorytractNOS" }, { - "@id": "bts:CancerIncidenceLocation" + "@id": "bts:Upperthirdofesophagus" }, { - "@id": "bts:Ethnicity" + "@id": "bts:Upper-innerquadrantofbreast" }, { - "@id": "bts:Gender" + "@id": "bts:Upper-outerquadrantofbreast" }, { - "@id": "bts:Race" + "@id": "bts:Urachus" }, { - "@id": "bts:VitalStatus" + "@id": "bts:Ureter" }, { - "@id": "bts:AgeatDiagnosis" + "@id": "bts:Uretericorifice" }, { - "@id": "bts:DaystoLastFollowup" + "@id": "bts:Urethra" }, { - "@id": "bts:DaystoLastKnownDiseaseStatus" + "@id": "bts:UrinarysystemNOS" }, { - "@id": "bts:DaystoRecurrence" + "@id": "bts:Uterineadnexa" }, { - "@id": "bts:LastKnownDiseaseStatus" + "@id": "bts:UterusNOS" }, { - "@id": "bts:Morphology" + "@id": "bts:Uvula" }, { - "@id": "bts:PrimaryDiagnosis" + "@id": "bts:VaginaNOS" }, { - "@id": "bts:ProgressionorRecurrence" + "@id": "bts:Vallecula" }, { - "@id": "bts:SiteofResectionorBiopsy" + "@id": "bts:VentralsurfaceoftongueNOS" }, { - "@id": "bts:TissueorOrganofOrigin" + "@id": "bts:VentricleNOS" }, { - "@id": "bts:NCIAtlasCancerSite" + "@id": "bts:Vertebralcolumn" }, { - "@id": "bts:TumorGrade" + "@id": "bts:Vestibuleofmouth" }, { - "@id": "bts:PackYearsSmoked" + "@id": "bts:VulvaNOS" }, { - "@id": "bts:YearsSmoked" + "@id": "bts:Waldeyerring" }, { - "@id": "bts:DaystoFollowUp" + "@id": "bts:BiliarytractNOS" }, { - "@id": "bts:GeneSymbol" + "@id": "bts:Cheekmucosa" }, { - "@id": "bts:MolecularAnalysisMethod" + "@id": "bts:Clitoris" }, { - "@id": "bts:TestResult" + "@id": "bts:Overlappinglesionofbiliarytract" }, { - "@id": "bts:TreatmentType" + "@id": "bts:Unknown" }, { - "@id": "bts:TumorLargestDimensionDiameter" + "@id": "bts:NotReported" } ], + "sms:displayName": "Site of Resection or Biopsy", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Ethnicity", + "@id": "bts:TissueorOrganofOrigin", "@type": "rdfs:Class", - "rdfs:comment": "An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.", - "rdfs:label": "Ethnicity", + "rdfs:comment": "The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", + "rdfs:label": "TissueorOrganofOrigin", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -9684,1826 +13113,1992 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Hispanicorlatino" + "@id": "bts:AbdomenNOS" }, { - "@id": "bts:Nothispanicorlatino" + "@id": "bts:Abdominalesophagus" }, { - "@id": "bts:Unknown" + "@id": "bts:AccessorysinusNOS" }, { - "@id": "bts:NotReported" + "@id": "bts:Acousticnerve" }, { - "@id": "bts:Notallowedtocollect" - } - ], - "sms:displayName": "Ethnicity", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Gender", - "@type": "rdfs:Class", - "rdfs:comment": "Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc.]", - "rdfs:label": "Gender", - "rdfs:subClassOf": [ + "@id": "bts:AdrenalglandNOS" + }, { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:AmpullaofVater" + }, { - "@id": "bts:Female" + "@id": "bts:Analcanal" }, { - "@id": "bts:Male" + "@id": "bts:Anterior2/3oftongueNOS" }, { - "@id": "bts:Unknown" + "@id": "bts:Anteriorfloorofmouth" }, { - "@id": "bts:Unspecified" + "@id": "bts:Anteriormediastinum" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Gender", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Race", - "@type": "rdfs:Class", - "rdfs:comment": "An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation withina a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution.", - "rdfs:label": "Race", - "rdfs:subClassOf": [ + "@id": "bts:Anteriorsurfaceofepiglottis" + }, { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Anteriorwallofbladder" + }, { - "@id": "bts:White" + "@id": "bts:Anteriorwallofnasopharynx" }, { - "@id": "bts:Americanindianoralaskanative" + "@id": "bts:AnusNOS" }, { - "@id": "bts:Blackorafricanamerican" + "@id": "bts:Aorticbodyandotherparaganglia" }, { - "@id": "bts:Asian" + "@id": "bts:Appendix" }, { - "@id": "bts:Nativehawaiianorotherpacificislander" + "@id": "bts:Ascendingcolon" }, { - "@id": "bts:Other" + "@id": "bts:AutonomicnervoussystemNOS" }, { - "@id": "bts:Unknown" + "@id": "bts:Axillarytailofbreast" }, { - "@id": "bts:NotReported" + "@id": "bts:BaseoftongueNOS" }, { - "@id": "bts:Notallowedtocollect" - } - ], - "sms:displayName": "Race", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:VitalStatus", - "@type": "rdfs:Class", - "rdfs:comment": "The survival state of the person registered on the protocol.", - "rdfs:label": "VitalStatus", - "rdfs:subClassOf": [ + "@id": "bts:Bladderneck" + }, { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:BladderNOS" + }, { - "@id": "bts:Alive" + "@id": "bts:Blood" }, { - "@id": "bts:Dead" + "@id": "bts:Bodyofpancreas" }, { - "@id": "bts:Unknown" + "@id": "bts:Bodyofpenis" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Vital Status", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:AgeatDiagnosis", - "@type": "rdfs:Class", - "rdfs:comment": "Age at the time of diagnosis expressed in number of days since birth.", - "rdfs:label": "AgeatDiagnosis", - "rdfs:subClassOf": [ + "@id": "bts:Bodyofstomach" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Age at Diagnosis", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:DaystoLastFollowup", - "@type": "rdfs:Class", - "rdfs:comment": "Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoLastFollowup", - "rdfs:subClassOf": [ + "@id": "bts:Bonemarrow" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Last Follow up", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:DaystoLastKnownDiseaseStatus", - "@type": "rdfs:Class", - "rdfs:comment": "Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoLastKnownDiseaseStatus", - "rdfs:subClassOf": [ + "@id": "bts:BoneoflimbNOS" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Last Known Disease Status", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:DaystoRecurrence", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date the patient's disease recurred. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoRecurrence", - "rdfs:subClassOf": [ + "@id": "bts:BoneNOS" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Recurrence", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:LastKnownDiseaseStatus", - "@type": "rdfs:Class", - "rdfs:comment": "Text term that describes the last known state or condition of an individual's neoplasm.", - "rdfs:label": "LastKnownDiseaseStatus", - "rdfs:subClassOf": [ + "@id": "bts:Bonesofskullandfaceandassociatedjoints" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Borderoftongue" + }, { - "@id": "bts:Distantmetrecurrence/progression" + "@id": "bts:Brainstem" }, { - "@id": "bts:Loco-regionalrecurrence/progression" + "@id": "bts:BrainNOS" }, { - "@id": "bts:Biochemicalevidenceofdiseasewithoutstructuralcorrelate" + "@id": "bts:Branchialcleft" }, { - "@id": "bts:Tumorfree" + "@id": "bts:BreastNOS" }, { - "@id": "bts:Unknowntumorstatus" + "@id": "bts:Broadligament" }, { - "@id": "bts:Withtumor" + "@id": "bts:CardiaNOS" }, { - "@id": "bts:NotReported" + "@id": "bts:Carotidbody" }, { - "@id": "bts:NotAllowedToCollect" + "@id": "bts:Caudaequina" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Last Known Disease Status", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Morphology", - "@type": "rdfs:Class", - "rdfs:comment": "The third edition of the International Classification of Diseases for Oncology, published in 2000 used principally in tumor and cancer registries for coding the site (topography) and the histology (morphology) of neoplasms. The study of the structure of the cells and their arrangement to constitute tissues and, finally, the association among these to form organs. In pathology, the microscopic process of identifying normal and abnormal morphologic characteristics in tissues, by employing various cytochemical and immunocytochemical stains. A system of numbered categories for representation of data.", - "rdfs:label": "Morphology", - "rdfs:subClassOf": [ + "@id": "bts:Cecum" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Morphology", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:PrimaryDiagnosis", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the patient's histologic diagnosis, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", - "rdfs:label": "PrimaryDiagnosis", - "rdfs:subClassOf": [ + "@id": "bts:Centralportionofbreast" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:CerebellumNOS" + }, { - "@id": "bts:Acinarcellcarcinoma" + "@id": "bts:Cerebralmeninges" }, { - "@id": "bts:Acutebasophilicleukaemia" + "@id": "bts:Cerebrum" }, { - "@id": "bts:AcuteleukemiaBurkitttype" + "@id": "bts:Cervicalesophagus" }, { - "@id": "bts:AcuteleukemiaNOS" + "@id": "bts:Cervixuteri" }, { - "@id": "bts:Acutelymphaticleukemia" + "@id": "bts:Choroid" }, { - "@id": "bts:Acutelymphoblasticleukemia-lymphomaNOS" + "@id": "bts:Ciliarybody" }, { - "@id": "bts:AcutelymphoblasticleukemiamatureB-celltype" + "@id": "bts:Cloacogeniczone" }, { - "@id": "bts:AcutelymphoblasticleukemiaNOS" + "@id": "bts:ColonNOS" }, { - "@id": "bts:Acutelymphoblasticleukemiaprecursorcelltype" + "@id": "bts:Commissureoflip" }, { - "@id": "bts:Acutelymphocyticleukemia" + "@id": "bts:Conjunctiva" }, { - "@id": "bts:Acutelymphoidleukemia" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofabdomen" }, { - "@id": "bts:Acutemyeloidleukemiaminimaldifferentiation" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofheadfaceandneck" }, { - "@id": "bts:AcutemyeloidleukemiaMLL" + "@id": "bts:Connectivesubcutaneousandothersofttissuesoflowerlimbandhip" }, { - "@id": "bts:AcutemyeloidleukemiaNOS" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofpelvis" }, { - "@id": "bts:Acutemyelomonocyticleukemia" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofthorax" }, { - "@id": "bts:AcutepromyelocyticleukemiaNOS" + "@id": "bts:ConnectivesubcutaneousandothersofttissuesoftrunkNOS" }, { - "@id": "bts:Adenocarcinoidtumor" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofupperlimbandshoulder" }, { - "@id": "bts:Adenocarcinomacombinedwithothertypesofcarcinoma" + "@id": "bts:ConnectivesubcutaneousandothersofttissuesNOS" }, { - "@id": "bts:AdenocarcinomainapolypNOS" + "@id": "bts:CorneaNOS" }, { - "@id": "bts:Adenocarcinomainadenomatouspolyp" + "@id": "bts:Corpusuteri" }, { - "@id": "bts:Adenocarcinomainpolypoidadenoma" + "@id": "bts:Cortexofadrenalgland" }, { - "@id": "bts:AdenocarcinomainsituinapolypNOS" + "@id": "bts:CranialnerveNOS" }, { - "@id": "bts:Adenocarcinomainsituinadenomatouspolyp" + "@id": "bts:Craniopharyngealduct" }, { - "@id": "bts:Adenocarcinomainsituintubularadenoma" + "@id": "bts:Descendedtestis" }, { - "@id": "bts:Adenocarcinomainsitumucinous" + "@id": "bts:Descendingcolon" }, { - "@id": "bts:Adenocarcinomainsitunon-mucinous" + "@id": "bts:Domeofbladder" }, { - "@id": "bts:AdenocarcinomainsituNOS" + "@id": "bts:DorsalsurfaceoftongueNOS" }, { - "@id": "bts:Adenocarcinomaintubularadenoma" + "@id": "bts:Duodenum" }, { - "@id": "bts:Adenocarcinomainvillousadenoma" + "@id": "bts:Endocervix" }, { - "@id": "bts:Adenocarcinomaofanalducts" + "@id": "bts:EndocrineglandNOS" }, { - "@id": "bts:Adenocarcinomaofanalglands" + "@id": "bts:Endometrium" }, { - "@id": "bts:Adenocarcinomadiffusetype" + "@id": "bts:Epididymis" }, { - "@id": "bts:Adenocarcinomaendocervicaltype" + "@id": "bts:EsophagusNOS" }, { - "@id": "bts:Adenocarcinomaintestinaltype" + "@id": "bts:Ethmoidsinus" }, { - "@id": "bts:AdenocarcinomametastaticNOS" + "@id": "bts:Exocervix" }, { - "@id": "bts:AdenocarcinomaNOS" + "@id": "bts:Externalear" }, { - "@id": "bts:Adenocarcinomapancreatobiliarytype" + "@id": "bts:ExternallipNOS" }, { - "@id": "bts:Adultrhabdomyoma" + "@id": "bts:Externallowerlip" }, { - "@id": "bts:AdultT-celllymphoma" + "@id": "bts:Externalupperlip" }, { - "@id": "bts:AdultT-celllymphoma/leukemia" + "@id": "bts:Extrahepaticbileduct" }, { - "@id": "bts:Astrocytomaanaplastic" + "@id": "bts:EyeNOS" }, { - "@id": "bts:Astrocytomalowgrade" + "@id": "bts:Eyelid" }, { - "@id": "bts:AstrocytomaNOS" + "@id": "bts:Fallopiantube" }, { - "@id": "bts:BcelllymphomaNOS" + "@id": "bts:FemalegenitaltractNOS" }, { - "@id": "bts:Blymphoblasticleukemia/lymphomawithhyperdiploidy" + "@id": "bts:FloorofmouthNOS" }, { - "@id": "bts:Blymphoblasticleukemia/lymphomawithhypodiploidy(HypodiploidALL)" + "@id": "bts:Frontallobe" }, { - "@id": "bts:Blymphoblasticleukemia/lymphomaNOS" + "@id": "bts:Frontalsinus" }, { - "@id": "bts:B-ALL" + "@id": "bts:Fundusofstomach" }, { - "@id": "bts:B-celllymphocyticleukemia/smalllymphocyticlymphoma" + "@id": "bts:Fundusuteri" }, { - "@id": "bts:Basalcelladenocarcinoma" + "@id": "bts:Gallbladder" }, { - "@id": "bts:Basalcelladenoma" + "@id": "bts:Gastricantrum" }, { - "@id": "bts:BasalcellcarcinomaNOS" + "@id": "bts:GastrointestinaltractNOS" }, { - "@id": "bts:Basalcellepithelioma" + "@id": "bts:Glanspenis" }, { - "@id": "bts:Basalcelltumor" + "@id": "bts:Glottis" }, { - "@id": "bts:Basophiladenocarcinoma" + "@id": "bts:GreatercurvatureofstomachNOS" }, { - "@id": "bts:Basophiladenoma" + "@id": "bts:GumNOS" }, { - "@id": "bts:Basophilcarcinoma" + "@id": "bts:Hardpalate" }, { - "@id": "bts:Bileductadenocarcinoma" + "@id": "bts:Headofpancreas" }, { - "@id": "bts:Bileductadenoma" + "@id": "bts:HeadfaceorneckNOS" }, { - "@id": "bts:Bileductcarcinoma" + "@id": "bts:Heart" }, { - "@id": "bts:Bileductcystadenocarcinoma" + "@id": "bts:HematopoieticsystemNOS" }, { - "@id": "bts:Bileductcystadenoma" + "@id": "bts:Hepaticflexureofcolon" }, { - "@id": "bts:Bronchialadenomacarcinoid" + "@id": "bts:Hypopharyngealaspectofaryepiglotticfold" }, { - "@id": "bts:Bronchialadenomacylindroid" + "@id": "bts:HypopharynxNOS" }, { - "@id": "bts:BronchialadenomaNOS" + "@id": "bts:Ileum" }, { - "@id": "bts:Bronchial-associatedlymphoidtissuelymphoma" + "@id": "bts:Ill-definedsiteswithinrespiratorysystem" }, { - "@id": "bts:Bronchio-alveolarcarcinomamixedmucinousandnon-mucinous" + "@id": "bts:IntestinaltractNOS" }, { - "@id": "bts:Bronchio-alveolarcarcinomamucinous" + "@id": "bts:Intra-abdominallymphnodes" }, { - "@id": "bts:Bronchiolaradenocarcinoma" + "@id": "bts:Intrahepaticbileduct" }, { - "@id": "bts:Bronchiolarcarcinoma" + "@id": "bts:Intrathoraciclymphnodes" }, { - "@id": "bts:Bronchiolo-alveolaradenocarcinomaNOS" + "@id": "bts:IsletsofLangerhans" }, { - "@id": "bts:Bronchiolo-alveolarcarcinomaClaracell" + "@id": "bts:Isthmusuteri" }, { - "@id": "bts:Bronchiolo-alveolarcarcinomaClaracellandgobletcelltype" + "@id": "bts:Jejunum" }, { - "@id": "bts:Bronchiolo-alveolarcarcinomagobletcelltype" + "@id": "bts:KidneyNOS" }, { - "@id": "bts:Bronchiolo-alveolarcarcinomaindeterminatetype" + "@id": "bts:Labiummajus" }, { - "@id": "bts:Bronchiolo-alveolarcarcinomanon-mucinous" + "@id": "bts:Labiumminus" }, { - "@id": "bts:Bronchiolo-alveolarcarcinomaNOS" + "@id": "bts:Lacrimalgland" }, { - "@id": "bts:Burkittcellleukemia" + "@id": "bts:Laryngealcartilage" }, { - "@id": "bts:BurkittlymphomaNOS(Includesallvariants)" + "@id": "bts:LarynxNOS" }, { - "@id": "bts:Burkitttumor" + "@id": "bts:Lateralfloorofmouth" }, { - "@id": "bts:Burkitt-likelymphoma" + "@id": "bts:Lateralwallofbladder" }, { - "@id": "bts:C-ALL" + "@id": "bts:Lateralwallofnasopharynx" }, { - "@id": "bts:Cancer" + "@id": "bts:Lateralwalloforopharynx" }, { - "@id": "bts:Capillaryhemangioma" + "@id": "bts:LessercurvatureofstomachNOS" }, { - "@id": "bts:Capillarylymphangioma" + "@id": "bts:Lingualtonsil" }, { - "@id": "bts:CarcinomainapolypNOS" + "@id": "bts:LipNOS" }, { - "@id": "bts:Carcinomainadenomatouspolyp" + "@id": "bts:Liver" }, { - "@id": "bts:Carcinomainpleomorphicadenoma" + "@id": "bts:Longbonesoflowerlimbandassociatedjoints" }, { - "@id": "bts:CarcinomainsituinapolypNOS" + "@id": "bts:Longbonesofupperlimbscapulaandassociatedjoints" }, { - "@id": "bts:Carcinomainsituinadenomatouspolyp" + "@id": "bts:Lowergum" }, { - "@id": "bts:CarcinomainsituNOS" + "@id": "bts:LowerlimbNOS" }, { - "@id": "bts:CarcinomaanaplasticNOS" + "@id": "bts:Lowerlobelung" }, { - "@id": "bts:Carcinomadiffusetype" + "@id": "bts:Lowerthirdofesophagus" }, { - "@id": "bts:Carcinomaintestinaltype" + "@id": "bts:Lower-innerquadrantofbreast" }, { - "@id": "bts:CarcinomametastaticNOS" + "@id": "bts:Lower-outerquadrantofbreast" }, { - "@id": "bts:CarcinomaNOS" + "@id": "bts:LungNOS" }, { - "@id": "bts:CarcinosarcomaNOS" + "@id": "bts:LymphnodeNOS" }, { - "@id": "bts:CarcinomaundifferentiatedNOS" + "@id": "bts:Lymphnodesofaxillaorarm" }, { - "@id": "bts:CementomaNOS" + "@id": "bts:Lymphnodesofheadfaceandneck" }, { - "@id": "bts:Centralneuroblastoma" + "@id": "bts:Lymphnodesofinguinalregionorleg" }, { - "@id": "bts:Centralneurocytoma" + "@id": "bts:Lymphnodesofmultipleregions" }, { - "@id": "bts:Cerebellarliponeurocytoma" + "@id": "bts:Mainbronchus" }, { - "@id": "bts:CerebellarsarcomaNOS" + "@id": "bts:MajorsalivaryglandNOS" }, { - "@id": "bts:CervicalintraepithelialneoplasiagradeIII" + "@id": "bts:MalegenitalorgansNOS" }, { - "@id": "bts:Cervicalintraepithelialneoplasialowgrade" + "@id": "bts:Mandible" }, { - "@id": "bts:ChondromaNOS" + "@id": "bts:Maxillarysinus" }, { - "@id": "bts:Chondrosarcomagrade2/3" + "@id": "bts:Meckeldiverticulum" }, { - "@id": "bts:ChronicgranulocyticleukemiaBCR/ABL" + "@id": "bts:MediastinumNOS" }, { - "@id": "bts:ChronicgranulocyticleukemiaNOS" + "@id": "bts:Medullaofadrenalgland" }, { - "@id": "bts:ChronicgranulocyticleukemiaPhiladelphiachromosome(Ph1)positive" + "@id": "bts:MeningesNOS" }, { - "@id": "bts:ChronicleukemiaNOS" + "@id": "bts:Middleear" }, { - "@id": "bts:Chroniclymphaticleukemia" + "@id": "bts:Middlelobelung" }, { - "@id": "bts:Chroniclymphocyticleukemia" + "@id": "bts:Middlethirdofesophagus" }, { - "@id": "bts:ChroniclymphocyticleukemiaB-celltype(includesallvariantsofBCLL)" + "@id": "bts:MouthNOS" }, { - "@id": "bts:Chroniclymphoidleukemia" + "@id": "bts:MucosaoflipNOS" }, { - "@id": "bts:Chronicmonocyticleukemia" + "@id": "bts:Mucosaoflowerlip" }, { - "@id": "bts:ChronicmyelocyticleukemiaNOS" + "@id": "bts:Mucosaofupperlip" }, { - "@id": "bts:ChronicmyelogenousleukemiaBCR-ABLpositive" + "@id": "bts:Myometrium" }, { - "@id": "bts:ChronicmyelogenousleukemiaPhiladelphiachromosome(Ph1)positive" + "@id": "bts:Nasalcavity" }, { - "@id": "bts:ChronicmyeloidleukemiaNOS" + "@id": "bts:NasopharynxNOS" }, { - "@id": "bts:Chronicmyelomonocyticleukemiaintransformation" + "@id": "bts:NervoussystemNOS" }, { - "@id": "bts:ChronicmyelomonocyticleukemiaNOS" + "@id": "bts:Nipple" }, { - "@id": "bts:ChronicmyelomonocyticleukemiaType1" + "@id": "bts:Occipitallobe" }, { - "@id": "bts:ChronicmyelomonocyticleukemiaTypeII" + "@id": "bts:Olfactorynerve" }, { - "@id": "bts:ChronicmyeloproliferativediseaseNOS" + "@id": "bts:Opticnerve" }, { - "@id": "bts:Chronicmyeloproliferativedisorder" + "@id": "bts:OrbitNOS" }, { - "@id": "bts:Chronicneutrophilicleukemia" + "@id": "bts:OropharynxNOS" }, { - "@id": "bts:ClassicalHodgkinlymphomalymphocytedepletiondiffusefibrosis" + "@id": "bts:Otherill-definedsites" }, { - "@id": "bts:ClassicalHodgkinlymphomalymphocytedepletionNOS" + "@id": "bts:Otherspecifiedpartsoffemalegenitalorgans" }, { - "@id": "bts:ClassicalHodgkinlymphomalymphocytedepletionreticular" + "@id": "bts:Otherspecifiedpartsofmalegenitalorgans" }, { - "@id": "bts:ClassicalHodgkinlymphomalymphocyte-rich" + "@id": "bts:Otherspecifiedpartsofpancreas" }, { - "@id": "bts:ClassicalHodgkinlymphomamixedcellularityNOS" + "@id": "bts:Ovary" }, { - "@id": "bts:ClassicalHodgkinlymphomanodularsclerosiscellularphase" + "@id": "bts:Overlappinglesionofaccessorysinuses" }, { - "@id": "bts:ClassicalHodgkinlymphomanodularsclerosisgrade1" + "@id": "bts:Overlappinglesionofbladder" }, { - "@id": "bts:ClassicalHodgkinlymphomanodularsclerosisgrade2" + "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilage" }, { - "@id": "bts:ClassicalHodgkinlymphomanodularsclerosisNOS" + "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilageoflimbs" + }, + { + "@id": "bts:Overlappinglesionofbrain" }, { - "@id": "bts:Combinedhepatocellularcarcinomaandcholangiocarcinoma" + "@id": "bts:Overlappinglesionofbrainandcentralnervoussystem" }, { - "@id": "bts:Combinedlargecellneuroendocrinecarcinoma" + "@id": "bts:Overlappinglesionofbreast" }, { - "@id": "bts:Combinedsmallcellcarcinoma" + "@id": "bts:Overlappinglesionofcervixuteri" }, { - "@id": "bts:Combinedsmallcell-adenocarcinoma" + "@id": "bts:Overlappinglesionofcolon" }, { - "@id": "bts:Combinedsmallcell-largecarcinoma" + "@id": "bts:Overlappinglesionofconnectivesubcutaneousandothersofttissues" }, { - "@id": "bts:Combinedsmallcell-squamouscellcarcinoma" + "@id": "bts:Overlappinglesionofcorpusuteri" }, { - "@id": "bts:Combined/mixedcarcinoidandadenocarcinoma" + "@id": "bts:Overlappinglesionofdigestivesystem" }, { - "@id": "bts:CompositeHodgkinandnon-Hodgkinlymphoma" + "@id": "bts:Overlappinglesionofendocrineglandsandrelatedstructures" }, { - "@id": "bts:Dermalnevus" + "@id": "bts:Overlappinglesionofesophagus" }, { - "@id": "bts:DermatofibromaNOS" + "@id": "bts:Overlappinglesionofeyeandadnexa" }, { - "@id": "bts:DiffuseastrocytomaIDH-mutant" + "@id": "bts:Overlappinglesionoffemalegenitalorgans" }, { - "@id": "bts:DiffuseastrocytomaIDH-wildtype" + "@id": "bts:Overlappinglesionoffloorofmouth" }, { - "@id": "bts:Diffuseastrocytomalowgrade" + "@id": "bts:Overlappinglesionofheartmediastinumandpleura" }, { - "@id": "bts:DiffuselargeB-celllymphomaNOS" + "@id": "bts:Overlappinglesionofhypopharynx" }, { - "@id": "bts:Diffusemelanocytosis" + "@id": "bts:Overlappinglesionofill-definedsites" }, { - "@id": "bts:DuctadenocarcinomaNOS" + "@id": "bts:Overlappinglesionoflarynx" }, { - "@id": "bts:DuctadenomaNOS" + "@id": "bts:Overlappinglesionoflip" }, { - "@id": "bts:Ductcarcinomadesmoplastictype" + "@id": "bts:Overlappinglesionofliporalcavityandpharynx" }, { - "@id": "bts:DuctcarcinomaNOS" + "@id": "bts:Overlappinglesionoflung" }, { - "@id": "bts:Ductcellcarcinoma" + "@id": "bts:Overlappinglesionofmajorsalivaryglands" }, { - "@id": "bts:DuctalcarcinomainsituNOS" + "@id": "bts:Overlappinglesionofmalegenitalorgans" }, { - "@id": "bts:DuctalcarcinomaNOS" + "@id": "bts:Overlappinglesionofnasopharynx" }, { - "@id": "bts:Dysplasticnevus" + "@id": "bts:Overlappinglesionofotherandunspecifiedpartsofmouth" }, { - "@id": "bts:EndometrialsarcomaNOS" + "@id": "bts:Overlappinglesionofpalate" }, { - "@id": "bts:EndometrioidadenocarcinomaNOS" + "@id": "bts:Overlappinglesionofpancreas" }, { - "@id": "bts:EndometrioidadenofibromaNOS" + "@id": "bts:Overlappinglesionofpenis" }, { - "@id": "bts:EndometrioidadenomaNOS" + "@id": "bts:Overlappinglesionofperipheralnervesandautonomicnervoussystem" }, { - "@id": "bts:EndometrioidcarcinomaNOS" + "@id": "bts:Overlappinglesionofrectumanusandanalcanal" }, { - "@id": "bts:Eosinophiladenocarcinoma" + "@id": "bts:Overlappinglesionofrespiratorysystemandintrathoracicorgans" }, { - "@id": "bts:Eosinophiladenoma" + "@id": "bts:Overlappinglesionofretroperitoneumandperitoneum" }, { - "@id": "bts:Eosinophilcarcinoma" + "@id": "bts:Overlappinglesionofskin" }, { - "@id": "bts:Eosinophilicgranuloma" + "@id": "bts:Overlappinglesionofsmallintestine" }, { - "@id": "bts:Eosinophilicleukemia" + "@id": "bts:Overlappinglesionofstomach" }, { - "@id": "bts:EpendymomaNOS" + "@id": "bts:Overlappinglesionoftongue" }, { - "@id": "bts:EpidermoidcarcinomainsituNOS" + "@id": "bts:Overlappinglesionoftonsil" }, { - "@id": "bts:EpidermoidcarcinomaNOS" + "@id": "bts:Overlappinglesionofurinaryorgans" }, { - "@id": "bts:Epithelialtumorbenign" + "@id": "bts:Overlappinglesionofvulva" }, { - "@id": "bts:Epithelialtumormalignant" + "@id": "bts:Overlappinglesionsoforopharynx" }, { - "@id": "bts:Esophagealglandulardysplasia(intraepithelialneoplasia)highgrade" + "@id": "bts:PalateNOS" }, { - "@id": "bts:Esophagealglandulardysplasia(intraepithelialneoplasia)lowgrade" + "@id": "bts:PancreasNOS" }, { - "@id": "bts:Esophagealintraepithelialneoplasiahighgrade" + "@id": "bts:Pancreaticduct" }, { - "@id": "bts:Esophagealsquamousintraepithelialneoplasia(dysplasia)highgrade" + "@id": "bts:Parametrium" }, { - "@id": "bts:Esophagealsquamousintraepithelialneoplasia(dysplasia)lowgrade" + "@id": "bts:Paraspinal" }, { - "@id": "bts:Ewingsarcoma" + "@id": "bts:Parathyroidgland" }, { - "@id": "bts:GangliogliomaNOS" + "@id": "bts:Paraurethralgland" }, { - "@id": "bts:Familialadenomatouspolyposis" + "@id": "bts:Parietallobe" }, { - "@id": "bts:Gastrincelltumor" + "@id": "bts:Parotidgland" }, { - "@id": "bts:Gastrincelltumormalignant" + "@id": "bts:Pelvicbonessacrumcoccyxandassociatedjoints" }, { - "@id": "bts:Gastrinomamalignant" + "@id": "bts:Pelviclymphnodes" }, { - "@id": "bts:GastrinomaNOS" + "@id": "bts:PelvisNOS" }, { - "@id": "bts:Gastrointestinalstromaltumormalignant" + "@id": "bts:PenisNOS" }, { - "@id": "bts:Glioblastoma" + "@id": "bts:Peripheralnervesandautonomicnervoussystemofabdomen" }, { - "@id": "bts:Gliomamalignant" + "@id": "bts:Peripheralnervesandautonomicnervoussystemofheadfaceandneck" }, { - "@id": "bts:GliomaNOS" + "@id": "bts:Peripheralnervesandautonomicnervoussystemoflowerlimbandhip" }, { - "@id": "bts:Haemangioblastoma" + "@id": "bts:Peripheralnervesandautonomicnervoussystemofpelvis" }, { - "@id": "bts:Haemangiosarcoma" + "@id": "bts:Peripheralnervesandautonomicnervoussystemofthorax" }, { - "@id": "bts:Hepatocarcinoma" + "@id": "bts:PeripheralnervesandautonomicnervoussystemoftrunkNOS" }, { - "@id": "bts:Hepatocellularadenoma" + "@id": "bts:Peripheralnervesandautonomicnervoussystemofupperlimbandshoulder" }, { - "@id": "bts:HepatocellularcarcinomaNOS" + "@id": "bts:PeritoneumNOS" }, { - "@id": "bts:Hepatocholangiocarcinoma" + "@id": "bts:PharynxNOS" }, { - "@id": "bts:Hepatoidadenocarcinoma" + "@id": "bts:Pinealgland" }, { - "@id": "bts:Hepatoidcarcinoma" + "@id": "bts:Pituitarygland" }, { - "@id": "bts:HodgkindiseaseNOS" + "@id": "bts:Placenta" }, { - "@id": "bts:Hodgkingranuloma" + "@id": "bts:PleuraNOS" }, { - "@id": "bts:HodgkinlymphomamixedcellularityNOS" + "@id": "bts:Postcricoidregion" }, { - "@id": "bts:HodgkinlymphomanodularsclerosisNOS" + "@id": "bts:Posteriormediastinum" }, { - "@id": "bts:HodgkinlymphomaNOS" + "@id": "bts:Posteriorwallofbladder" }, { - "@id": "bts:HodgkinparagranulomaNOS" + "@id": "bts:Posteriorwallofhypopharynx" }, { - "@id": "bts:Hodgkinsarcoma" + "@id": "bts:Posteriorwallofnasopharynx" }, { - "@id": "bts:InfiltratingbasalcellcarcinomaNOS" + "@id": "bts:Posteriorwalloforopharynx" }, { - "@id": "bts:InfiltratingductcarcinomaNOS" + "@id": "bts:Prepuce" }, { - "@id": "bts:Infiltratingductandcolloidcarcinoma" + "@id": "bts:Prostategland" }, { - "@id": "bts:Infiltratingductandcribriformcarcinoma" + "@id": "bts:Pylorus" }, { - "@id": "bts:Inflammatoryadenocarcinoma" + "@id": "bts:Pyriformsinus" }, { - "@id": "bts:Inflammatorycarcinoma" + "@id": "bts:Rectosigmoidjunction" }, { - "@id": "bts:Interstitialcelltumorbenign" + "@id": "bts:RectumNOS" }, { - "@id": "bts:Interstitialcelltumormalignant" + "@id": "bts:Renalpelvis" }, { - "@id": "bts:InterstitialcelltumorNOS" + "@id": "bts:ReticuloendothelialsystemNOS" }, { - "@id": "bts:Intracysticpapilloma" + "@id": "bts:Retina" }, { - "@id": "bts:Intradermalnevus" + "@id": "bts:Retromolararea" }, { - "@id": "bts:IntraductaladenocarcinomanoninfiltratingNOS" + "@id": "bts:Retroperitoneum" }, { - "@id": "bts:Intraductalandlobularcarcinoma" + "@id": "bts:Ribsternumclavicleandassociatedjoints" }, { - "@id": "bts:Intraductalcarcinomaandlobularcarcinomainsitu" + "@id": "bts:Roundligament" }, { - "@id": "bts:Intraductalcarcinomaclinging" + "@id": "bts:ScrotumNOS" }, { - "@id": "bts:IntraductalcarcinomanoninfiltratingNOS" + "@id": "bts:Shortbonesoflowerlimbandassociatedjoints" }, { - "@id": "bts:IntraductalcarcinomaNOS" + "@id": "bts:Shortbonesofupperlimbandassociatedjoints" }, { - "@id": "bts:Intraductalcarcinomasolidtype" + "@id": "bts:Sigmoidcolon" }, { - "@id": "bts:Intraductalmicropapillarycarcinoma" + "@id": "bts:SkinoflipNOS" }, { - "@id": "bts:Intraductalpapillaryadenocarcinomawithinvasion" + "@id": "bts:Skinoflowerlimbandhip" }, { - "@id": "bts:IntraductalpapillaryadenocarcinomaNOS" + "@id": "bts:Skinofotherandunspecifiedpartsofface" }, { - "@id": "bts:Intraductalpapillarycarcinoma" + "@id": "bts:Skinofscalpandneck" }, { - "@id": "bts:Intraductaltubular-papillaryneoplasmhighgrade" + "@id": "bts:Skinoftrunk" }, { - "@id": "bts:Intraductaltubular-papillaryneoplasmlowgrade" + "@id": "bts:Skinofupperlimbandshoulder" }, { - "@id": "bts:Intraductaltubulopapillaryneoplasm" + "@id": "bts:SkinNOS" }, { - "@id": "bts:IntraepidermalcarcinomaNOS" + "@id": "bts:SmallintestineNOS" }, { - "@id": "bts:IntraepidermalsquamouscellcarcinomaBowentype" + "@id": "bts:SoftpalateNOS" }, { - "@id": "bts:IntravascularB-celllymphoma" + "@id": "bts:Specifiedpartsofperitoneum" }, { - "@id": "bts:Juvenilemyelomonocyticleukemia" + "@id": "bts:Spermaticcord" }, { - "@id": "bts:Kaposisarcoma" + "@id": "bts:Sphenoidsinus" }, { - "@id": "bts:LargecellcarcinomaNOS" + "@id": "bts:Spinalcord" }, { - "@id": "bts:Liposarcomadifferentiated" + "@id": "bts:Spinalmeninges" }, { - "@id": "bts:LiposarcomaNOS" + "@id": "bts:Spleen" }, { - "@id": "bts:Liposarcomawelldifferentiated" + "@id": "bts:Splenicflexureofcolon" }, { - "@id": "bts:Livercelladenoma" + "@id": "bts:StomachNOS" }, { - "@id": "bts:Livercellcarcinoma" + "@id": "bts:Subglottis" }, { - "@id": "bts:Lobularadenocarcinoma" + "@id": "bts:Sublingualgland" }, { - "@id": "bts:Lobularandductalcarcinoma" + "@id": "bts:Submandibulargland" }, { - "@id": "bts:LobularcarcinomainsituNOS" + "@id": "bts:Superiorwallofnasopharynx" }, { - "@id": "bts:Lobularcarcinomanoninfiltrating" + "@id": "bts:Supraglottis" }, { - "@id": "bts:LobularcarcinomaNOS" + "@id": "bts:Tailofpancreas" }, { - "@id": "bts:LymphaticleukemicNOS" + "@id": "bts:Temporallobe" }, { - "@id": "bts:LymphoblasticleukemiaNOS" + "@id": "bts:TestisNOS" }, { - "@id": "bts:Lymphoblastoma" + "@id": "bts:Thoracicesophagus" }, { - "@id": "bts:LymphocyticleukemiaNOS" + "@id": "bts:ThoraxNOS" }, { - "@id": "bts:LymphomaNOS" + "@id": "bts:Thymus" }, { - "@id": "bts:Malignancy" + "@id": "bts:Thyroidgland" }, { - "@id": "bts:MalignantlymphomadiffuseNOS" + "@id": "bts:TongueNOS" }, { - "@id": "bts:MalignantlymphomaHodgkin" + "@id": "bts:TonsilNOS" }, { - "@id": "bts:MalignantlymphomaimmunoblasticNOS" + "@id": "bts:Tonsillarfossa" }, { - "@id": "bts:MalignantlymphomalargeB-celldiffuseNOS" + "@id": "bts:Tonsillarpillar" }, { - "@id": "bts:MalignantlymphomalargeB-cellNOS" + "@id": "bts:Trachea" }, { - "@id": "bts:MalignantlymphomalargecellNOS" + "@id": "bts:Transversecolon" }, { - "@id": "bts:MalignantlymphomalymphoblasticNOS" + "@id": "bts:Trigoneofbladder" }, { - "@id": "bts:MalignantlymphomalymphocyticdiffuseNOS" + "@id": "bts:Undescendedtestis" }, { - "@id": "bts:MalignantlymphomalymphocyticnodularNOS" + "@id": "bts:Unknownprimarysite" }, { - "@id": "bts:MalignantlymphomalymphocyticNOS" + "@id": "bts:Uppergum" }, { - "@id": "bts:Malignantlymphomamixedcelltypediffuse" + "@id": "bts:UpperlimbNOS" }, { - "@id": "bts:Malignantlymphomamixedcelltypefollicular" + "@id": "bts:Upperlobelung" }, { - "@id": "bts:Malignantlymphomamixedcelltypenodular" + "@id": "bts:UpperrespiratorytractNOS" }, { - "@id": "bts:MalignantlymphomanodularNOS" + "@id": "bts:Upperthirdofesophagus" }, { - "@id": "bts:Malignantlymphomanon-HodgkinNOS" + "@id": "bts:Upper-innerquadrantofbreast" }, { - "@id": "bts:MalignantlymphomaNOS" + "@id": "bts:Upper-outerquadrantofbreast" }, { - "@id": "bts:MalignantlymphomasmallBlymphocyticNOS" + "@id": "bts:Urachus" }, { - "@id": "bts:Malignantmelanomaincongenitalmelanocyticnevus" + "@id": "bts:Ureter" }, { - "@id": "bts:Malignantmelanomaingiantpigmentednevus" + "@id": "bts:Uretericorifice" }, { - "@id": "bts:MalignantmelanomainHutchinsonmelanoticfreckle" + "@id": "bts:Urethra" }, { - "@id": "bts:Malignantmelanomainjunctionalnevus" + "@id": "bts:UrinarysystemNOS" }, { - "@id": "bts:Malignantmelanomainprecancerousmelanosis" + "@id": "bts:Uterineadnexa" }, { - "@id": "bts:MalignantmelanomaNOS" + "@id": "bts:UterusNOS" }, { - "@id": "bts:Malignantmelanomaregressing" + "@id": "bts:Uvula" }, { - "@id": "bts:Mammarycarcinomainsitu" + "@id": "bts:VaginaNOS" }, { - "@id": "bts:Medullaryadenocarcinoma" + "@id": "bts:Vallecula" }, { - "@id": "bts:MedullarycarcinomaNOS" + "@id": "bts:VentralsurfaceoftongueNOS" }, { - "@id": "bts:Medullaryosteosarcoma" + "@id": "bts:VentricleNOS" }, { - "@id": "bts:MedulloblastomaNOS" + "@id": "bts:Vertebralcolumn" }, { - "@id": "bts:Melanoameloblastoma" + "@id": "bts:Vestibuleofmouth" }, { - 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If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoFollowUp", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Days to Follow Up", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:GeneSymbol", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe a gene targeted or included in molecular analysis. For rearrangements, this is should be used to represent the reference gene. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "GeneSymbol", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Gene Symbol", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:MolecularAnalysisMethod", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the method used for molecular analysis. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "MolecularAnalysisMethod", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:ComparativeGenomicHybridization" }, { - "@id": "bts:Neoplasmmetastatic" + "@id": "bts:CytogeneticsNOS" }, { - "@id": "bts:NeoplasmNOS" + "@id": "bts:FISH" }, { - "@id": "bts:Neoplasmsecondary" + "@id": "bts:FlowCytometry" }, { - "@id": "bts:Neoplasmuncertainwhetherbenignormalignant" + "@id": "bts:IHC" }, { - "@id": "bts:NephroblastomaNOS" + "@id": "bts:ISH" }, { - "@id": "bts:NeuroblastomaNOS" + "@id": "bts:Karyotype" }, { - "@id": "bts:NeuroendocrinecarcinomaNOS" + "@id": "bts:Microarray" }, { - "@id": "bts:NeuroepitheliomaNOS" + "@id": "bts:MicrosatelliteAnalysis" }, { - "@id": "bts:NeurofibromaNOS" + "@id": "bts:NuclearStaining" }, { - "@id": "bts:NeurofibromatosisNOS" + "@id": "bts:Other" }, { - "@id": "bts:Neurofibrosarcoma" + "@id": "bts:RNASequencing" }, { - "@id": "bts:Neurosarcoma" + "@id": "bts:RT-PCR" }, { - "@id": "bts:NevusNOS" + "@id": "bts:SequencingNOS" }, { - "@id": "bts:Non-HodgkinlymphomaNOS" + "@id": "bts:SouthernBlotting" }, { - "@id": "bts:Non-invasivelowgradeserouscarcinoma" + "@id": "bts:TargetedSequencing" }, { - "@id": "bts:Non-lymphocyticleukemiaNOS" + "@id": "bts:WGS" }, { - "@id": "bts:Non-smallcellcarcinoma" + "@id": "bts:WXS" }, { - "@id": "bts:Nonpigmentednevus" + "@id": "bts:Unknown" }, { "@id": "bts:NotReported" }, { - "@id": "bts:Oatcellcarcinoma" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Molecular Analysis Method", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:TestResult", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the result of the molecular test. If the test result was a numeric value see test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "TestResult", + "rdfs:subClassOf": [ { - "@id": "bts:Osteoblastomamalignant" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:OsteoblastomaNOS" + "@id": "bts:AbnormalNOS" }, { - "@id": "bts:OsteosarcomaNOS" + "@id": "bts:CopyNumberReported" }, { - "@id": "bts:Pagetdiseaseandinfiltratingductcarcinomaofbreast" + "@id": "bts:Equivocal" }, { - "@id": "bts:Pagetdiseaseandintraductalcarcinomaofbreast" + "@id": "bts:High" }, { - "@id": "bts:Pagetdiseaseofbreast" + "@id": "bts:Intermediate" }, { - "@id": "bts:Pagetdiseaseextramammary" + "@id": "bts:LossofExpression" }, { - "@id": "bts:Pagetdiseasemammary" + "@id": "bts:Low" }, { - "@id": "bts:Pagetoidreticulosis" + "@id": "bts:Negative" }, { - "@id": "bts:Pancreaticendocrinetumorbenign" + "@id": "bts:Normal" }, { - "@id": "bts:Pancreaticendocrinetumormalignant" + "@id": "bts:Overexpressed" }, { - 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"@id": "bts:SerouscystadenocarcinomaNOS" + "@id": "bts:LungWedgeResectionBilateral" }, { - "@id": "bts:Seroussurfacepapillarycarcinoma" + "@id": "bts:LungWedgeResectionLeft" }, { - "@id": "bts:High-gradeserouscarcinoma" + "@id": "bts:LungWedgeResectionMultiple" }, { - "@id": "bts:Skinappendagecarcinoma" + "@id": "bts:LungWedgeResectionRight" }, { - "@id": "bts:SmallcellcarcinomaNOS" + "@id": "bts:PneumonectomyLeft" }, { - "@id": "bts:Smallcellneuroendocrinecarcinoma" + "@id": "bts:PneumonectomyRight" }, { - "@id": "bts:Smallcellosteosarcoma" + "@id": "bts:Endobronchialbiopsy" }, { - "@id": "bts:Smallcellsarcoma" + "@id": "bts:Mediastinoscopy" }, { - "@id": "bts:Smallcongenitalnevus" + "@id": "bts:VATSSclerosis" }, { - "@id": "bts:SpindlecellcarcinomaNOS" + "@id": "bts:Brainresection" }, { - "@id": "bts:SpindlecellmelanomaNOS" + "@id": "bts:Segmentectomy" }, { - "@id": "bts:SplenicB-celllymphoma/leukemiaunclassifiable" + "@id": "bts:Unknown" }, { - "@id": "bts:SplenicdiffuseredpulpsmallB-celllymphoma" + "@id": "bts:Other" }, { - "@id": "bts:Spleniclymphomawithvillouslymphocytes" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Lung Cancer Participant Procedure History", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:LungAdjacentHistologyType", + "@type": "rdfs:Class", + "rdfs:comment": "The type of morphologic characteristics observed by microscope in the tissue next to a benign or malignant tissue growth", + "rdfs:label": "LungAdjacentHistologyType", + "rdfs:subClassOf": [ + { + "@id": "bts:LungCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Lungadenocarcinoma" }, { - "@id": "bts:SplenicmarginalzoneB-celllymphoma" + "@id": "bts:Adenosquamouscarcinoma" }, { - "@id": "bts:SplenicmarginalzonelymphomaNOS" + "@id": "bts:Carcinoidtumorandlungatypicalcarcinoidtumor" }, { - "@id": "bts:SquamouscellcarcinomainsituNOS" + "@id": "bts:Lungadenocarcinomainsitu" }, { - "@id": "bts:Squamouscellcarcinomaadenoid" + "@id": "bts:Largecelllungcarcinoma" }, { - "@id": "bts:Squamouscellcarcinomaclearcelltype" + "@id": "bts:Largecellneuroendocrinecarcinoma" }, { - "@id": "bts:SquamouscellcarcinomaNOS" + "@id": "bts:Lunglymphoepithelioma-likecarcinoma" }, { - "@id": "bts:Tlymphoblasticleukemia/lymphoma" + "@id": "bts:Bronchioalveolarcarcinoma" }, { - "@id": "bts:T-celllargegranularlymphocyticleukemia" + "@id": "bts:ThoracicNUTcarcinoma" }, { - "@id": "bts:T-celllargegranularlymphocytosis" + "@id": "bts:Sarcomatoidcarcinoma" }, { - "@id": "bts:T-celllymphomaNOS" + "@id": "bts:Smallcelllungcarcinoma" }, { - "@id": "bts:TeratomamalignantNOS" + "@id": "bts:Squamouscelllungcarcinoma" }, { - "@id": "bts:TeratomaNOS" + "@id": "bts:Lungsquamouscellcarcinomainsitu" }, { - "@id": "bts:Therapyrelatedmyeloidneoplasm" + "@id": "bts:Other" }, { - "@id": "bts:Transitionalcarcinoma" + "@id": "bts:Unknown" }, { - "@id": "bts:Transitionalcellcarcinoma" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Lung Adjacent Histology Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:LungTumorLocationAnatomicSite", + "@type": "rdfs:Class", + "rdfs:comment": "Anatomic location of the tumor inside the lung", + "rdfs:label": "LungTumorLocationAnatomicSite", + "rdfs:subClassOf": [ + { + "@id": "bts:LungCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Maincarina" }, { - "@id": "bts:Transitionalcellcarcinomainsitu" + "@id": "bts:Left" }, { - "@id": "bts:Tubularadenocarcinoma" + "@id": "bts:Right" }, { - "@id": "bts:TubularadenomaNOS" + "@id": "bts:Unknown" }, { - "@id": "bts:Tubularandroblastomawithlipidstorage" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Lung Tumor Location Anatomic Site", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:LungTumorLobeBronchialLocation", + "@type": "rdfs:Class", + "rdfs:comment": "Anatomic lobe and bronchial location of the tumor inside the lung", + "rdfs:label": "LungTumorLobeBronchialLocation", + "rdfs:subClassOf": [ + { + "@id": "bts:LungCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Upperlobe" }, { - "@id": "bts:TubularandroblastomaNOS" + "@id": "bts:Middlelobe" }, { - "@id": "bts:Tubularcarcinoid" + "@id": "bts:Lowerlobe" }, { - "@id": "bts:Tubularcarcinoma" + "@id": "bts:Stump" }, { - "@id": "bts:Tubulo-papillaryadenoma" + "@id": "bts:Bronchus" }, { - "@id": "bts:Tubulocysticrenalcellcarcinoma" + "@id": "bts:Unknown" }, { - "@id": "bts:Tubulolobularcarcinoma" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Lung Tumor Lobe Bronchial Location", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CurrentLungCancerSymptoms", + "@type": "rdfs:Class", + "rdfs:comment": "Reported lung cancer related symptoms person is currently experiencing", + "rdfs:label": "CurrentLungCancerSymptoms", + "rdfs:subClassOf": [ + { + "@id": "bts:LungCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Asbestosis" }, { - "@id": "bts:Tubulopapillaryadenocarcinoma" + "@id": "bts:Productivecough" }, { - "@id": "bts:TubulovillousadenomaNOS" + "@id": "bts:Non-productivecough" }, { - "@id": "bts:Tumorcellsbenign" + "@id": "bts:Wheezing" }, { - "@id": "bts:Tumorcellsmalignant" + "@id": "bts:Rhonci" }, { - "@id": "bts:TumorcellsNOS" + "@id": "bts:Crackles" }, { - "@id": "bts:Tumorcellsuncertainwhetherbenignormalignant" + "@id": "bts:Hemoptysis" }, { - "@id": "bts:Tumorembolus" + "@id": "bts:Dyspnea" }, { - "@id": "bts:Tumorbenign" + "@id": "bts:Unexplainedweightloss" }, { - "@id": "bts:TumormalignantNOS" + "@id": "bts:Unexplainedlossofenergy/fatigue" }, { - "@id": "bts:Tumormetastatic" + "@id": "bts:Chestpainordiscomfort" }, { - "@id": "bts:TumorNOS" + "@id": "bts:Dysphagia" }, { - "@id": "bts:Tumorsecondary" + "@id": "bts:Pneumonia" }, { - "@id": "bts:Tumorletbenign" + "@id": "bts:Hoarseness/laryngitis/vocalcordinflammation" }, { - "@id": "bts:Typicalcarcinoid" + "@id": "bts:Airentrydecreased/fair/poor/diminished" }, { - "@id": "bts:Unclassifiedtumorbenign" + "@id": "bts:Fair/pooraeration" }, { - "@id": "bts:Unclassifiedtumorborderlinemalignancy" + "@id": "bts:Shallowinspiration" }, { - "@id": "bts:Unclassifiedtumormalignant" + "@id": "bts:Breathsoundscoarse/diminished" }, { - "@id": "bts:Unclassifiedtumormalignantuncertainwhetherprimaryormetastatic" + "@id": "bts:Dullnesstopercussion" }, { - "@id": "bts:Unclassifiedtumoruncertainwhetherbenignormalignant" + "@id": "bts:Abnormalbreathsounds" }, { - "@id": "bts:Undifferentiatedepithelioidsarcoma" + "@id": "bts:Clearlungstoauscultationorpercussion" }, { - "@id": "bts:Undifferentiatedhigh-gradepleomorphicsarcoma" + "@id": "bts:Unlabored/normalbreathing" }, { - "@id": "bts:Undifferentiatedleukaemia" + "@id": "bts:Coldsymptoms/flu/sinus/nasalcongestion" }, { - "@id": "bts:Undifferentiatedpleomorphicsarcoma" + "@id": "bts:Sinuspain/infection" }, { - "@id": "bts:Undifferentiatedroundcellsarcoma" + "@id": "bts:Fingerclubbing" }, { - "@id": "bts:Undifferentiatedsarcoma" + "@id": "bts:Noevidenceoflungcancerrecurrence" }, { - "@id": "bts:Undifferentiatedspindlecellsarcoma" + "@id": "bts:PatientisNED" }, { - "@id": "bts:Undifferentiateduterinesarcoma" + "@id": "bts:Oxygensupplemental-portableO2atnightorcontinuous" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Primary Diagnosis", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ProgressionorRecurrence", - "@type": "rdfs:Class", - "rdfs:comment": "Yes/No/unknown indicator to identify whether a patient has had a new tumor event after initial treatment.", - "rdfs:label": "ProgressionorRecurrence", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes-ProgressionorRecurrence" + "@id": "bts:Prolongedexpiration-long/forcedexpiratoryphase" }, { - "@id": "bts:No" + "@id": "bts:Other" }, { "@id": "bts:Unknown" @@ -11512,18 +15107,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Progression or Recurrence", - "sms:required": "sms:true", + "sms:displayName": "Current Lung Cancer Symptoms", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SiteofResectionorBiopsy", + "@id": "bts:LungTopography", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the anatomic site of the resection or biopsy of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", - "rdfs:label": "SiteofResectionorBiopsy", + "rdfs:comment": "Lung PCA specific topography (not covered in previous tiers)", + "rdfs:label": "LungTopography", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:LungCancerTier3" } ], "schema:isPartOf": { @@ -11531,1017 +15126,1534 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:AbdomenNOS" + "@id": "bts:MC-Carinabetweenrightandleftlungs(maincarina)" }, { - "@id": "bts:Abdominalesophagus" + "@id": "bts:TR-Trachea(airwaywallbetweentracheo-esophagealbifurcationandmaincarina)" }, { - "@id": "bts:AccessorysinusNOS" + "@id": "bts:CarinaNOS(Carinanototherwisespecified)" }, { - "@id": "bts:Acousticnerve" + "@id": "bts:LUDB-Carinabetweenthelingulaandupperdivisionleftupperlobe" }, { - "@id": "bts:AdrenalglandNOS" + "@id": "bts:CarinabetweenLUDBorificeandlingulaorifice" }, { - "@id": "bts:AmpullaofVater" + "@id": "bts:LUDB-orificeairwaywallbetweenLUDBandLB3(LB1+2carinae)" }, { - "@id": "bts:Analcanal" + "@id": "bts:LingulaorificeairwaywallbetweenLUDBandLB4/5carinae" }, { - "@id": "bts:Anterior2/3oftongueNOS" + "@id": "bts:RMB-Rightmainstembronchus(airwaywallbetweenMC&RULcarina)" }, { - "@id": "bts:Anteriorfloorofmouth" + "@id": "bts:LMB-Leftmainstembronchus(airwaywallbetweenMC&LULcarina)" }, { - "@id": "bts:Anteriormediastinum" + "@id": "bts:RLNOS(Rightlungnototherwisespecified)" }, { - "@id": "bts:Anteriorsurfaceofepiglottis" + "@id": "bts:RB1/2-Carinabetweenapicalandposteriorsegmentsrightupperlobe(CarinabetweenRB1orificeandRB2orifice)" }, { - "@id": "bts:Anteriorwallofbladder" + "@id": "bts:RB6A/B-CarinabetweenapicalandlateralsubsegmentssuperiorsegmentRLL" }, { - "@id": "bts:Anteriorwallofnasopharynx" + "@id": "bts:RB6A/C-CarinabetweenapicalandmedialsubsegmentssuperiorsegmentRLL" }, { - "@id": "bts:AnusNOS" + "@id": "bts:RB6B/C-CarinabetweenmedialandlateralsubsegmentssuperiorsegmentRLL" }, { - "@id": "bts:Aorticbodyandotherparaganglia" + "@id": "bts:RB7A/B-CarinabetweenmedialandlateralsubsegmentsmedialbasalsegmentRLL" }, { - "@id": "bts:Appendix" + "@id": "bts:RB8/9-CarinabetweenanteriorandlateralsegmentsRLL(CarinabetweenRB8orificeandRB9orifice)" }, { - "@id": "bts:Ascendingcolon" + "@id": "bts:RB8A/B-CarinabetweenmedialandlateralsubsegmentsanteriorsegmentRLL" }, { - "@id": "bts:AutonomicnervoussystemNOS" + "@id": "bts:RB9/10-CarinabetweenlateralandposteriorsegmentsRLL" }, { - "@id": "bts:Axillarytailofbreast" + "@id": "bts:RB9A/B-CarinabetweenmedialandlateralsubsegmentslateralsegmentRLL" }, { - "@id": "bts:BaseoftongueNOS" + "@id": "bts:RB10A/B-CarinabetweenmedialandlateralsubsegmentsposteriorsegmentRLL" }, { - "@id": "bts:Bladderneck" + "@id": "bts:RB10A/C-CarinabetweenmedialandapicalsubsegmentsposteriorsegmentRLL" }, { - "@id": "bts:BladderNOS" + "@id": "bts:RB1A/B-CarinabetweenmedialandlateralsubsegmentsapicalsegmentRUL" }, { - "@id": "bts:Blood" + "@id": "bts:RB10B/C-CarinabetweenmedialandlateralsubsegmentsposteriorsegmentRLL" }, { - "@id": "bts:Bodyofpancreas" + "@id": "bts:RB6-CarinaofsuperiorsegmentRLL(CarinabetweenRB6orificeandlowerportionofRLLorifice)" }, { - "@id": "bts:Bodyofpenis" + "@id": "bts:RB6orificeAirwaywallbetweenRB6andRB6A/B/Ccarinae" }, { - "@id": "bts:Bodyofstomach" + "@id": "bts:BronchusIntermediusBronchus(airwaywall)betweenrightupperandrightmiddlelobes" }, { - "@id": "bts:Bonemarrow" + "@id": "bts:RB1/3-CarinabetweenapicalandanteriorsegmentsRUL(CarinabetweenRB1orificeandRB3orifice)" }, { - "@id": "bts:BoneoflimbNOS" + "@id": "bts:RB2/3-CarinabetweenanteriorandposteriorsegmentsRUL(CarinabetweenRB2orificeandRB3orifice)" }, { - "@id": "bts:BoneNOS" + "@id": "bts:RB2A/B-Carinabetweenthemedialandlateralsubsegmentsoftheposteriorsegment(RUL)" }, { - "@id": "bts:Bonesofskullandfaceandassociatedjoints" + "@id": "bts:RB3A/B-CarinabetweenthemedialandlateralsubsegmentsoftheanteriorsegmentRUL" }, { - "@id": "bts:Borderoftongue" + "@id": "bts:RB4/5-Carinabetweenthelateralandmedialsegmentsrightmiddlelobe(CarinabetweenRB4orificeandRB5orifice)" }, { - "@id": "bts:Brainstem" + "@id": "bts:RB4A/B-Carinabetweenthemedialandlateralsubsegmentsofthelateralsegmentoftherightmiddlelobe" }, { - "@id": "bts:BrainNOS" + "@id": "bts:RB5A/B-Carinabetweenthemedialandlateralsubsegmentsofthemedialsegmentoftherightmiddlelobe" }, { - "@id": "bts:Branchialcleft" + "@id": "bts:RULCarinaebetweenRULorificeandbronchusintermedius" }, { - "@id": "bts:BreastNOS" + "@id": "bts:RULorificeAirwaywallbetweenRULandRB1/RB2/RB3" }, { - "@id": "bts:Broadligament" + "@id": "bts:RB1orificeApicalsegment-rightupperlobe(airwaywallbetweenRB1andRB1A/Bcarinae)" }, { - "@id": "bts:CardiaNOS" + "@id": "bts:RB2orificePosteriorsegment-rightupperlobe(airwaywallbetweenRB2andRB2A/Bcarinae)" }, { - "@id": "bts:Carotidbody" + "@id": "bts:RB3orificeAnteriorsegment-rightupperlobe(airwaywallbetweenRB3andRB3A/Bcarinae)" }, { - "@id": "bts:Caudaequina" + "@id": "bts:RML-CarinabetweenRMLorificeandRLLorifice" }, { - "@id": "bts:Cecum" + "@id": "bts:RMLorificeAirwaywallbetweenRMLandRB4/5" }, { - "@id": "bts:Centralportionofbreast" + "@id": "bts:RB4orificeLateralsegmentrightmiddlelobe(airwaywallbetweenRB4andRB4A/Bcarinae)" }, { - "@id": "bts:CerebellumNOS" + "@id": "bts:RB5orificeMedialsegmentrightmiddlelobe(airwaywallbetweenRB5andRB5A/Bcarinae)" }, { - "@id": "bts:Cerebralmeninges" + "@id": "bts:RLLorificeAirwaywallbetweenRMLandRB6-10carinae" }, { - "@id": "bts:Cerebrum" + "@id": "bts:RB7Medialbasalsegmentrightlowerlobe(CarinaatRB7orificetakeofffromRLLorifice)" }, { - "@id": "bts:Cervicalesophagus" + "@id": "bts:RB7orificeAirwaywallbetweenRB7andRB7A/Bcarinae" }, { - "@id": "bts:Cervixuteri" + "@id": "bts:RB8orificeAnteriorsegmentrightlowerlobe(airwaywallbetweenRB8andRB8A/Bcarinae)" }, { - "@id": "bts:Choroid" + "@id": "bts:RB9orificeLateralsegmentrightlowerlobe(airwaywallbetweenRB9andRB9A/Bcarinae)" }, { - "@id": "bts:Ciliarybody" + "@id": "bts:RB10Posteriorsegmentrightlowerlobe(CarinaatRB10orificetakeofffromRLLorifice)" }, { - "@id": "bts:Cloacogeniczone" + "@id": "bts:RB10orificeAirwaywallbetweenRB10andRB10A/Bcarinae" }, { - "@id": "bts:ColonNOS" + "@id": "bts:LLNOS(Leftlungnototherwisespecified)" }, { - "@id": "bts:Commissureoflip" + "@id": "bts:LB1/2Carinabetweenapicalandposteriorsegmentleftupperlobe(CarinabetweenLB1orificeandLB2orifice)" }, { - "@id": "bts:Conjunctiva" + "@id": "bts:LB4/5Carinabetweensuperiorandinferiorsegmentlingula(CarinabetweenLB4orificeandLB5orifice)" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofabdomen" + "@id": "bts:LB4A/BCarinabetweenmedialandlateralsubsegmentssuperiorsegmentlingula" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofheadfaceandneck" + "@id": "bts:LB5A/BCarinabetweenthemedialandlateralsubsegmentsinferiorsegmentlingula" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesoflowerlimbandhip" + "@id": "bts:LB6A/BCarinabetweenthesuperiorandlateralsubsegmentssuperiorsegmentLLL" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofpelvis" + "@id": "bts:LB6A/CCarinabetweenthesuperiorandmedialsubsegmentsofsuperiorsegmentLLL" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofthorax" + "@id": "bts:LB6B/CCarinabetweenthemedialandlateralsubsegmentsofthesuperiorsegmentLLL" }, { - "@id": "bts:ConnectivesubcutaneousandothersofttissuesoftrunkNOS" + "@id": "bts:LB8/9CarinabetweentheanteriorandlateralsegmentsLLL(CarinabetweenLB8orificeandLB9orifice)" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofupperlimbandshoulder" + "@id": "bts:LB8A/BCarinabetweenthemedialandlateralsubsegmentsoftheanteriorsegmentLLL" }, { - "@id": "bts:ConnectivesubcutaneousandothersofttissuesNOS" + "@id": "bts:LB9/10CarinabetweenthelateralandposteriorsegmentsLLL(CarinabetweenLB9orificeandLB10orifice)" }, { - "@id": "bts:CorneaNOS" + "@id": "bts:LB9A/BCarinabetweenthemedialandlateralsubsegmentsofthelateralsegmentLLL" }, { - "@id": "bts:Corpusuteri" + "@id": "bts:LB1A/BCarinabetweenthelateralandmedialsubsegmentsoftheapicalsegmentoftheLUL" }, { - "@id": "bts:Cortexofadrenalgland" + "@id": "bts:LB10A/BCarinabetweentheapicalandlateralsubsegmentsoftheposteriorsegmentoftheLLL" }, { - "@id": "bts:CranialnerveNOS" + "@id": "bts:LB10A/CCarinabetweentheapicalandmedialsegmentsoftheposteriorsegmentoftheLLL" }, { - "@id": "bts:Craniopharyngealduct" + "@id": "bts:LB10B/CCarinabetweenthemedialandlateralsubsegmentsoftheposteriorsegmentoftheLLL" }, { - "@id": "bts:Descendedtestis" + "@id": "bts:LB1+2orificeTheapico-posteriorsegmentoftheleftupperlobe(airwaywallbetweenLB1+2/3carinaandLB1orLB2)" }, { - "@id": "bts:Descendingcolon" + "@id": "bts:LB6Thesuperiorsegmentoftheleftlowerlobe(CarinabetweenLB6orificeandlowerportionofLLLorifice)" }, { - 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"@id": "bts:VulvaNOS" + "@id": "bts:EstrogenreceptorIHC" }, { - "@id": "bts:Waldeyerring" + "@id": "bts:ProgesteronereceptorIHC" }, { - "@id": "bts:BiliarytractNOS" + "@id": "bts:HER2IHC" }, { - "@id": "bts:Cheekmucosa" + "@id": "bts:HER2FISH-CISH" }, { - "@id": "bts:Clitoris" + "@id": "bts:HER2FISH" }, { - "@id": "bts:Overlappinglesionofbiliarytract" + "@id": "bts:Other" }, { "@id": "bts:Unknown" }, { - "@id": "bts:NotReported" + "@id": "bts:Datanotavailable" } ], - "sms:displayName": "Site of Resection or Biopsy", - "sms:required": "sms:true", + "sms:displayName": "Breast Cancer Assessment Tests", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TissueorOrganofOrigin", + "@id": "bts:BreastCancerGenomicTestPerformed", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", - "rdfs:label": "TissueorOrganofOrigin", + "rdfs:comment": "Text term that represents the name of the genomic test performed for breast cancer.", + "rdfs:label": "BreastCancerGenomicTestPerformed", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { @@ -12549,997 +16661,1652 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:AbdomenNOS" - }, - { - "@id": "bts:Abdominalesophagus" - }, - { - "@id": "bts:AccessorysinusNOS" - }, - { - "@id": "bts:Acousticnerve" - }, - { - "@id": "bts:AdrenalglandNOS" - }, - { - "@id": "bts:AmpullaofVater" + "@id": "bts:Oncotype" }, { - "@id": "bts:Analcanal" + "@id": "bts:MammaPrint" }, { - "@id": "bts:Anterior2/3oftongueNOS" + "@id": "bts:Other" }, { - "@id": "bts:Anteriorfloorofmouth" + "@id": "bts:Datanotavailable" }, { - "@id": "bts:Anteriormediastinum" + "@id": "bts:Unknown" }, { - "@id": "bts:Anteriorsurfaceofepiglottis" - }, + "@id": "bts:Notperformed" + } + ], + "sms:displayName": "Breast Cancer Genomic Test Performed", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MammaprintRiskGroup", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that represents the risk group for breast cancer as determined by assessment of the MammaPrint test.", + "rdfs:label": "MammaprintRiskGroup", + "rdfs:subClassOf": [ { - "@id": "bts:Anteriorwallofbladder" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Anteriorwallofnasopharynx" + "@id": "bts:Highrisk" }, { - "@id": "bts:AnusNOS" + "@id": "bts:Intermediaterisk" }, { - "@id": "bts:Aorticbodyandotherparaganglia" + "@id": "bts:Lowrisk" }, { - "@id": "bts:Appendix" + "@id": "bts:Datanotavailable" }, { - "@id": "bts:Ascendingcolon" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Mammaprint Risk Group", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:OncotypeRiskGroup", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that represents the risk group for breast cancer as determined by assessment of the Oncotype recurrence score.", + "rdfs:label": "OncotypeRiskGroup", + "rdfs:subClassOf": [ { - "@id": "bts:AutonomicnervoussystemNOS" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - 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}, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Connectivesubcutaneousandothersofttissuesoflowerlimbandhip" + "@id": "bts:DCIS" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofpelvis" + "@id": "bts:LCIS" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofthorax" + "@id": "bts:Invasivebreastcancer(unrelatedtothecurrentcancer)" }, { - "@id": "bts:ConnectivesubcutaneousandothersofttissuesoftrunkNOS" + "@id": "bts:Other" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofupperlimbandshoulder" + "@id": "bts:Unknown" }, { - "@id": "bts:ConnectivesubcutaneousandothersofttissuesNOS" - }, + "@id": "bts:Datanotavailable" + } + ], + "sms:displayName": "Prior Invasive Breast Disease", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaERStatusPercentageValue", + "@type": "rdfs:Class", + "rdfs:comment": "A numerical quantity measured or assigned or computed which captures the estrogen receptor level measured in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaERStatusPercentageValue", + "rdfs:subClassOf": [ { - "@id": "bts:CorneaNOS" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Breast Carcinoma ER Status Percentage Value", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaPRStatusPercentageValue", + "@type": "rdfs:Class", + "rdfs:comment": "A numerical quantity measured or assigned or computed which captures the progesterone receptor level measured in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaPRStatusPercentageValue", + "rdfs:subClassOf": [ { - "@id": "bts:Corpusuteri" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Breast Carcinoma PR Status Percentage Value", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HER2BreastCarcinomaCopyNumberTotal", + "@type": "rdfs:Class", + "rdfs:comment": "Result of HER2 Copy Number testing (in a participant with breast cancer), expressed as a range of values.", + "rdfs:label": "HER2BreastCarcinomaCopyNumberTotal", + "rdfs:subClassOf": [ { - "@id": "bts:Cortexofadrenalgland" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "HER2 Breast Carcinoma Copy Number Total", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaCentromere17CopyNumber", + "@type": "rdfs:Class", + "rdfs:comment": "Result of Centromere 17 testing in a sample or specimen of metastatic breast carcinoma, expressed as a range of values.", + "rdfs:label": "BreastCarcinomaCentromere17CopyNumber", + "rdfs:subClassOf": [ { - "@id": "bts:CranialnerveNOS" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Breast Carcinoma Centromere 17 Copy Number", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaHER2Centromere17CopynumberTotal", + "@type": "rdfs:Class", + "rdfs:comment": "Number of Cells Counted for HER2 & Centromere 17 Copy Numbers in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaHER2Centromere17CopynumberTotal", + "rdfs:subClassOf": [ { - "@id": "bts:Craniopharyngealduct" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Breast Carcinoma HER2 Centromere17 Copynumber Total", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaHER2Chromosome17Ratio", + "@type": "rdfs:Class", + "rdfs:comment": "HER2 chromosome 17 ratio in participants with breast cancer", + "rdfs:label": "BreastCarcinomaHER2Chromosome17Ratio", + "rdfs:subClassOf": [ { - "@id": "bts:Descendedtestis" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Breast Carcinoma HER2 Chromosome17 Ratio", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaSurgicalProcedureName", + "@type": "rdfs:Class", + "rdfs:comment": "Text name of a surgical procedure performed for a person with a diagnosis of breast cancer", + "rdfs:label": "BreastCarcinomaSurgicalProcedureName", + "rdfs:subClassOf": [ { - "@id": "bts:Descendingcolon" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Domeofbladder" + "@id": "bts:Lumpectomy" }, { - "@id": "bts:DorsalsurfaceoftongueNOS" + "@id": "bts:Radicalmastectomy" }, { - "@id": "bts:Duodenum" + "@id": "bts:Modifiedradicalmastectomy" }, { - "@id": "bts:Endocervix" + "@id": "bts:Other" }, { - "@id": "bts:EndocrineglandNOS" + "@id": "bts:Partialmastectomy" }, { - "@id": "bts:Endometrium" + "@id": "bts:Re-excision" }, { - "@id": "bts:Epididymis" + "@id": "bts:Simplemastectomy" }, { - "@id": "bts:EsophagusNOS" + "@id": "bts:Surgerynotperformed" }, { - "@id": "bts:Ethmoidsinus" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Breast Carcinoma Surgical Procedure Name", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaHER2RatioDiagnosis", + "@type": "rdfs:Class", + "rdfs:comment": "HER2 ratio of the participant at diagnosis", + "rdfs:label": "BreastCarcinomaHER2RatioDiagnosis", + "rdfs:subClassOf": [ { - 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"@id": "bts:Retina" + "@id": "bts:Platinum-refractory" }, { - "@id": "bts:Retromolararea" + "@id": "bts:Platinum-sensitive" }, { - "@id": "bts:Retroperitoneum" + "@id": "bts:Platinum-resistant" }, { - "@id": "bts:Ribsternumclavicleandassociatedjoints" + "@id": "bts:Datanotavailable" }, { - "@id": "bts:Roundligament" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Ovarian Cancer Platinum Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ProstateCancerTier3", + "@type": "rdfs:Class", + "rdfs:comment": "Prostate cancer specific attributes in Clinical Data Tier 3", + "rdfs:label": "ProstateCancerTier3", + "rdfs:subClassOf": [ { - "@id": "bts:ScrotumNOS" - }, + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Prostate Cancer Tier 3", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:Shortbonesoflowerlimbandassociatedjoints" + "@id": "bts:Component" }, { - "@id": "bts:Shortbonesofupperlimbandassociatedjoints" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:Sigmoidcolon" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:SkinoflipNOS" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:Skinoflowerlimbandhip" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:Skinofotherandunspecifiedpartsofface" + "@id": "bts:LocationExtentExtraprostaticExtension" }, { - "@id": "bts:Skinofscalpandneck" + "@id": "bts:LocationNaturePositiveMargins" }, { - "@id": "bts:Skinoftrunk" + "@id": "bts:SeminalVesicleInvasion" }, { - "@id": "bts:Skinofupperlimbandshoulder" + "@id": "bts:ProstateCarcinomaHistologicType" }, { - "@id": "bts:SkinNOS" + "@id": "bts:ProstateCancerLocalExtent" }, { - "@id": "bts:SmallintestineNOS" + "@id": "bts:AdditonalFindingsUninvolvedProstate" }, { - "@id": "bts:SoftpalateNOS" - }, + "@id": "bts:ProstateCancerCytologicMorphologicSubtypes" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:LocationExtentExtraprostaticExtension", + "@type": "rdfs:Class", + "rdfs:comment": "Location and extent of extraprostatic extension", + "rdfs:label": "LocationExtentExtraprostaticExtension", + "rdfs:subClassOf": [ { - "@id": "bts:Specifiedpartsofperitoneum" - }, + "@id": "bts:ProstateCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Spermaticcord" + "@id": "bts:LeftAnterior" }, { - "@id": "bts:Sphenoidsinus" + "@id": "bts:LeftLateral" }, { - "@id": "bts:Spinalcord" + "@id": "bts:LeftPosterolateral" }, { - "@id": "bts:Spinalmeninges" + "@id": "bts:LeftPosterior" }, { - "@id": "bts:Spleen" + "@id": "bts:LeftApex" }, { - "@id": "bts:Splenicflexureofcolon" + "@id": "bts:LeftMid" }, { - "@id": "bts:StomachNOS" + "@id": "bts:LeftBase" }, { - "@id": "bts:Subglottis" + "@id": "bts:LeftFocal" }, { - "@id": "bts:Sublingualgland" + "@id": "bts:LeftNon-focal(established)" }, { - "@id": "bts:Submandibulargland" + "@id": "bts:RightAnterior" }, { - "@id": "bts:Superiorwallofnasopharynx" + "@id": "bts:RightLateral" }, { - "@id": "bts:Supraglottis" + "@id": "bts:RightPosterolateral" }, { - "@id": "bts:Tailofpancreas" + "@id": "bts:RightPosterior" }, { - "@id": "bts:Temporallobe" + "@id": "bts:RightApex" }, { - "@id": "bts:TestisNOS" + "@id": "bts:RightMid" }, { - "@id": "bts:Thoracicesophagus" + "@id": "bts:RightBase" }, { - "@id": "bts:ThoraxNOS" + "@id": "bts:RightFocal" }, { - "@id": "bts:Thymus" + "@id": "bts:RightNon-focal(established)" }, { - "@id": "bts:Thyroidgland" + "@id": "bts:Unknown" }, { - "@id": "bts:TongueNOS" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Location Extent Extraprostatic Extension", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:LocationNaturePositiveMargins", + "@type": "rdfs:Class", + "rdfs:comment": "Location and nature of positive margins", + "rdfs:label": "LocationNaturePositiveMargins", + "rdfs:subClassOf": [ { - "@id": "bts:TonsilNOS" - }, + "@id": "bts:ProstateCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Tonsillarfossa" + "@id": "bts:LeftAnterior" }, { - "@id": "bts:Tonsillarpillar" + "@id": "bts:LeftLateral" }, { - "@id": "bts:Trachea" + "@id": "bts:LeftPosterolateral" }, { - "@id": "bts:Transversecolon" + "@id": "bts:LeftPosterior" }, { - "@id": "bts:Trigoneofbladder" + "@id": "bts:LeftApex" }, { - "@id": "bts:Undescendedtestis" + "@id": "bts:LeftMid" }, { - "@id": "bts:Unknownprimarysite" + "@id": "bts:LeftBase" }, { - "@id": "bts:Uppergum" + "@id": "bts:LeftFocal" }, { - "@id": "bts:UpperlimbNOS" + "@id": "bts:LeftExtensive" }, { - "@id": "bts:Upperlobelung" + "@id": "bts:LeftPositiveinanareaofextraprostaticextension(EPE)" }, { - "@id": "bts:UpperrespiratorytractNOS" + "@id": "bts:LeftPositiveinanareaofintraprostaticincision(II)" }, { - "@id": "bts:Upperthirdofesophagus" + "@id": "bts:LeftPositivewhereitisdifficulttodistinguishEPEvsII" }, { - "@id": "bts:Upper-innerquadrantofbreast" + "@id": "bts:RightAnterior" }, { - "@id": "bts:Upper-outerquadrantofbreast" + "@id": "bts:RightLateral" }, { - "@id": "bts:Urachus" + "@id": "bts:RightPosterolateral" }, { - "@id": "bts:Ureter" + "@id": "bts:RightPosterior" }, { - "@id": "bts:Uretericorifice" + "@id": "bts:RightApex" }, { - "@id": "bts:Urethra" + "@id": "bts:RightMid" }, { - "@id": "bts:UrinarysystemNOS" + "@id": "bts:RightBase" }, { - "@id": "bts:Uterineadnexa" + "@id": "bts:RightFocal" }, { - "@id": "bts:UterusNOS" + "@id": "bts:RightExtensive" }, { - "@id": "bts:Uvula" + "@id": "bts:RightPositiveinanareaofextraprostaticextension(EPE)" }, { - "@id": "bts:VaginaNOS" + "@id": "bts:RightPositiveinanareaofintraprostaticincision(II)" }, { - "@id": "bts:Vallecula" + "@id": "bts:RightPositivewhereitisdifficulttodistinguishEPEvsII" }, { - "@id": "bts:VentralsurfaceoftongueNOS" + "@id": "bts:Bladderneck(blockPUM)" }, { - "@id": "bts:VentricleNOS" + "@id": "bts:Vasdeferens" }, { - "@id": "bts:Vertebralcolumn" + "@id": "bts:Apicalmargin(blockDUM)" }, { - "@id": "bts:Vestibuleofmouth" + "@id": "bts:Unknown" }, { - "@id": "bts:VulvaNOS" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Location Nature Positive Margins", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SeminalVesicleInvasion", + "@type": "rdfs:Class", + "rdfs:comment": "An anatomic position identifying a side of the body where local spread of malignant neoplasm is found to infiltrate tissue in the saclike glandular diverticulum on the ductus deferens in a male.", + "rdfs:label": "SeminalVesicleInvasion", + "rdfs:subClassOf": [ { - "@id": "bts:Waldeyerring" - }, + "@id": "bts:ProstateCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:BiliarytractNOS" + "@id": "bts:None" }, { - "@id": "bts:Cheekmucosa" + "@id": "bts:Left" }, { - "@id": "bts:Clitoris" + "@id": "bts:Right" }, { - "@id": "bts:Overlappinglesionofbiliarytract" + "@id": "bts:Bothsides" }, { "@id": "bts:Unknown" @@ -13548,18 +18315,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Tissue or Organ of Origin", - "sms:required": "sms:true", + "sms:displayName": "Seminal Vesicle Invasion", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NCIAtlasCancerSite", + "@id": "bts:ProstateCarcinomaHistologicType", "@type": "rdfs:Class", - "rdfs:comment": "The primary tumor site used to calculate the incidence rate using the NCI Cancer Atlas, a digital atlas which provides geographical data related to cancer utilizing the Surveillance, Epidemiology, and End Results (SEER) Program cancer incidence rates for 2013 to 2017", - "rdfs:label": "NCIAtlasCancerSite", + "rdfs:comment": "The diagnostic subclassification of an invasive prostate carcinoma.", + "rdfs:label": "ProstateCarcinomaHistologicType", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:ProstateCancerTier3" } ], "schema:isPartOf": { @@ -13567,84 +18334,119 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Bladder" + "@id": "bts:Prostaticadenocarcinoma(conventionalNOS)" }, { - "@id": "bts:BrainAndOtherNervousSystem" + "@id": "bts:Prostaticductadenocarcinoma" }, { - "@id": "bts:FemaleBreast" + "@id": "bts:Acinarprostatemucinous(colloid)adenocarcinoma" }, { - "@id": "bts:InsituFemaleBreast" + "@id": "bts:Acinarprostateadenocarcinoma-signet-ringvariant" }, { - "@id": "bts:CervixUteri" + "@id": "bts:Prostaticadenosquamouscarcinoma" }, { - "@id": "bts:LessThanAge" + "@id": "bts:Acinarprostatemucinousadenocarcinoma" }, { - "@id": "bts:MalignantChildhoodNeoplasm" + "@id": "bts:Prostaticsmallcellcarcinoma" }, { - "@id": "bts:ColonAndRectum" + "@id": "bts:Acinarprostateadenocarcinoma-sarcomatoidvariant" }, { - "@id": "bts:Esophagus" + "@id": "bts:UndifferentiatedcarcinomaNOS" }, { - "@id": "bts:KidneyAndRenalPelvis" - }, + "@id": "bts:Other" + } + ], + "sms:displayName": "Prostate Carcinoma Histologic Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ProstateCancerLocalExtent", + "@type": "rdfs:Class", + "rdfs:comment": "The response used to categorize the local extent of disease for prostate cancer.", + "rdfs:label": "ProstateCancerLocalExtent", + "rdfs:subClassOf": [ { - "@id": "bts:Leukemia" - }, + "@id": "bts:ProstateCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:LiverAndBileDuct" + "@id": "bts:OrganConfined" }, { - "@id": "bts:LungAndBronchus" + "@id": "bts:Extraprostaticextension" }, { - "@id": "bts:CutaneousMelanoma" + "@id": "bts:Unknown" }, { - "@id": "bts:Non-Hodgkin'sLymphoma" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Prostate Cancer Local Extent", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AdditonalFindingsUninvolvedProstate", + "@type": "rdfs:Class", + "rdfs:comment": "Additional findings, uninvolved prostate", + "rdfs:label": "AdditonalFindingsUninvolvedProstate", + "rdfs:subClassOf": [ { - "@id": "bts:OralCavityAndPharynx" + "@id": "bts:ProstateCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:High-gradeprostaticintraepithelialneoplasia(PIN)" }, { - "@id": "bts:Ovary" + "@id": "bts:Inflammation" }, { - "@id": "bts:Pancreas" + "@id": "bts:Benignprostatichyperplasia(BPH)" }, { - "@id": "bts:ProstateGland" + "@id": "bts:ProstaticIntraductaladenocarcinoma" }, { - "@id": "bts:Stomach" + "@id": "bts:Other" }, { - "@id": "bts:ThyroidGland" + "@id": "bts:Unknown" }, { - "@id": "bts:Uterus" + "@id": "bts:NotReported" } ], - "sms:displayName": "NCI Atlas Cancer Site", + "sms:displayName": "Additonal Findings Uninvolved Prostate", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TumorGrade", + "@id": "bts:ProstateCancerCytologicMorphologicSubtypes", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.", - "rdfs:label": "TumorGrade", + "rdfs:comment": "Text term that describes various morphological and cytological subtypes in protate tumors.", + "rdfs:label": "ProstateCancerCytologicMorphologicSubtypes", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:ProstateCancerTier3" } ], "schema:isPartOf": { @@ -13652,124 +18454,131 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:G1" - }, - { - "@id": "bts:G2" - }, - { - "@id": "bts:G3" - }, - { - "@id": "bts:G4" + "@id": "bts:Prostaticbasalcellhyperplasia" }, { - "@id": "bts:GX" + "@id": "bts:Prostaticclearcellcribiformhyperplasia" }, { - "@id": "bts:GB" + "@id": "bts:Prostaticatypicaladenomatoushyperplasia(adenosisorAAH)" }, { - "@id": "bts:HighGrade" + "@id": "bts:Lowgradeprostaticintraepithelialneoplasia(PIN)/(PINI)" }, { - "@id": "bts:IntermediateGrade" + "@id": "bts:Highgradeprostaticintraepithelialneoplasia(HGPIN)/(PINII&PINIII)" }, { - "@id": "bts:LowGrade" + "@id": "bts:Other" }, { "@id": "bts:Unknown" }, { "@id": "bts:NotReported" - }, - { - "@id": "bts:NotApplicable" } ], - "sms:displayName": "Tumor Grade", + "sms:displayName": "Prostate Cancer Cytologic Morphologic Subtypes", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PackYearsSmoked", + "@id": "bts:SarcomaTier3", "@type": "rdfs:Class", - "rdfs:comment": "Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes smoked per day x number of years smoked divided by 20.", - "rdfs:label": "PackYearsSmoked", + "rdfs:comment": "Sarcoma specific attributes in Clinical Data Tier 3", + "rdfs:label": "SarcomaTier3", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:Patient" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Pack Years Smoked", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:YearsSmoked", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value (or unknown) to represent the number of years a person has been smoking.", - "rdfs:label": "YearsSmoked", - "rdfs:subClassOf": [ + "sms:displayName": "Sarcoma Tier 3", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:Exposure" + "@id": "bts:Component" + }, + { + "@id": "bts:HTANParticipantID" + }, + { + "@id": "bts:TimepointLabel" + }, + { + "@id": "bts:StartDaysfromIndex" + }, + { + "@id": "bts:StopDaysfromIndex" + }, + { + "@id": "bts:SarcomaSubtype" + }, + { + "@id": "bts:SarcomaDiagnosisClassificationCategory" + }, + { + "@id": "bts:SarcomaTumorExtensionType" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Years Smoked", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:DaystoFollowUp", + "@id": "bts:SarcomaSubtype", "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date of the patient's last follow-up appointment or contact. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoFollowUp", + "rdfs:comment": "The subtype related to the scientific determination and investigation, analysis and recognition of the presence and nature of disease, condition, or injury from expressed signs and symptoms of tissue growth resulting from uncontrolled cell proliferation.", + "rdfs:label": "SarcomaSubtype", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:SarcomaTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Days to Follow Up", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:GeneSymbol", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a gene targeted or included in molecular analysis. For rearrangements, this is should be used to represent the reference gene. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "GeneSymbol", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ + { + "@id": "bts:Undifferentiatedpleomorphicsarcoma" + }, + { + "@id": "bts:Leiomyosarcoma(uterineorextra-uterine)" + }, + { + "@id": "bts:OtherSynovialSarcomaOrMalignantPeripheralNerveSheathTumorSarcoma" + }, + { + "@id": "bts:GastrointestinalStromalTumor" + }, + { + "@id": "bts:Liposarcoma" + }, { - "@id": "bts:MolecularTest" + "@id": "bts:Undifferentiatedpleomorphicsarcomaormalignantfibroushistiosarcoma" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Gene Symbol", - "sms:required": "sms:true", + "sms:displayName": "Sarcoma Subtype", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MolecularAnalysisMethod", + "@id": "bts:SarcomaDiagnosisClassificationCategory", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the method used for molecular analysis. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "MolecularAnalysisMethod", + "rdfs:comment": "High level grouping to describe a diagnostic grouping or category for sarcoma, a malignant mesenchymal cell tumor most commonly arising from muscle, fat, fibrous tissue, bone, cartilage, and blood vessels.", + "rdfs:label": "SarcomaDiagnosisClassificationCategory", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:SarcomaTier3" } ], "schema:isPartOf": { @@ -13777,81 +18586,119 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:ComparativeGenomicHybridization" + "@id": "bts:BoneSarcoma" }, { - "@id": "bts:CytogeneticsNOS" + "@id": "bts:MusculoskeletalSarcoma" }, { - "@id": "bts:FISH" + "@id": "bts:SoftTissueSarcoma" }, { - "@id": "bts:FlowCytometry" + "@id": "bts:Unknown" }, { - "@id": "bts:IHC" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Sarcoma Diagnosis Classification Category", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SarcomaTumorExtensionType", + "@type": "rdfs:Class", + "rdfs:comment": "The field to indicate the organs and structures to which the tumor has become adherent or has invaded.", + "rdfs:label": "SarcomaTumorExtensionType", + "rdfs:subClassOf": [ { - "@id": "bts:ISH" + "@id": "bts:SarcomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Extraosseous" }, { - "@id": "bts:Karyotype" + "@id": "bts:Intracranial" }, { - "@id": "bts:Microarray" + "@id": "bts:Lymphnodes" }, { - "@id": "bts:MicrosatelliteAnalysis" + "@id": "bts:Parameningeal" }, { - "@id": "bts:NuclearStaining" + "@id": "bts:Thoraciccavity" }, { "@id": "bts:Other" }, { - "@id": "bts:RNASequencing" + "@id": "bts:Unknown" }, { - "@id": "bts:RT-PCR" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Sarcoma Tumor Extension Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PancreaticCancerTier3", + "@type": "rdfs:Class", + "rdfs:comment": "Pancreatic cancer specific attributes in Clinical Tier Data 3", + "rdfs:label": "PancreaticCancerTier3", + "rdfs:subClassOf": [ { - "@id": "bts:SequencingNOS" + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Pancreatic Cancer Tier 3", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:SouthernBlotting" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:TargetedSequencing" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:WGS" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:WXS" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:Unknown" + "@id": "bts:PancreasPrecancerHistopathologicGrade" }, { - "@id": "bts:NotReported" + "@id": "bts:PancreaticIPMNPathologyEpithelialSubtype" }, { - "@id": "bts:NotApplicable" + "@id": "bts:PancreaticDuctFinalPathologyType" } ], - "sms:displayName": "Molecular Analysis Method", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TestResult", + "@id": "bts:PancreasPrecancerHistopathologicGrade", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the result of the molecular test. If the test result was a numeric value see test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "TestResult", + "rdfs:comment": "The grade of precancerous pancreatic tissue based on microscopic study of characteristic tissue abnormalities by employing various cytochemical and immunocytochemical stains.", + "rdfs:label": "PancreasPrecancerHistopathologicGrade", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:PancreaticCancerTier3" } ], "schema:isPartOf": { @@ -13859,63 +18706,51 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:AbnormalNOS" - }, - { - "@id": "bts:CopyNumberReported" - }, - { - "@id": "bts:Equivocal" - }, - { - "@id": "bts:High" + "@id": "bts:IPMN-Adenoma" }, { - "@id": "bts:Intermediate" + "@id": "bts:IPMN-Borderline" }, { - "@id": "bts:LossofExpression" + "@id": "bts:IPMN-Carcinomainsitu" }, { - "@id": "bts:Low" + "@id": "bts:IPMN-Invasivecarcinoma" }, { - "@id": "bts:Negative" + "@id": "bts:PanIN1" }, { - "@id": "bts:Normal" + "@id": "bts:PanIN1A" }, { - "@id": "bts:Overexpressed" + "@id": "bts:PanIN1B" }, { - "@id": "bts:Positive" + "@id": "bts:PanIN2" }, { - "@id": "bts:TestValueReported" + "@id": "bts:PanIN3" }, { "@id": "bts:Unknown" }, { "@id": "bts:NotReported" - }, - { - "@id": "bts:NotApplicable" } ], - "sms:displayName": "Test Result", - "sms:required": "sms:true", + "sms:displayName": "Pancreas Precancer Histopathologic Grade", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TreatmentType", + "@id": "bts:PancreaticIPMNPathologyEpithelialSubtype", "@type": "rdfs:Class", - "rdfs:comment": "Text term that describes the kind of treatment administered.", - "rdfs:label": "TreatmentType", + "rdfs:comment": "The Intraductal Papillary Mucinous Neoplasm (IPMN) epithelial cell subtype based on the gross and microscopic examination of a pancreatic neoplasm specimen", + "rdfs:label": "PancreaticIPMNPathologyEpithelialSubtype", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:PancreaticCancerTier3" } ], "schema:isPartOf": { @@ -13923,178 +18758,268 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:AblationCryo" - }, - { - "@id": "bts:AblationEthanolInjection" - }, - { - "@id": "bts:AblationMicrowave" + "@id": "bts:GastricFoveolar" }, { - "@id": "bts:AblationNOS" + "@id": "bts:Intestinal" }, { - "@id": "bts:AblationRadiofrequency" + "@id": "bts:IntraductalTubopapillary" }, { - "@id": "bts:AblationRadiosurgical" + "@id": "bts:Pancreatobiliary" }, { - "@id": "bts:AncillaryTreatment" + "@id": "bts:Oncocytic" }, { - "@id": "bts:AntiseizureTreatment" + "@id": "bts:Other" }, { - "@id": "bts:BisphosphonateTherapy" + "@id": "bts:Unknown" }, { - "@id": "bts:BlindedStudyTreatmentunknown" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Pancreatic IPMN Pathology Epithelial Subtype", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PancreaticDuctFinalPathologyType", + "@type": "rdfs:Class", + "rdfs:comment": "The final pathology result of the pancreatic duct communication type.", + "rdfs:label": "PancreaticDuctFinalPathologyType", + "rdfs:subClassOf": [ { - "@id": "bts:BrachytherapyHighDose" - }, + "@id": "bts:PancreaticCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:BrachytherapyLowDose" + "@id": "bts:Side-Branch" }, { - "@id": "bts:BrachytherapyNOS" + "@id": "bts:MainDuct" }, { - "@id": "bts:Chemoembolization" + "@id": "bts:Mixed" }, { - "@id": "bts:Chemoprotectant" + "@id": "bts:NotSpecified" }, { - "@id": "bts:Chemotherapy" + "@id": "bts:None" }, { - "@id": "bts:ConcurrentChemoradiation" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Pancreatic Duct Final Pathology Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MelanomaTier3", + "@type": "rdfs:Class", + "rdfs:comment": "Melanoma specific attributes in Clinical Data Tier 3", + "rdfs:label": "MelanomaTier3", + "rdfs:subClassOf": [ { - "@id": "bts:Cryoablation" - }, + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Melanoma Tier 3", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:Embolization" + "@id": "bts:Component" }, { - "@id": "bts:EthanolInjectionAblation" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:ExternalBeamRadiation" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:HormoneTherapy" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:I-131RadiationTherapy" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:InternalRadiation" + "@id": "bts:CutaneousMelanomaTumorInfiltratingLymphocytes" }, { - "@id": "bts:Immunotherapy(IncludingVaccines)" + "@id": "bts:CutaneousMelanomaTumorRegressionRange" }, { - "@id": "bts:IsolatedLimbPerfusion(ILP)" + "@id": "bts:MelanomaSpecimenClarkLevelValue" }, { - "@id": "bts:OrganTransplantation" + "@id": "bts:CutaneousMelanomaSurgicalMargins" }, { - "@id": "bts:Other" + "@id": "bts:MelanomaLesionSize" }, { - "@id": "bts:PharmaceuticalTherapyNOS" + "@id": "bts:HistoryofAtypicalNevi" }, { - "@id": "bts:Pleurodesis" + "@id": "bts:FitzpatrickSkinTone" }, { - "@id": "bts:Radiation2DConventional" + "@id": "bts:HistoryofChronicUVExposure" }, { - "@id": "bts:Radiation3DConformal" + "@id": "bts:HistoryofBlisteringSunburn" }, { - "@id": "bts:RadiationCombination" + "@id": "bts:HistoryofTanningBedUse" }, { - "@id": "bts:RadiationCyberknife" + "@id": "bts:ImmediateFamilyHistoryMelanoma" }, { - "@id": "bts:RadiationExternalBeam" + "@id": "bts:MelanomaBiopsyResectionSites" }, { - "@id": "bts:RadiationImplants" + "@id": "bts:CutaneousMelanomaUlceration" }, { - "@id": "bts:RadiationIntensity-ModulatedRadiotherapy" - }, + "@id": "bts:CutaneousMelanomaAdditionalFindings" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:CutaneousMelanomaTumorInfiltratingLymphocytes", + "@type": "rdfs:Class", + "rdfs:comment": "Description of degree of lymphocytic infiltration surrounding and disrupting tumor cells of the vertical growth phase in a cutaneous melanoma.", + "rdfs:label": "CutaneousMelanomaTumorInfiltratingLymphocytes", + "rdfs:subClassOf": [ { - "@id": "bts:RadiationInternal" - }, + "@id": "bts:MelanomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:RadiationProtonBeam" + "@id": "bts:Absent" }, { - "@id": "bts:RadiationRadioisotope" + "@id": "bts:Brisk" }, { - "@id": "bts:RadiationStereotactic/GammaKnife/SRS" + "@id": "bts:Nonbrisk" }, { - "@id": "bts:RadiationSystemic" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Cutaneous Melanoma Tumor Infiltrating Lymphocytes", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CutaneousMelanomaTumorRegressionRange", + "@type": "rdfs:Class", + "rdfs:comment": "Description of the degree to which tumor cells are replaced by lymphocytic inflammation with or without dermal melanophages and fibrosis._Range; the difference between the lowest and highest numerical values.", + "rdfs:label": "CutaneousMelanomaTumorRegressionRange", + "rdfs:subClassOf": [ { - "@id": "bts:RadiationTherapyNOS" - }, + "@id": "bts:MelanomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:RadioactiveIodineTherapy" + "@id": "bts:Absent" }, { - "@id": "bts:Radioembolization" + "@id": "bts:Presentinvolving75%ormore" }, { - "@id": "bts:RadiosensitizingAgent" + "@id": "bts:Presentinvolvinglessthan75%" }, { - "@id": "bts:StemCellTreatment" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Cutaneous Melanoma Tumor Regression Range", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MelanomaSpecimenClarkLevelValue", + "@type": "rdfs:Class", + "rdfs:comment": "Definition of the Clark level or depth of involvement of a melanoma in the skin or a specimen.", + "rdfs:label": "MelanomaSpecimenClarkLevelValue", + "rdfs:subClassOf": [ { - "@id": "bts:StemCellTransplantationAutologous" - }, + "@id": "bts:MelanomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:StemCellTransplantationDoubleAutologous" + "@id": "bts:I" }, { - "@id": "bts:StemCellTransplantationAllogeneic" + "@id": "bts:II" }, { - "@id": "bts:StemCellTransplantationNon-Myeloablative" + "@id": "bts:III" }, { - "@id": "bts:StemCellTransplantationSyngenic" + "@id": "bts:IV" }, { - "@id": "bts:StemCellTransplantationHaploidentical" + "@id": "bts:V" }, { - "@id": "bts:StemCellTransplantationNOS" + "@id": "bts:NoSourceDocumentation" }, { - "@id": "bts:StereotacticRadiosurgery" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Melanoma Specimen Clark Level Value", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CutaneousMelanomaSurgicalMargins", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to indicate presence of tumor at resection margins", + "rdfs:label": "CutaneousMelanomaSurgicalMargins", + "rdfs:subClassOf": [ { - "@id": "bts:SteroidTherapy" - }, + "@id": "bts:MelanomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Surgery" + "@id": "bts:Positive" }, { - "@id": "bts:TargetedMolecularTherapy" + "@id": "bts:Negative" }, { "@id": "bts:Unknown" @@ -14103,95 +19028,112 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Treatment Type", + "sms:displayName": "Cutaneous Melanoma Surgical Margins", "sms:required": "sms:false", - "sms:validationRules": [ - "list like" - ] + "sms:validationRules": [] }, { - "@id": "bts:TumorLargestDimensionDiameter", + "@id": "bts:MelanomaLesionSize", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the maximum diameter or dimension of the primary tumor, measured in centimeters.", - "rdfs:label": "TumorLargestDimensionDiameter", + "rdfs:comment": "Diameter of lesion determined on skin examination (pre-bx), in mm", + "rdfs:label": "MelanomaLesionSize", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:MelanomaTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Tumor Largest Dimension Diameter", + "sms:displayName": "Melanoma Lesion Size", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LungCancerTier3", + "@id": "bts:HistoryofAtypicalNevi", "@type": "rdfs:Class", - "rdfs:comment": "Lung cancer specific attributes in Clinical Data Tier 3", - "rdfs:label": "LungCancerTier3", + "rdfs:comment": "Patient has a history of atypical nevi", + "rdfs:label": "HistoryofAtypicalNevi", "rdfs:subClassOf": [ { - "@id": "bts:Patient" + "@id": "bts:MelanomaTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Lung Cancer Tier 3", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "schema:rangeIncludes": [ { - "@id": "bts:Component" + "@id": "bts:Yes(morethan50)" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:Yes(lessthan50)" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:No" }, { - "@id": "bts:StartDaysfromIndex" + "@id": "bts:Unknown" }, { - "@id": "bts:StopDaysfromIndex" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "History of Atypical Nevi", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:FitzpatrickSkinTone", + "@type": "rdfs:Class", + "rdfs:comment": "The Fitzpatrick classification of skin phototype", + "rdfs:label": "FitzpatrickSkinTone", + "rdfs:subClassOf": [ { - "@id": "bts:LungCancerDetectionMethodType" + "@id": "bts:MelanomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:I" }, { - "@id": "bts:LungCancerParticipantProcedureHistory" + "@id": "bts:II" }, { - "@id": "bts:LungAdjacentHistologyType" + "@id": "bts:III" }, { - "@id": "bts:LungTumorLocationAnatomicSite" + "@id": "bts:IV" }, { - "@id": "bts:LungTumorLobeBronchialLocation" + "@id": "bts:V" }, { - "@id": "bts:CurrentLungCancerSymptoms" + "@id": "bts:VI" }, { - "@id": "bts:LungTopography" + "@id": "bts:Unknown" }, { - "@id": "bts:LungCancerHarboringGenomicAberrations" + "@id": "bts:NotReported" } ], + "sms:displayName": "Fitzpatrick Skin Tone", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LungCancerDetectionMethodType", + "@id": "bts:HistoryofChronicUVExposure", "@type": "rdfs:Class", - "rdfs:comment": "The means, manner of procedure, or systematic course of actions performed in order to discover or identify lung cancer", - "rdfs:label": "LungCancerDetectionMethodType", + "rdfs:comment": "History of chronic UV exposure", + "rdfs:label": "HistoryofChronicUVExposure", "rdfs:subClassOf": [ { - "@id": "bts:LungCancerTier3" + "@id": "bts:MelanomaTier3" } ], "schema:isPartOf": { @@ -14199,36 +19141,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:LowDoseComputedTomography(LDCT)" - }, - { - "@id": "bts:ChestX-ray" + "@id": "bts:Outdooroccupational" }, { - "@id": "bts:ChestCT" + "@id": "bts:Outdoorrecreational" }, { - "@id": "bts:Unknown" + "@id": "bts:Therapeutic" }, { - "@id": "bts:Datanotavailable" + "@id": "bts:None" }, { - "@id": "bts:Other" + "@id": "bts:NotReported" } ], - "sms:displayName": "Lung Cancer Detection Method Type", + "sms:displayName": "History of Chronic UV Exposure", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LungCancerParticipantProcedureHistory", + "@id": "bts:HistoryofBlisteringSunburn", "@type": "rdfs:Class", - "rdfs:comment": "Text name of a surgical or operative procedure used in a natural history protocol of a lung cancer participant.", - "rdfs:label": "LungCancerParticipantProcedureHistory", + "rdfs:comment": "Patient has history of blistering sunburn", + "rdfs:label": "HistoryofBlisteringSunburn", "rdfs:subClassOf": [ { - "@id": "bts:LungCancerTier3" + "@id": "bts:MelanomaTier3" } ], "schema:isPartOf": { @@ -14236,69 +19175,95 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:LobectomyBilateral" + "@id": "bts:Yes" }, { - "@id": "bts:LobectomyLeft" + "@id": "bts:No" }, { - "@id": "bts:LobectomyRight" + "@id": "bts:Unknown" }, { - "@id": "bts:LungWedgeResectionBilateral" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "History of Blistering Sunburn", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HistoryofTanningBedUse", + "@type": "rdfs:Class", + "rdfs:comment": "History of tanning bed use of the patient", + "rdfs:label": "HistoryofTanningBedUse", + "rdfs:subClassOf": [ { - "@id": "bts:LungWedgeResectionLeft" - }, + "@id": "bts:MelanomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:LungWedgeResectionMultiple" + "@id": "bts:Never" }, { - "@id": "bts:LungWedgeResectionRight" + "@id": "bts:Lessthan10times" }, { - "@id": "bts:PneumonectomyLeft" + "@id": "bts:10-50times" }, { - "@id": "bts:PneumonectomyRight" + "@id": "bts:50-100times" }, { - "@id": "bts:Endobronchialbiopsy" + "@id": "bts:Morethan100times" }, { - "@id": "bts:Mediastinoscopy" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "History of Tanning Bed Use", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ImmediateFamilyHistoryMelanoma", + "@type": "rdfs:Class", + "rdfs:comment": "Text that describes the age at which the family member was diagnosed with melanoma skin cancer in relationship to their 50th birthday.", + "rdfs:label": "ImmediateFamilyHistoryMelanoma", + "rdfs:subClassOf": [ { - "@id": "bts:VATSSclerosis" - }, + "@id": "bts:MelanomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Brainresection" + "@id": "bts:Beforeage50" }, { - "@id": "bts:Segmentectomy" + "@id": "bts:Notbeforeage50" }, { "@id": "bts:Unknown" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:NotReported" } ], - "sms:displayName": "Lung Cancer Participant Procedure History", + "sms:displayName": "Immediate Family History Melanoma", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LungAdjacentHistologyType", + "@id": "bts:MelanomaBiopsyResectionSites", "@type": "rdfs:Class", - "rdfs:comment": "The type of morphologic characteristics observed by microscope in the tissue next to a benign or malignant tissue growth", - "rdfs:label": "LungAdjacentHistologyType", + "rdfs:comment": "Biopsy resection sites specific to melanoma (not covered in Tiers 1 and 2)", + "rdfs:label": "MelanomaBiopsyResectionSites", "rdfs:subClassOf": [ { - "@id": "bts:LungCancerTier3" + "@id": "bts:MelanomaTier3" } ], "schema:isPartOf": { @@ -14306,66 +19271,84 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Lungadenocarcinoma" + "@id": "bts:Skinofscalp" }, { - "@id": "bts:Adenosquamouscarcinoma" + "@id": "bts:Skinofeyelid" }, { - "@id": "bts:Carcinoidtumorandlungatypicalcarcinoidtumor" + "@id": "bts:Skinofnose" }, { - "@id": "bts:Lungadenocarcinomainsitu" + "@id": "bts:Skinoflip" }, { - "@id": "bts:Largecelllungcarcinoma" + "@id": "bts:Skinofear" }, { - "@id": "bts:Largecellneuroendocrinecarcinoma" + "@id": "bts:Skinofneck" }, { - "@id": "bts:Lunglymphoepithelioma-likecarcinoma" + "@id": "bts:Skinofotherpartsofface" }, { - "@id": "bts:Bronchioalveolarcarcinoma" + "@id": "bts:Skinofchest" }, { - "@id": "bts:ThoracicNUTcarcinoma" + "@id": "bts:Skinofback" }, { - "@id": "bts:Sarcomatoidcarcinoma" + "@id": "bts:Skinofabdomen" }, { - "@id": "bts:Smallcelllungcarcinoma" + "@id": "bts:Skinoftrunk-other" }, { - "@id": "bts:Squamouscelllungcarcinoma" + "@id": "bts:Skinofbreast" }, { - "@id": "bts:Lungsquamouscellcarcinomainsitu" + "@id": "bts:Skinofupperlimbandshoulder" }, { - "@id": "bts:Other" + "@id": "bts:Skinofpalm" }, { - "@id": "bts:Unknown" + "@id": "bts:Skinoflowerlimbandhip" + }, + { + "@id": "bts:Skinofsole" + }, + { + "@id": "bts:Skinofpenis" + }, + { + "@id": "bts:Skinofscrotum" + }, + { + "@id": "bts:Skinofvulva" + }, + { + "@id": "bts:Skinother" + }, + { + "@id": "bts:SkinNOS" }, { "@id": "bts:NotReported" } ], - "sms:displayName": "Lung Adjacent Histology Type", + "sms:displayName": "Melanoma Biopsy Resection Sites", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LungTumorLocationAnatomicSite", + "@id": "bts:CutaneousMelanomaUlceration", "@type": "rdfs:Class", - "rdfs:comment": "Anatomic location of the tumor inside the lung", - "rdfs:label": "LungTumorLocationAnatomicSite", + "rdfs:comment": "Description of extent of disruption to the surface of the skin caused by the cutaneous melanoma.", + "rdfs:label": "CutaneousMelanomaUlceration", "rdfs:subClassOf": [ { - "@id": "bts:LungCancerTier3" + "@id": "bts:MelanomaTier3" } ], "schema:isPartOf": { @@ -14373,13 +19356,10 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Maincarina" - }, - { - "@id": "bts:Left" + "@id": "bts:Absent" }, { - "@id": "bts:Right" + "@id": "bts:Present" }, { "@id": "bts:Unknown" @@ -14388,18 +19368,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Lung Tumor Location Anatomic Site", + "sms:displayName": "Cutaneous Melanoma Ulceration", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LungTumorLobeBronchialLocation", + "@id": "bts:CutaneousMelanomaAdditionalFindings", "@type": "rdfs:Class", - "rdfs:comment": "Anatomic lobe and bronchial location of the tumor inside the lung", - "rdfs:label": "LungTumorLobeBronchialLocation", + "rdfs:comment": "Significant pathologic finding present in addition to the cutaneous melanoma.", + "rdfs:label": "CutaneousMelanomaAdditionalFindings", "rdfs:subClassOf": [ { - "@id": "bts:LungCancerTier3" + "@id": "bts:MelanomaTier3" } ], "schema:isPartOf": { @@ -14407,39 +19387,67 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Upperlobe" + "@id": "bts:ActinicKeratosis" }, { - "@id": "bts:Middlelobe" + "@id": "bts:NevusRemnant" }, { - "@id": "bts:Lowerlobe" + "@id": "bts:SolarElastosis" }, { - "@id": "bts:Stump" + "@id": "bts:FibrosingRegression" }, { - "@id": "bts:Bronchus" + "@id": "bts:NestingMelanoma" + }, + { + "@id": "bts:PagetoidSpread" + }, + { + "@id": "bts:VascularProliferation" + }, + { + "@id": "bts:Other" }, { "@id": "bts:Unknown" }, { - "@id": "bts:NotReported" + "@id": "bts:NotApplicable" } ], - "sms:displayName": "Lung Tumor Lobe Bronchial Location", + "sms:displayName": "Cutaneous Melanoma Additional Findings", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CurrentLungCancerSymptoms", + "@id": "bts:DaystoBirth", "@type": "rdfs:Class", - "rdfs:comment": "Reported lung cancer related symptoms person is currently experiencing", - "rdfs:label": "CurrentLungCancerSymptoms", + "rdfs:comment": "Number of days between the date used for index and the date from a person's date of birth represented as a calculated negative number of days. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoBirth", "rdfs:subClassOf": [ { - "@id": "bts:LungCancerTier3" + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Days to Birth", + "sms:required": "sms:false", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:CountryofResidence", + "@type": "rdfs:Class", + "rdfs:comment": "Country of Residence at enrollment", + "rdfs:label": "CountryofResidence", + "rdfs:subClassOf": [ + { + "@id": "bts:Demographics" } ], "schema:isPartOf": { @@ -14447,670 +19455,714 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Asbestosis" + "@id": "bts:Afghanistan" }, { - "@id": "bts:Productivecough" + "@id": "bts:Albania" }, { - "@id": "bts:Non-productivecough" + "@id": "bts:Algeria" }, { - "@id": "bts:Wheezing" + "@id": "bts:Andorra" }, { - "@id": "bts:Rhonci" + "@id": "bts:Angola" }, { - "@id": "bts:Crackles" + "@id": "bts:Anguilla" }, { - "@id": "bts:Hemoptysis" + "@id": "bts:AntiguaandBarbuda" }, { - "@id": "bts:Dyspnea" + "@id": "bts:Argentina" }, { - "@id": "bts:Unexplainedweightloss" + "@id": "bts:Armenia" }, { - "@id": "bts:Unexplainedlossofenergy/fatigue" + "@id": "bts:Aruba" }, { - "@id": "bts:Chestpainordiscomfort" + "@id": "bts:Australia" }, { - "@id": "bts:Dysphagia" + "@id": "bts:Austria" }, { - "@id": "bts:Pneumonia" + "@id": "bts:Azerbaijan" }, { - "@id": "bts:Hoarseness/laryngitis/vocalcordinflammation" + "@id": "bts:Bahamas" }, { - "@id": "bts:Airentrydecreased/fair/poor/diminished" + "@id": "bts:Bahrain" }, { - "@id": "bts:Fair/pooraeration" + "@id": "bts:Bangladesh" }, { - "@id": "bts:Shallowinspiration" + "@id": "bts:Barbados" }, { - "@id": "bts:Breathsoundscoarse/diminished" + "@id": "bts:Belarus" }, { - "@id": "bts:Dullnesstopercussion" + "@id": "bts:Belgium" }, { - "@id": "bts:Abnormalbreathsounds" + "@id": "bts:Belize" }, { - "@id": "bts:Clearlungstoauscultationorpercussion" + "@id": "bts:Benin" }, { - "@id": "bts:Unlabored/normalbreathing" + "@id": "bts:Bermuda" }, { - "@id": "bts:Coldsymptoms/flu/sinus/nasalcongestion" + "@id": "bts:Bhutan" }, { - "@id": "bts:Sinuspain/infection" + "@id": "bts:Bolivia" }, { - "@id": "bts:Fingerclubbing" + "@id": "bts:BosniaandHerzegovina" }, { - "@id": "bts:Noevidenceoflungcancerrecurrence" + "@id": "bts:Botswana" }, { - "@id": "bts:PatientisNED" + "@id": "bts:Brazil" }, { - "@id": "bts:Oxygensupplemental-portableO2atnightorcontinuous" + "@id": "bts:Brunei" }, { - "@id": "bts:Prolongedexpiration-long/forcedexpiratoryphase" + "@id": "bts:Bulgaria" }, { - "@id": "bts:Other" + "@id": "bts:BurkinaFaso" }, { - "@id": "bts:Unknown" + "@id": "bts:Burundi" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Current Lung Cancer Symptoms", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LungTopography", - "@type": "rdfs:Class", - "rdfs:comment": "Lung PCA specific topography (not covered in previous tiers)", - "rdfs:label": "LungTopography", - "rdfs:subClassOf": [ + "@id": "bts:Cambodia" + }, { - "@id": "bts:LungCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Cameroon" + }, { - "@id": "bts:MC-Carinabetweenrightandleftlungs(maincarina)" + "@id": "bts:Canada" }, { - "@id": "bts:TR-Trachea(airwaywallbetweentracheo-esophagealbifurcationandmaincarina)" + "@id": "bts:CapeVerde" }, { - "@id": "bts:CarinaNOS(Carinanototherwisespecified)" + "@id": "bts:CaymanIslands" }, { - "@id": "bts:LUDB-Carinabetweenthelingulaandupperdivisionleftupperlobe" + "@id": "bts:CentralAfricanRepublic" }, { - "@id": "bts:CarinabetweenLUDBorificeandlingulaorifice" + "@id": "bts:Chad" }, { - "@id": "bts:LUDB-orificeairwaywallbetweenLUDBandLB3(LB1+2carinae)" + "@id": "bts:Chile" }, { - "@id": "bts:LingulaorificeairwaywallbetweenLUDBandLB4/5carinae" + "@id": "bts:China" }, { - "@id": "bts:RMB-Rightmainstembronchus(airwaywallbetweenMC&RULcarina)" + "@id": "bts:Colombia" }, { - "@id": "bts:LMB-Leftmainstembronchus(airwaywallbetweenMC&LULcarina)" + "@id": "bts:Comoros" }, { - "@id": "bts:RLNOS(Rightlungnototherwisespecified)" + "@id": "bts:Congo" }, { - "@id": "bts:RB1/2-Carinabetweenapicalandposteriorsegmentsrightupperlobe(CarinabetweenRB1orificeandRB2orifice)" + "@id": "bts:CookIslands" }, { - "@id": "bts:RB6A/B-CarinabetweenapicalandlateralsubsegmentssuperiorsegmentRLL" + "@id": "bts:CostaRica" }, { - "@id": "bts:RB6A/C-CarinabetweenapicalandmedialsubsegmentssuperiorsegmentRLL" + "@id": "bts:Coted'Ivoire" }, { - "@id": "bts:RB6B/C-CarinabetweenmedialandlateralsubsegmentssuperiorsegmentRLL" + "@id": "bts:Croatia" }, { - "@id": "bts:RB7A/B-CarinabetweenmedialandlateralsubsegmentsmedialbasalsegmentRLL" + "@id": "bts:Cuba" }, { - "@id": "bts:RB8/9-CarinabetweenanteriorandlateralsegmentsRLL(CarinabetweenRB8orificeandRB9orifice)" + "@id": "bts:Curacao" }, { - "@id": "bts:RB8A/B-CarinabetweenmedialandlateralsubsegmentsanteriorsegmentRLL" + "@id": "bts:Cyprus" }, { - "@id": "bts:RB9/10-CarinabetweenlateralandposteriorsegmentsRLL" + "@id": "bts:CzechRepublic(Czechia)" }, { - "@id": "bts:RB9A/B-CarinabetweenmedialandlateralsubsegmentslateralsegmentRLL" + "@id": "bts:DemocraticRepublicoftheCongo" }, { - "@id": "bts:RB10A/B-CarinabetweenmedialandlateralsubsegmentsposteriorsegmentRLL" + "@id": "bts:Denmark" }, { - "@id": "bts:RB10A/C-CarinabetweenmedialandapicalsubsegmentsposteriorsegmentRLL" + "@id": "bts:Djibouti" }, { - "@id": "bts:RB1A/B-CarinabetweenmedialandlateralsubsegmentsapicalsegmentRUL" + "@id": "bts:Dominica" }, { - "@id": "bts:RB10B/C-CarinabetweenmedialandlateralsubsegmentsposteriorsegmentRLL" + "@id": "bts:DominicanRepublic" }, { - "@id": "bts:RB6-CarinaofsuperiorsegmentRLL(CarinabetweenRB6orificeandlowerportionofRLLorifice)" + "@id": "bts:Ecuador" }, { - "@id": "bts:RB6orificeAirwaywallbetweenRB6andRB6A/B/Ccarinae" + "@id": "bts:Egypt" }, { - "@id": "bts:BronchusIntermediusBronchus(airwaywall)betweenrightupperandrightmiddlelobes" + "@id": "bts:ElSalvador" }, { - "@id": "bts:RB1/3-CarinabetweenapicalandanteriorsegmentsRUL(CarinabetweenRB1orificeandRB3orifice)" + "@id": "bts:EquatorialGuinea" }, { - "@id": "bts:RB2/3-CarinabetweenanteriorandposteriorsegmentsRUL(CarinabetweenRB2orificeandRB3orifice)" + "@id": "bts:Eritrea" }, { - "@id": "bts:RB2A/B-Carinabetweenthemedialandlateralsubsegmentsoftheposteriorsegment(RUL)" + "@id": "bts:Estonia" }, { - "@id": "bts:RB3A/B-CarinabetweenthemedialandlateralsubsegmentsoftheanteriorsegmentRUL" + "@id": "bts:Eswatini" }, { - "@id": "bts:RB4/5-Carinabetweenthelateralandmedialsegmentsrightmiddlelobe(CarinabetweenRB4orificeandRB5orifice)" + "@id": "bts:Ethiopia" }, { - "@id": "bts:RB4A/B-Carinabetweenthemedialandlateralsubsegmentsofthelateralsegmentoftherightmiddlelobe" + "@id": "bts:FalklandIslands(Malvinas)" }, { - "@id": "bts:RB5A/B-Carinabetweenthemedialandlateralsubsegmentsofthemedialsegmentoftherightmiddlelobe" + "@id": "bts:FaroeIslands" }, { - "@id": "bts:RULCarinaebetweenRULorificeandbronchusintermedius" + "@id": "bts:FederatedStatesofMicronesia" }, { - "@id": "bts:RULorificeAirwaywallbetweenRULandRB1/RB2/RB3" + "@id": "bts:Fiji" }, { - "@id": "bts:RB1orificeApicalsegment-rightupperlobe(airwaywallbetweenRB1andRB1A/Bcarinae)" + "@id": "bts:Finland" }, { - "@id": "bts:RB2orificePosteriorsegment-rightupperlobe(airwaywallbetweenRB2andRB2A/Bcarinae)" + "@id": "bts:France" }, { - "@id": "bts:RB3orificeAnteriorsegment-rightupperlobe(airwaywallbetweenRB3andRB3A/Bcarinae)" + "@id": "bts:FrenchGuiana" }, { - "@id": "bts:RML-CarinabetweenRMLorificeandRLLorifice" + "@id": "bts:FrenchPolynesia" }, { - "@id": "bts:RMLorificeAirwaywallbetweenRMLandRB4/5" + "@id": "bts:Gabon" }, { - "@id": "bts:RB4orificeLateralsegmentrightmiddlelobe(airwaywallbetweenRB4andRB4A/Bcarinae)" + "@id": "bts:Gambia" }, { - "@id": "bts:RB5orificeMedialsegmentrightmiddlelobe(airwaywallbetweenRB5andRB5A/Bcarinae)" + "@id": "bts:Georgia" }, { - "@id": "bts:RLLorificeAirwaywallbetweenRMLandRB6-10carinae" + "@id": "bts:Germany" }, { - "@id": "bts:RB7Medialbasalsegmentrightlowerlobe(CarinaatRB7orificetakeofffromRLLorifice)" + "@id": "bts:Ghana" }, { - "@id": "bts:RB7orificeAirwaywallbetweenRB7andRB7A/Bcarinae" + "@id": "bts:Gibraltar" }, { - "@id": "bts:RB8orificeAnteriorsegmentrightlowerlobe(airwaywallbetweenRB8andRB8A/Bcarinae)" + "@id": "bts:Greece" }, { - "@id": "bts:RB9orificeLateralsegmentrightlowerlobe(airwaywallbetweenRB9andRB9A/Bcarinae)" + "@id": "bts:Greenland" }, { - "@id": "bts:RB10Posteriorsegmentrightlowerlobe(CarinaatRB10orificetakeofffromRLLorifice)" + "@id": "bts:Grenada" }, { - "@id": "bts:RB10orificeAirwaywallbetweenRB10andRB10A/Bcarinae" + "@id": "bts:Guadeloupe" }, { - "@id": "bts:LLNOS(Leftlungnototherwisespecified)" + "@id": "bts:Guam" }, { - "@id": "bts:LB1/2Carinabetweenapicalandposteriorsegmentleftupperlobe(CarinabetweenLB1orificeandLB2orifice)" + "@id": "bts:Guatemala" }, { - "@id": "bts:LB4/5Carinabetweensuperiorandinferiorsegmentlingula(CarinabetweenLB4orificeandLB5orifice)" + "@id": "bts:Guernsey" }, { - "@id": "bts:LB4A/BCarinabetweenmedialandlateralsubsegmentssuperiorsegmentlingula" + "@id": "bts:Guinea" }, { - "@id": "bts:LB5A/BCarinabetweenthemedialandlateralsubsegmentsinferiorsegmentlingula" + "@id": "bts:Guinea-Bissau" }, { - "@id": "bts:LB6A/BCarinabetweenthesuperiorandlateralsubsegmentssuperiorsegmentLLL" + "@id": "bts:Guyana" }, { - "@id": "bts:LB6A/CCarinabetweenthesuperiorandmedialsubsegmentsofsuperiorsegmentLLL" + "@id": "bts:Haiti" + }, + { + "@id": "bts:HolySee" + }, + { + "@id": "bts:Honduras" + }, + { + "@id": "bts:HongKong" + }, + { + "@id": "bts:Hungary" + }, + { + "@id": "bts:Iceland" + }, + { + "@id": "bts:India" + }, + { + "@id": "bts:Indonesia" + }, + { + "@id": "bts:Iran" + }, + { + "@id": "bts:Iraq" + }, + { + "@id": "bts:Ireland" + }, + { + "@id": "bts:IsleofMan" + }, + { + "@id": "bts:Israel" + }, + { + "@id": "bts:Italy" + }, + { + "@id": "bts:Jamaica" + }, + { + "@id": "bts:Japan" + }, + { + "@id": "bts:Jersey" + }, + { + "@id": "bts:Jordan" + }, + { + "@id": "bts:Kazakhstan" + }, + { + "@id": "bts:Kenya" + }, + { + "@id": "bts:Kiribati" + }, + { + "@id": "bts:Kosovo" + }, + { + "@id": "bts:Kuwait" + }, + { + "@id": "bts:Kyrgyzstan" + }, + { + "@id": "bts:Laos" + }, + { + "@id": "bts:Latvia" + }, + { + "@id": "bts:Lebanon" + }, + { + "@id": "bts:Lesotho" + }, + { + "@id": "bts:Liberia" + }, + { + "@id": "bts:Libya" + }, + { + "@id": "bts:Liechtenstein" + }, + { + "@id": "bts:Lithuania" + }, + { + "@id": "bts:Luxembourg" + }, + { + "@id": "bts:Macau" + }, + { + "@id": "bts:Madagascar" + }, + { + "@id": "bts:Malawi" + }, + { + "@id": "bts:Malaysia" }, { - "@id": "bts:LB6B/CCarinabetweenthemedialandlateralsubsegmentsofthesuperiorsegmentLLL" + "@id": "bts:Maldives" }, { - "@id": "bts:LB8/9CarinabetweentheanteriorandlateralsegmentsLLL(CarinabetweenLB8orificeandLB9orifice)" + "@id": "bts:Mali" }, { - "@id": "bts:LB8A/BCarinabetweenthemedialandlateralsubsegmentsoftheanteriorsegmentLLL" + "@id": "bts:Malta" }, { - "@id": "bts:LB9/10CarinabetweenthelateralandposteriorsegmentsLLL(CarinabetweenLB9orificeandLB10orifice)" + "@id": "bts:MarshallIslands" }, { - "@id": "bts:LB9A/BCarinabetweenthemedialandlateralsubsegmentsofthelateralsegmentLLL" + "@id": "bts:Martinique" }, { - "@id": "bts:LB1A/BCarinabetweenthelateralandmedialsubsegmentsoftheapicalsegmentoftheLUL" + "@id": "bts:Mauritania" }, { - "@id": "bts:LB10A/BCarinabetweentheapicalandlateralsubsegmentsoftheposteriorsegmentoftheLLL" + "@id": "bts:Mauritius" }, { - "@id": "bts:LB10A/CCarinabetweentheapicalandmedialsegmentsoftheposteriorsegmentoftheLLL" + "@id": "bts:Mayotte" }, { - "@id": "bts:LB10B/CCarinabetweenthemedialandlateralsubsegmentsoftheposteriorsegmentoftheLLL" + "@id": "bts:Mexico" }, { - "@id": "bts:LB1+2orificeTheapico-posteriorsegmentoftheleftupperlobe(airwaywallbetweenLB1+2/3carinaandLB1orLB2)" + "@id": "bts:Moldova" }, { - "@id": "bts:LB6Thesuperiorsegmentoftheleftlowerlobe(CarinabetweenLB6orificeandlowerportionofLLLorifice)" + "@id": "bts:Monaco" }, { - "@id": "bts:LB6orificeAirwaywallbetweenLB6andLB6A/Bcarinae" + "@id": "bts:Mongolia" }, { - "@id": "bts:LB1A/CCarinabetweentheapicalandlateralsubsegmentsoftheapicalsegmentleftupperlobe" + "@id": "bts:Montenegro" }, { - "@id": "bts:LB1B/CCarinabetweenthemedialandlateralsubsegmentsoftheapicalsegmentoftheleftupperlobe" + "@id": "bts:Montserrat" }, { - "@id": "bts:LB2A/BCarinabetweentheapicalandlateralsubsegmentsoftheposteriorsegmentoftheleftupperlobe" + "@id": "bts:Morocco" }, { - "@id": "bts:LB2A/CCarinabetweentheapicalandmedialsubsegmentsoftheposteriorsegmentoftheleftupperlobe" + "@id": "bts:Mozambique" }, { - "@id": "bts:LB2B/CCarinabetweenthemedialandlateralsubsegmentsoftheposteriorsegmentleftupperlobe" + "@id": "bts:Myanmar" }, { - "@id": "bts:LB1+2/3Carinabetweentheapico-posteriorandanteriorsegmentsoftheleftupperlobe(CarinabetweenLB1+2orificeandLB3orifice)" + "@id": "bts:Namibia" }, { - "@id": "bts:LB3A/BCarinabetweentheapicalandlateralsubsegmentsoftheanteriorsegmentoftheleftupperlobe" + "@id": "bts:Nauru" }, { - "@id": "bts:LULCarinabetweentheLULorificeandLLLorifice(airways)" + "@id": "bts:Nepal" }, { - "@id": "bts:LULorificeAirwaywallbetweenLULandLUDB" + "@id": "bts:Netherlands" }, { - "@id": "bts:LB3orificeAnteriorsegmentleftupperlobe(airwaywallbetweenLB3andLB3A/Bcarinae)" + "@id": "bts:NewCaledonia" }, { - "@id": "bts:LB4orificeSuperiorsegmentlingula(airwaywallbetweenLB4andLB4A/Bcarinae)" + "@id": "bts:NewZealand" }, { - "@id": "bts:LB5orificeInferiorsegmentlingula(airwaywallbetweenLB5andLB5A/Bcarinae)" + "@id": "bts:Nicaragua" }, { - "@id": "bts:LLLorificeAirwaywallbetweenLULcarinaandLB6-10carinae" + "@id": "bts:Niger" }, { - "@id": "bts:LB9orificeLateralsegmentleftlowerlobe(airwaywallbetweenLB9andLB9A/Bcarinae)" + "@id": "bts:Nigeria" }, { - "@id": "bts:LB8orificeAnteriorsegmentleftlowerlobe(airwaywallbetweenLB8andLB8A/Bcarinae)" + "@id": "bts:Niue" }, { - "@id": "bts:LB10orificePosteriorsegmentleftlowerlobe(airwaywallbetweenLB10andLB10A/Bcarinae)" + "@id": "bts:NorthKorea" }, { - "@id": "bts:Other" + "@id": "bts:NorthMacedonia" }, { - "@id": "bts:Unknown" + "@id": "bts:NorthernMarianaIslands" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Lung Topography", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LungCancerHarboringGenomicAberrations", - "@type": "rdfs:Class", - "rdfs:comment": "Genomic aberrations in participants with lung cancer (specific lung cancer associated gene mutations not covered in Tiers 1 and 2)", - "rdfs:label": "LungCancerHarboringGenomicAberrations", - "rdfs:subClassOf": [ + "@id": "bts:Norway" + }, { - "@id": "bts:LungCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Oman" + }, { - "@id": "bts:G12AKRASmutation" + "@id": "bts:Pakistan" }, { - "@id": "bts:G12CKRASmutation" + "@id": "bts:Palau" }, { - "@id": "bts:G12DKRASmutation" + "@id": "bts:Panama" }, { - "@id": "bts:G12RKRASmutation" + "@id": "bts:PapuaNewGuinea" }, { - "@id": "bts:G12SKRASmutation" + "@id": "bts:Paraguay" }, { - "@id": "bts:G12VKRASmutation" + "@id": "bts:Peru" }, { - "@id": "bts:G13DKRASmutation" + "@id": "bts:Philippines" }, { - "@id": "bts:G13RKRASmutation" + "@id": "bts:Poland" }, { - "@id": "bts:G13CKRASmutation" + "@id": "bts:Portugal" }, { - "@id": "bts:G13AKRASmutation" + "@id": "bts:PuertoRico" }, { - "@id": "bts:G13VKRASmutation" + "@id": "bts:Qatar" }, { - "@id": "bts:Q61LKRASmutation" + "@id": "bts:Reunion" }, { - "@id": "bts:Q61HKRASmutation" + "@id": "bts:Romania" }, { - "@id": "bts:A146TKRASmutation" + "@id": "bts:Russia" }, { - "@id": "bts:G719XEGFRmutation" + "@id": "bts:Rwanda" }, { - "@id": "bts:T790MEGFRmutation" + "@id": "bts:SaintHelenaAscensionandTristandaCunha" }, { - "@id": "bts:C797SEGFRmutation" + "@id": "bts:SaintKittsandNevis" }, { - "@id": "bts:L858REGFRmutation" + "@id": "bts:SaintLucia" }, { - "@id": "bts:L861QEGFRmutation" + "@id": "bts:SaintPierreandMiquelon" }, { - "@id": "bts:Exon19deletion" + "@id": "bts:SaintVincentandtheGrenadines" }, { - "@id": "bts:Exon20insertion" + "@id": "bts:Samoa" }, { - "@id": "bts:EML4-ALKtranslocation-variant1" + "@id": "bts:SanMarino" }, { - "@id": "bts:EML4-ALKtranslocation-variant2" + "@id": "bts:SaoTomeandPrincipe" }, { - "@id": "bts:EML4-ALKtranslocation-variant3" + "@id": "bts:SaudiArabia" }, { - "@id": "bts:EML4-ALKtranslocation-variant4" + "@id": "bts:Senegal" }, { - "@id": "bts:EML4-ALKtranslocation-variant5" + "@id": "bts:Serbia" }, { - "@id": "bts:V600EBRAFmutation" + "@id": "bts:Seychelles" }, { - "@id": "bts:V600DBRAFmutation" + "@id": "bts:SierraLeone" }, { - "@id": "bts:V600KBRAFmutation" + "@id": "bts:Singapore" }, { - "@id": "bts:V600RBRAFmutation" + "@id": "bts:Slovakia" }, { - "@id": "bts:K601EBRAFmutation" + "@id": "bts:Slovenia" }, { - "@id": "bts:D963spliceMETmutation" + "@id": "bts:SolomonIslands" }, { - "@id": "bts:D1010NMETmutation" + "@id": "bts:Somalia" }, { - "@id": "bts:D1010spliceMETmutation" + "@id": "bts:SouthAfrica" }, { - "@id": "bts:Intron13mutation" + "@id": "bts:SouthKorea" }, { - "@id": "bts:Intron14mutation" + "@id": "bts:SouthSudan" }, { - "@id": "bts:Exon14mutation" + "@id": "bts:Spain" }, { - "@id": "bts:Exon14deletion" + "@id": "bts:SriLanka" }, { - "@id": "bts:Other" + "@id": "bts:StateofPalestine" }, { - "@id": "bts:Unknown" + "@id": "bts:Sudan" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Lung Cancer Harboring Genomic Aberrations", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ColorectalCancerTier3", - "@type": "rdfs:Class", - "rdfs:comment": "Colorectal cancer specific attributes in Clinical Data Tier 3", - "rdfs:label": "ColorectalCancerTier3", - "rdfs:subClassOf": [ + "@id": "bts:Suriname" + }, { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Colorectal Cancer Tier 3", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "@id": "bts:Svalbard&JanMayenIslands" + }, { - "@id": "bts:Component" + "@id": "bts:Sweden" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:Switzerland" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:Syria" }, { - "@id": "bts:StartDaysfromIndex" + "@id": "bts:Taiwan" }, { - "@id": "bts:StopDaysfromIndex" + "@id": "bts:Tajikistan" }, { - "@id": "bts:ColorectalCancerDetectionMethodType" + "@id": "bts:Tanzania" }, { - "@id": "bts:HistoryofPriorColonPolyps" + "@id": "bts:Thailand" }, { - "@id": "bts:FamilyColonCancerHistoryIndicator" + "@id": "bts:Timor-Leste" }, { - "@id": "bts:FamilyMedicalHistoryColorectalPolypDiagnosis" + "@id": "bts:Togo" }, { - "@id": "bts:ImmediateFamilyHistoryEndometrialCancer" + "@id": "bts:Tokelau" }, { - "@id": "bts:ImmediateFamilyHistoryOvarianCancer" + "@id": "bts:Tonga" }, { - "@id": "bts:PatientInflammatoryBowelDiseasePersonalMedicaHistory" + "@id": "bts:TrinidadandTobago" }, { - "@id": "bts:PatientColonoscopyPerformedIndicator" + "@id": "bts:Tunisia" }, { - "@id": "bts:ColorectalCancerTumorBorderConfiguration" + "@id": "bts:Turkey" }, { - "@id": "bts:MLH1PromoterMethylationStatus" + "@id": "bts:Turkmenistan" }, { - "@id": "bts:ColorectalCancerKRASIndicator" + "@id": "bts:Tuvalu" }, { - "@id": "bts:ColonPolypOccurenceIndicator" + "@id": "bts:Uganda" }, { - "@id": "bts:FamilyHistoryColorectalPolyp" + "@id": "bts:Ukraine" }, { - "@id": "bts:ColorectalPolypNewIndicator" + "@id": "bts:UnitedArabEmirates" }, { - "@id": "bts:ColorectalPolypShape" + "@id": "bts:UnitedKingdom" }, { - "@id": "bts:SizeofPolypRemoved" + "@id": "bts:UnitedStates" }, { - "@id": "bts:ColorectalPolypCount" + "@id": "bts:Uruguay" }, { - "@id": "bts:ColorectalPolypType" + "@id": "bts:Uzbekistan" }, { - "@id": "bts:ColorectalPolypAdenomaType" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:ColorectalCancerDetectionMethodType", - "@type": "rdfs:Class", - "rdfs:comment": "The means, manner of procedure, or systematic course of actions performed in order to discover or identify colorectal cancer", - "rdfs:label": "ColorectalCancerDetectionMethodType", - "rdfs:subClassOf": [ + "@id": "bts:Vanuatu" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Venezuela" + }, { - "@id": "bts:Fecaloccultbloodtest" + "@id": "bts:Vietnam" }, { - "@id": "bts:Sigmoidoscopy" + "@id": "bts:VirginIslandsBritish" }, { - "@id": "bts:Colonoscopy" + "@id": "bts:VirginIslandsU.S." }, { - "@id": "bts:Virtualcolonoscopy" + "@id": "bts:WallisandFutuna" }, { - "@id": "bts:DNAstooltest" + "@id": "bts:WesternSahara" }, { - "@id": "bts:Other" + "@id": "bts:Yemen" }, { - "@id": "bts:Unknown" + "@id": "bts:Zambia" }, { - "@id": "bts:Datanotavailable" + "@id": "bts:Zimbabwe" } ], - "sms:displayName": "Colorectal Cancer Detection Method Type", + "sms:displayName": "Country of Residence", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HistoryofPriorColonPolyps", + "@id": "bts:AgeIsObfuscated", "@type": "rdfs:Class", - "rdfs:comment": "Yes/No indicator to describe if the subject had a previous history of colon polyps as noted in the history/physical or previous endoscopic report (s).", - "rdfs:label": "HistoryofPriorColonPolyps", + "rdfs:comment": "The age of the patient has been modified for compliance reasons. The actual age differs from what is reported. Other date intervals for this patient may also be modified.", + "rdfs:label": "AgeIsObfuscated", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:Demographics" } ], "schema:isPartOf": { @@ -15118,92 +20170,58 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:NotApplicable" + "@id": "bts:True" }, { - "@id": "bts:Unknown" + "@id": "bts:False" } ], - "sms:displayName": "History of Prior Colon Polyps", + "sms:displayName": "Age Is Obfuscated", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FamilyColonCancerHistoryIndicator", + "@id": "bts:YearOfBirth", "@type": "rdfs:Class", - "rdfs:comment": "The indicator to designate if any first degree relative has a history of colorectal cancer.", - "rdfs:label": "FamilyColonCancerHistoryIndicator", + "rdfs:comment": "Numeric value to represent the calendar year in which an individual was born.", + "rdfs:label": "YearOfBirth", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:Demographics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:NotApplicable" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Family Colon Cancer History Indicator", + "sms:displayName": "Year Of Birth", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FamilyMedicalHistoryColorectalPolypDiagnosis", + "@id": "bts:OccupationDurationYears", "@type": "rdfs:Class", - "rdfs:comment": "A yes/no/unknown/not applicable indicator related to family medical history diagnosis of polypoid lesion that arises from the colon or rectum and protrudes into the lumen.", - "rdfs:label": "FamilyMedicalHistoryColorectalPolypDiagnosis", + "rdfs:comment": "The number of years a patient worked in a specific occupation.", + "rdfs:label": "OccupationDurationYears", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:Demographics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:NotApplicable" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Family Medical History Colorectal Polyp Diagnosis", + "sms:displayName": "Occupation Duration Years", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ImmediateFamilyHistoryEndometrialCancer", + "@id": "bts:PrematureAtBirth", "@type": "rdfs:Class", - "rdfs:comment": "Text that describes the age at which the family member was diagnosed with endometrial or uterine cancer in relationship to their 50th birthday.", - "rdfs:label": "ImmediateFamilyHistoryEndometrialCancer", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was premature (less than 37 weeks gestation) at birth.", + "rdfs:label": "PrematureAtBirth", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:Demographics" } ], "schema:isPartOf": { @@ -15211,61 +20229,47 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Beforeage50" + "@id": "bts:Yes" }, { - "@id": "bts:Notbeforeage50" + "@id": "bts:No" }, { "@id": "bts:Unknown" }, { - "@id": "bts:NotApplicable" + "@id": "bts:NotReported" } ], - "sms:displayName": "Immediate Family History Endometrial Cancer", + "sms:displayName": "Premature At Birth", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ImmediateFamilyHistoryOvarianCancer", + "@id": "bts:WeeksGestationatBirth", "@type": "rdfs:Class", - "rdfs:comment": "Text that describes the age at which the family member was diagnosed with ovarian cancer in relationship to their 50th birthday.", - "rdfs:label": "ImmediateFamilyHistoryOvarianCancer", + "rdfs:comment": "Numeric value used to describe the number of weeks starting from the approximate date of the biological mother's last menstrual period and ending with the birth of the patient.", + "rdfs:label": "WeeksGestationatBirth", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:Demographics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Beforeage50" - }, - { - "@id": "bts:Notbeforeage50" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Immediate Family History Ovarian Cancer", + "sms:displayName": "Weeks Gestation at Birth", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PatientInflammatoryBowelDiseasePersonalMedicaHistory", + "@id": "bts:RelativewithCancerHistory", "@type": "rdfs:Class", - "rdfs:comment": "The indicator for patient's personal medical history of inflammatory bowel disease (chronic, non-specific disorders of unknown etiology, including Crohn disease and ulcerative colitis).", - "rdfs:label": "PatientInflammatoryBowelDiseasePersonalMedicaHistory", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether any of the patient's relatives have a history of cancer.", + "rdfs:label": "RelativewithCancerHistory", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:FamilyHistory" } ], "schema:isPartOf": { @@ -15273,33 +20277,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes-Crohn'sdisease" - }, - { - "@id": "bts:Yes-Ulcerativecolitis" + "@id": "bts:Yes-CancerHistoryRelative" }, { - "@id": "bts:No" + "@id": "bts:None" }, { "@id": "bts:Unknown" }, { - "@id": "bts:NotApplicable" + "@id": "bts:NotReported" } ], - "sms:displayName": "Patient Inflammatory Bowel Disease Personal Medica History", + "sms:displayName": "Relative with Cancer History", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PatientColonoscopyPerformedIndicator", + "@id": "bts:SmokingExposure", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no indicator that records if the subject has undergone a previous colonoscopy.", - "rdfs:label": "PatientColonoscopyPerformedIndicator", + "rdfs:comment": "Indicate if individual has smoking exposure", + "rdfs:label": "SmokingExposure", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:Exposure" } ], "schema:isPartOf": { @@ -15307,30 +20308,27 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" + "@id": "bts:Yes-SmokingExposure" }, { - "@id": "bts:NotApplicable" + "@id": "bts:No-SmokingExposure" }, { - "@id": "bts:Unknown" + "@id": "bts:NotReported" } ], - "sms:displayName": "Patient Colonoscopy Performed Indicator", - "sms:required": "sms:false", + "sms:displayName": "Smoking Exposure", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ColorectalCancerTumorBorderConfiguration", + "@id": "bts:AlcoholExposure", "@type": "rdfs:Class", - "rdfs:comment": "The description of the border configuration of a colorectal tumor at pathologic assessment.", - "rdfs:label": "ColorectalCancerTumorBorderConfiguration", + "rdfs:comment": "Indicate if individual has alcohol exposure", + "rdfs:label": "AlcoholExposure", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:Exposure" } ], "schema:isPartOf": { @@ -15338,33 +20336,27 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Indeterminate" - }, - { - "@id": "bts:Infiltrating" - }, - { - "@id": "bts:Other" + "@id": "bts:Yes-AlcoholExposure" }, { - "@id": "bts:Pushing" + "@id": "bts:No-AlcoholExposure" }, { - "@id": "bts:NotApplicable" + "@id": "bts:NotReported" } ], - "sms:displayName": "Colorectal Cancer Tumor Border Configuration", - "sms:required": "sms:false", + "sms:displayName": "Alcohol Exposure", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MLH1PromoterMethylationStatus", + "@id": "bts:AsbestosExposure", "@type": "rdfs:Class", - "rdfs:comment": "Text term to define the status of promoter methylation for the MLH1 gene. Note: MLH1 gene is commonly associated with hereditary nonpolyposis colorectal cancer. Testing for methylation of the MLH1 promoter can help distinguish sporadic from inherited cancers.", - "rdfs:label": "MLH1PromoterMethylationStatus", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was exposed to asbestos.", + "rdfs:label": "AsbestosExposure", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:Exposure" } ], "schema:isPartOf": { @@ -15372,30 +20364,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Absent" + "@id": "bts:Yes" }, { - "@id": "bts:Indeterminate" + "@id": "bts:No" }, { - "@id": "bts:NotAssessed" + "@id": "bts:Unknown" }, { - "@id": "bts:Present" + "@id": "bts:NotReported" } ], - "sms:displayName": "MLH1 Promoter Methylation Status", + "sms:displayName": "Asbestos Exposure", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ColorectalCancerKRASIndicator", + "@id": "bts:CoalDustExposure", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/not applicable indicator that describes if patient has diagnosis of colorectal cancer with known KRAS.", - "rdfs:label": "ColorectalCancerKRASIndicator", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposed to fine powder derived by the crushing of coal.", + "rdfs:label": "CoalDustExposure", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:Exposure" } ], "schema:isPartOf": { @@ -15410,23 +20402,20 @@ }, { "@id": "bts:Unknown" - }, - { - "@id": "bts:NotApplicable" } ], - "sms:displayName": "Colorectal Cancer KRAS Indicator", + "sms:displayName": "Coal Dust Exposure", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ColonPolypOccurenceIndicator", + "@id": "bts:EnvironmentalTobaccoSmokeExposure", "@type": "rdfs:Class", - "rdfs:comment": "Yes/No indicator to describe if the subject had a previous history of colon polyps as noted in the history/physical or previous endoscopic report (s).", - "rdfs:label": "ColonPolypOccurenceIndicator", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposed to smoke that is emitted from burning tobacco, including cigarettes, pipes, and cigars. This includes tobacco smoke exhaled by smokers.", + "rdfs:label": "EnvironmentalTobaccoSmokeExposure", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:Exposure" } ], "schema:isPartOf": { @@ -15441,23 +20430,20 @@ }, { "@id": "bts:Unknown" - }, - { - "@id": "bts:NotApplicable" } ], - "sms:displayName": "Colon Polyp Occurence Indicator", + "sms:displayName": "Environmental Tobacco Smoke Exposure", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FamilyHistoryColorectalPolyp", + "@id": "bts:RadonExposure", "@type": "rdfs:Class", - "rdfs:comment": "A yes/no/unknown/not applicable indicator related to family medical history diagnosis of polypoid lesion that arises from the colon or rectum and protrudes into the lumen.", - "rdfs:label": "FamilyHistoryColorectalPolyp", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was exposed to radon.", + "rdfs:label": "RadonExposure", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:Exposure" } ], "schema:isPartOf": { @@ -15474,21 +20460,21 @@ "@id": "bts:Unknown" }, { - "@id": "bts:NotApplicable" + "@id": "bts:NotReported" } ], - "sms:displayName": "Family History Colorectal Polyp", + "sms:displayName": "Radon Exposure", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ColorectalPolypNewIndicator", + "@id": "bts:RespirableCrystallineSilicaExposure", "@type": "rdfs:Class", - "rdfs:comment": "A yes/no response to a question that asks whether any new polyps greater or equal to two millimeter were identified.", - "rdfs:label": "ColorectalPolypNewIndicator", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposured to respirable crystalline silica, a widespread, naturally occurring, crystalline metal oxide that consists of different forms including quartz, cristobalite, tridymite, tripoli, ganister, chert and novaculite.", + "rdfs:label": "RespirableCrystallineSilicaExposure", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:Exposure" } ], "schema:isPartOf": { @@ -15503,23 +20489,20 @@ }, { "@id": "bts:Unknown" - }, - { - "@id": "bts:NotApplicable" } ], - "sms:displayName": "Colorectal Polyp New Indicator", + "sms:displayName": "Respirable Crystalline Silica Exposure", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ColorectalPolypShape", + "@id": "bts:AdverseEvent", "@type": "rdfs:Class", - "rdfs:comment": "Shape of polyp identified in the participant", - "rdfs:label": "ColorectalPolypShape", + "rdfs:comment": "Text that represents the Common Terminology Criteria for Adverse Events low level term name for an adverse event.", + "rdfs:label": "AdverseEvent", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -15527,4078 +20510,2913 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Pedunculated" + "@id": "bts:AbdominalDistension" }, { - "@id": "bts:Sessile" + "@id": "bts:AbdominalInfection" }, { - "@id": "bts:Flat" + "@id": "bts:AbdominalPain" }, { - "@id": "bts:Notstated" + "@id": "bts:AbdominalSoftTissueNecrosis" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Colorectal Polyp Shape", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SizeofPolypRemoved", - "@type": "rdfs:Class", - "rdfs:comment": "Size of the polyp removed in cm", - "rdfs:label": "SizeofPolypRemoved", - "rdfs:subClassOf": [ + "@id": "bts:AbducensNerveDisorder" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Size of Polyp Removed", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ColorectalPolypCount", - "@type": "rdfs:Class", - "rdfs:comment": "The total number of polyps detected", - "rdfs:label": "ColorectalPolypCount", - "rdfs:subClassOf": [ + "@id": "bts:AccessoryNerveDisorder" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Colorectal Polyp Count", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ColorectalPolypType", - "@type": "rdfs:Class", - "rdfs:comment": "Type of polyp found in the participant", - "rdfs:label": "ColorectalPolypType", - "rdfs:subClassOf": [ + "@id": "bts:Acidosis" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:AcousticNerveDisorderNOS" + }, { - "@id": "bts:Adenoma" + "@id": "bts:ActivatedPartialThromboplastinTimeProlonged" }, { - "@id": "bts:Hyperplastic" + "@id": "bts:AcuteCoronarySyndrome" }, { - "@id": "bts:Mixed" + "@id": "bts:AcuteKidneyInjury" }, { - "@id": "bts:Papillomatous" + "@id": "bts:AdrenalInsufficiency" }, { - "@id": "bts:Normal" + "@id": "bts:AdultRespiratoryDistressSyndrome" }, { - "@id": "bts:Cancer" + "@id": "bts:Agitation" }, { - "@id": "bts:Other" + "@id": "bts:Akathisia" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Colorectal Polyp Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ColorectalPolypAdenomaType", - "@type": "rdfs:Class", - "rdfs:comment": "Type of adenoma associated with the polyp", - "rdfs:label": "ColorectalPolypAdenomaType", - "rdfs:subClassOf": [ + "@id": "bts:AlanineAminotransferaseIncreased" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:AlcoholIntolerance" + }, { - "@id": "bts:Tubular" + "@id": "bts:AlkalinePhosphataseIncreased" }, { - "@id": "bts:Villous" + "@id": "bts:Alkalosis" }, { - "@id": "bts:Tubulovillous" + "@id": "bts:AllergicReaction" }, { - "@id": "bts:Sessileserrated" + "@id": "bts:AllergicRhinitis" }, { - "@id": "bts:Traditionalserrated" + "@id": "bts:Alopecia" }, { - "@id": "bts:Serratednotspecified" + "@id": "bts:Amnesia" }, { - "@id": "bts:Notstated" + "@id": "bts:AnalFistula" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Colorectal Polyp Adenoma Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BreastCancerTier3", - "@type": "rdfs:Class", - "rdfs:comment": "Breast cancer specific attributes in Clinical Data Tier 3", - "rdfs:label": "BreastCancerTier3", - "rdfs:subClassOf": [ + "@id": "bts:AnalHemorrhage" + }, { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Breast Cancer Tier 3", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "@id": "bts:AnalMucositis" + }, { - "@id": "bts:Component" + "@id": "bts:AnalNecrosis" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:AnalPain" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:AnalStenosis" }, { - "@id": "bts:StartDaysfromIndex" + "@id": "bts:AnalUlcer" }, { - "@id": "bts:StopDaysfromIndex" + "@id": "bts:Anaphylaxis" }, { - "@id": "bts:BreastCarcinomaDetectionMethodType" + "@id": "bts:Anemia" }, { - "@id": "bts:BreastCarcinomaHistologyCategory" + "@id": "bts:AnkleFracture" }, { - "@id": "bts:InvasiveLobularBreastCarcinomaHistologicCategory" + "@id": "bts:AnorectalInfection" }, { - "@id": "bts:InvasiveDuctalBreastCarcinomaHistologicCategory" + "@id": "bts:Anorexia" }, { - "@id": "bts:BreastBiopsyProcedureFindingType" + "@id": "bts:Anorgasmia" }, { - "@id": "bts:BreastQuadrantSite" + "@id": "bts:Anxiety" }, { - "@id": "bts:BreastCancerAssessmentTests" + "@id": "bts:AorticInjury" }, { - "@id": "bts:BreastCancerGenomicTestPerformed" + "@id": "bts:AorticValveDisease" }, { - "@id": "bts:MammaprintRiskGroup" + "@id": "bts:Aphonia" }, { - "@id": "bts:OncotypeRiskGroup" + "@id": "bts:Apnea" }, { - "@id": "bts:BreastCarcinomaEstrogenReceptorStatus" + "@id": "bts:Appendicitis" }, { - "@id": "bts:BreastCarcinomaProgesteronerReceptorStatus" + "@id": "bts:AppendicitisPerforated" }, { - "@id": "bts:BreastCancerAllredEstrogenReceptorScore" + "@id": "bts:Arachnoiditis" }, { - "@id": "bts:PriorInvasiveBreastDisease" + "@id": "bts:ArterialInjury" }, { - "@id": "bts:BreastCarcinomaERStatusPercentageValue" + "@id": "bts:ArteritisInfective" }, { - "@id": "bts:BreastCarcinomaPRStatusPercentageValue" + "@id": "bts:Arthralgia" }, { - "@id": "bts:HER2BreastCarcinomaCopyNumberTotal" + "@id": "bts:Arthritis" }, { - "@id": "bts:BreastCarcinomaCentromere17CopyNumber" + "@id": "bts:Ascites" }, { - "@id": "bts:BreastCarcinomaHER2Centromere17CopynumberTotal" + "@id": "bts:AspartateAminotransferaseIncreased" }, { - "@id": "bts:BreastCarcinomaHER2Chromosome17Ratio" + "@id": "bts:Aspiration" }, { - "@id": "bts:BreastCarcinomaSurgicalProcedureName" + "@id": "bts:Asystole" }, { - "@id": "bts:BreastCarcinomaHER2RatioDiagnosis" + "@id": "bts:Ataxia" }, { - "@id": "bts:BreastCarcinomaHER2Status" + "@id": "bts:Atelectasis" }, { - "@id": "bts:HormoneTherapyBreastCancerPreventionIndicator" + "@id": "bts:AtrialFibrillation" }, { - "@id": "bts:BreastCarcinomaERStainingIntensity" + "@id": "bts:AtrialFlutter" }, { - "@id": "bts:BreastCarcinomaPRStainingIntensity" + "@id": "bts:AtrioventricularBlockComplete" }, { - "@id": "bts:OncotypeScore" + "@id": "bts:AtrioventricularBlockFirstDegree" }, { - "@id": "bts:BreastImagingPerformedType" + "@id": "bts:AutoimmuneDisorder" }, { - "@id": "bts:MultifocalBreastCarcinomaPresentIndicator" + "@id": "bts:AvascularNecrosis" }, { - "@id": "bts:MulticentricBreastCarcinomaPresentIndicator" + "@id": "bts:Azoospermia" }, { - "@id": "bts:BIRADSMammographyBreastDensityCategory" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:BreastCarcinomaDetectionMethodType", - "@type": "rdfs:Class", - "rdfs:comment": "The means, manner of procedure, or systematic course of actions performed in order to discover or identify breast cancer.", - "rdfs:label": "BreastCarcinomaDetectionMethodType", - "rdfs:subClassOf": [ + "@id": "bts:BackPain" + }, { - "@id": "bts:BreastCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:BileDuctStenosis" + }, { - "@id": "bts:ClinicalExam" + "@id": "bts:BiliaryAnastomoticLeak" }, { - "@id": "bts:Datanotavailable" + "@id": "bts:BiliaryFistula" }, { - "@id": "bts:NippleDischarge" + "@id": "bts:BiliaryTractInfection" }, { - "@id": "bts:Other" + "@id": "bts:BladderAnastomoticLeak" }, { - "@id": "bts:ScreeningMammography" + "@id": "bts:BladderInfection" }, { - "@id": "bts:ScreeningMRI" + "@id": "bts:BladderPerforation" }, { - "@id": "bts:Selfexam" + "@id": "bts:BladderSpasm" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Breast Carcinoma Detection Method Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BreastCarcinomaHistologyCategory", - "@type": "rdfs:Class", - "rdfs:comment": "Classification of the type of invasive breast carcinoma diagnosed based on histologic attributes.", - "rdfs:label": "BreastCarcinomaHistologyCategory", - "rdfs:subClassOf": [ + "@id": "bts:Bloating" + }, { - "@id": "bts:BreastCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:BloodandLymphaticSystemDisordersOther" + }, { - "@id": "bts:Infiltratingductalcarcinoma" + "@id": "bts:BloodAntidiureticHormoneAbnormal" }, { - "@id": "bts:Infiltratinglobularcarcinoma" + "@id": "bts:BloodBilirubinIncreased" }, { - "@id": "bts:InvasivemammarycarcinomaNOS" + "@id": "bts:BloodCorticotrophinDecreased" }, { - "@id": "bts:Invasivemixedductalandlobularcarcinoma" + "@id": "bts:BloodGonadotrophinAbnormal" }, { - "@id": "bts:Other" - } - ], - "sms:displayName": "Breast Carcinoma Histology Category", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:InvasiveLobularBreastCarcinomaHistologicCategory", - "@type": "rdfs:Class", - "rdfs:comment": "The histologic subtype for an infiltrating lobular carcinoma of the breast.", - "rdfs:label": "InvasiveLobularBreastCarcinomaHistologicCategory", - "rdfs:subClassOf": [ + "@id": "bts:BloodProlactinAbnormal" + }, { - "@id": "bts:BreastCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:BlurredVision" + }, { - "@id": "bts:Alveolartype" + "@id": "bts:BodyOdor" }, { - "@id": "bts:Classicaltype" + "@id": "bts:BoneInfection" }, { - "@id": "bts:Datanotavailable" + "@id": "bts:BoneMarrowHypocellular" }, { - "@id": "bts:Pleomorphictype" + "@id": "bts:BonePain" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Invasive Lobular Breast Carcinoma Histologic Category", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:InvasiveDuctalBreastCarcinomaHistologicCategory", - "@type": "rdfs:Class", - "rdfs:comment": "The histologic subtype for the most common type of invasive breast carcinoma.", - "rdfs:label": "InvasiveDuctalBreastCarcinomaHistologicCategory", - "rdfs:subClassOf": [ + "@id": "bts:BrachialPlexopathy" + }, { - "@id": "bts:BreastCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:BreastAtrophy" + }, { - "@id": "bts:Classicaltype" + "@id": "bts:BreastInfection" }, { - "@id": "bts:Invasivecarcinoma-typecannotbedetermined" + "@id": "bts:BreastPain" }, { - "@id": "bts:Invasivecribriformcarcinoma" + "@id": "bts:BronchialFistula" }, { - "@id": "bts:Invasivemicropapillarycarcinoma" + "@id": "bts:BronchialInfection" }, { - "@id": "bts:Invasivepapillarycarcinoma" + "@id": "bts:BronchialObstruction" }, { - "@id": "bts:Invasivetubularcarcinoma" + "@id": "bts:BronchialStricture" }, { - "@id": "bts:Medullarycarcinoma" + "@id": "bts:BronchopleuralFistula" }, { - "@id": "bts:Mucinouscarcinoma" + "@id": "bts:BronchopulmonaryHemorrhage" }, { - "@id": "bts:Tubulolobularcarcinoma" + "@id": "bts:Bronchospasm" }, { - "@id": "bts:Other" + "@id": "bts:Bruising" }, { - "@id": "bts:Unknown" + "@id": "bts:BullousDermatitis" }, { - "@id": "bts:Datanotavailable" - } - ], - "sms:displayName": "Invasive Ductal Breast Carcinoma Histologic Category", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BreastBiopsyProcedureFindingType", - "@type": "rdfs:Class", - "rdfs:comment": "Text term to describe the result of the examination of the breast tissue specimen or fluid as related to the presence and nature of disease.", - "rdfs:label": "BreastBiopsyProcedureFindingType", - "rdfs:subClassOf": [ + "@id": "bts:Burn" + }, { - "@id": "bts:BreastCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:ButtockPain" + }, { - "@id": "bts:Atypicalhyperplasia" + "@id": "bts:CapillaryLeakSyndrome" }, { - "@id": "bts:DCIS" + "@id": "bts:CarbonMonoxideDiffusingCapacityDecreased" }, { - "@id": "bts:LCIS" + "@id": "bts:CardiacArrest" }, { - "@id": "bts:Cancer" + "@id": "bts:CardiacDisordersOther" }, { - "@id": "bts:Nocancer" + "@id": "bts:CardiacTroponinIIncreased" }, { - "@id": "bts:Other" - } - ], - "sms:displayName": "Breast Biopsy Procedure Finding Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BreastQuadrantSite", - "@type": "rdfs:Class", - "rdfs:comment": "The breast quadrant or structure from which the breast tissue specimen was removed for microscopic examination.", - "rdfs:label": "BreastQuadrantSite", - "rdfs:subClassOf": [ + "@id": "bts:CardiacTroponinTIncreased" + }, { - "@id": "bts:BreastCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Cataract" + }, + { + "@id": "bts:CatheterRelatedInfection" + }, + { + "@id": "bts:CD4LymphocytesDecreased" + }, + { + "@id": "bts:CecalHemorrhage" + }, + { + "@id": "bts:CecalInfection" + }, + { + "@id": "bts:CentralNervousSystemNecrosis" + }, + { + "@id": "bts:CerebrospinalFluidLeakage" + }, + { + "@id": "bts:CervicitisInfection" + }, + { + "@id": "bts:Cheilitis" + }, + { + "@id": "bts:ChestPainCardiac" + }, + { + "@id": "bts:ChestWallPain" + }, + { + "@id": "bts:Chills" + }, + { + "@id": "bts:Cholecystitis" + }, + { + "@id": "bts:CholesterolHigh" + }, + { + "@id": "bts:ChronicKidneyDisease" + }, + { + "@id": "bts:Chylothorax" + }, + { + "@id": "bts:CognitiveDisturbance" + }, + { + "@id": "bts:Colitis" + }, + { + "@id": "bts:ColonicFistula" + }, + { + "@id": "bts:ColonicHemorrhage" + }, + { + "@id": "bts:ColonicObstruction" + }, + { + "@id": "bts:ColonicPerforation" + }, + { + "@id": "bts:ColonicStenosis" + }, + { + "@id": "bts:ColonicUlcer" + }, + { + "@id": "bts:ConcentrationImpairment" + }, + { + "@id": "bts:ConductionDisorder" + }, + { + "@id": "bts:Confusion" + }, + { + "@id": "bts:Congenital" + }, { - "@id": "bts:Upperouterquadrant" + "@id": "bts:FamilialandGeneticDisordersOther" }, { - "@id": "bts:Lowerouterquadrant" + "@id": "bts:Conjunctivitis" }, { - "@id": "bts:Upperinnerquadrant" + "@id": "bts:ConjunctivitisInfective" }, { - "@id": "bts:Lowerinnerquadrant" + "@id": "bts:Constipation" }, { - "@id": "bts:Central" + "@id": "bts:ConstrictivePericarditis" }, { - "@id": "bts:Nipple" + "@id": "bts:CornealInfection" }, { - "@id": "bts:Unknown" + "@id": "bts:CornealUlcer" }, { - "@id": "bts:Datanotavailable" - } - ], - "sms:displayName": "Breast Quadrant Site", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BreastCancerAssessmentTests", - "@type": "rdfs:Class", - "rdfs:comment": "Text term to identify assessment tests done in participants during diagnosis", - "rdfs:label": "BreastCancerAssessmentTests", - "rdfs:subClassOf": [ + "@id": "bts:Cough" + }, { - "@id": "bts:BreastCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:CPKIncreased" + }, { - "@id": "bts:EstrogenreceptorIHC" + "@id": "bts:CranialNerveInfection" }, { - "@id": "bts:ProgesteronereceptorIHC" + "@id": "bts:CreatinineIncreased" }, { - "@id": "bts:HER2IHC" + "@id": "bts:Cushingoid" }, { - "@id": "bts:HER2FISH-CISH" + "@id": "bts:CystitisNoninfective" }, { - "@id": "bts:HER2FISH" + "@id": "bts:CytokineReleaseSyndrome" }, { - "@id": "bts:Other" + "@id": "bts:DeathNeonatal" }, { - "@id": "bts:Unknown" + "@id": "bts:DeathNOS" }, { - "@id": "bts:Datanotavailable" - } - ], - "sms:displayName": "Breast Cancer Assessment Tests", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BreastCancerGenomicTestPerformed", - "@type": "rdfs:Class", - "rdfs:comment": "Text term that represents the name of the genomic test performed for breast cancer.", - "rdfs:label": "BreastCancerGenomicTestPerformed", - "rdfs:subClassOf": [ + "@id": "bts:Dehydration" + }, { - "@id": "bts:BreastCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:DelayedOrgasm" + }, { - "@id": "bts:Oncotype" + "@id": "bts:DelayedPuberty" }, { - "@id": "bts:MammaPrint" + "@id": "bts:Delirium" }, { - "@id": "bts:Other" + "@id": "bts:Delusions" }, { - "@id": "bts:Datanotavailable" + "@id": "bts:DentalCaries" }, { - "@id": "bts:Unknown" + "@id": "bts:DepressedLevelofConsciousness" }, { - "@id": "bts:Notperformed" - } - ], - "sms:displayName": "Breast Cancer Genomic Test Performed", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MammaprintRiskGroup", - "@type": "rdfs:Class", - "rdfs:comment": "Text term that represents the risk group for breast cancer as determined by assessment of the MammaPrint test.", - "rdfs:label": "MammaprintRiskGroup", - "rdfs:subClassOf": [ + "@id": "bts:Depression" + }, { - "@id": "bts:BreastCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - 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}, - "schema:rangeIncludes": [ + "@id": "bts:Epistaxis" + }, { - "@id": "bts:DCIS" + "@id": "bts:ErectileDysfunction" }, { - "@id": "bts:LCIS" + "@id": "bts:ErythemaMultiforme" }, { - "@id": "bts:Invasivebreastcancer(unrelatedtothecurrentcancer)" + "@id": "bts:Erythroderma" }, { - "@id": "bts:Other" + "@id": "bts:EsophagealAnastomoticLeak" }, { - "@id": "bts:Unknown" + "@id": "bts:EsophagealFistula" }, { - "@id": "bts:Datanotavailable" - } - ], - "sms:displayName": "Prior Invasive Breast Disease", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BreastCarcinomaERStatusPercentageValue", - "@type": "rdfs:Class", - "rdfs:comment": "A numerical quantity measured or assigned or computed which captures the estrogen receptor level measured in a participant with breast cancer", - "rdfs:label": "BreastCarcinomaERStatusPercentageValue", - "rdfs:subClassOf": [ + "@id": "bts:EsophagealHemorrhage" + }, { - "@id": "bts:BreastCancerTier3" - } - ], - "schema:isPartOf": { - 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} - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:PortalHypertension" + }, { - "@id": "bts:GastricFoveolar" + "@id": "bts:PortalVeinThrombosis" }, { - "@id": "bts:Intestinal" + "@id": "bts:PostnasalDrip" }, { - "@id": "bts:IntraductalTubopapillary" + "@id": "bts:PostoperativeHemorrhage" }, { - "@id": "bts:Pancreatobiliary" + "@id": "bts:PostoperativeThoracicProcedureComplication" }, { - "@id": "bts:Oncocytic" + "@id": "bts:PrecociousPuberty" }, { - "@id": "bts:Other" + "@id": "bts:Pregnancy" }, { - "@id": "bts:Unknown" + "@id": "bts:PuerperiumandPerinatalConditionsOther" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Pancreatic IPMN Pathology Epithelial Subtype", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PancreaticDuctFinalPathologyType", - "@type": "rdfs:Class", - "rdfs:comment": "The final pathology result of the pancreatic duct communication type.", - "rdfs:label": "PancreaticDuctFinalPathologyType", - "rdfs:subClassOf": [ + "@id": "bts:PrematureDelivery" + }, { - "@id": "bts:PancreaticCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:PrematureMenopause" + }, { - "@id": "bts:Side-Branch" + "@id": "bts:Presyncope" }, { - "@id": "bts:MainDuct" + "@id": "bts:Proctitis" }, { - "@id": "bts:Mixed" + "@id": "bts:ProductiveCough" }, { - "@id": "bts:NotSpecified" + "@id": "bts:ProlapseofIntestinalStoma" }, { - "@id": "bts:None" + "@id": "bts:ProlapseofUrostomy" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Pancreatic Duct Final Pathology Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MelanomaTier3", - "@type": "rdfs:Class", - "rdfs:comment": "Melanoma specific attributes in Clinical Data Tier 3", - "rdfs:label": "MelanomaTier3", - "rdfs:subClassOf": [ + "@id": "bts:ProstateInfection" + }, { - "@id": "bts:Patient" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Melanoma Tier 3", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "@id": "bts:ProstaticHemorrhage" + }, { - "@id": "bts:Component" + "@id": "bts:ProstaticObstruction" }, { - "@id": "bts:HTANParticipantID" + "@id": "bts:ProstaticPain" }, { - "@id": "bts:TimepointLabel" + "@id": "bts:Proteinuria" + }, + { + "@id": "bts:Pruritus" + }, + { + "@id": "bts:PsychiatricDisordersOther" }, { - "@id": "bts:StartDaysfromIndex" + "@id": "bts:Psychosis" }, { - "@id": "bts:StopDaysfromIndex" + "@id": "bts:PulmonaryEdema" }, { - "@id": "bts:CutaneousMelanomaTumorInfiltratingLymphocytes" + "@id": "bts:PulmonaryFibrosis" }, { - "@id": "bts:CutaneousMelanomaTumorRegressionRange" + "@id": "bts:PulmonaryFistula" }, { - "@id": "bts:MelanomaSpecimenClarkLevelValue" + "@id": "bts:PulmonaryHypertension" }, { - "@id": "bts:CutaneousMelanomaSurgicalMargins" + "@id": "bts:PulmonaryValveDisease" }, { - "@id": "bts:MelanomaLesionSize" + "@id": "bts:Purpura" }, { - "@id": "bts:HistoryofAtypicalNevi" + "@id": "bts:PyramidalTractSyndrome" }, { - 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"@id": "bts:MelanomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:RectalMucositis" + }, { - "@id": "bts:Absent" + "@id": "bts:RectalNecrosis" }, { - "@id": "bts:Brisk" + "@id": "bts:RectalObstruction" }, { - "@id": "bts:Nonbrisk" + "@id": "bts:RectalPain" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Cutaneous Melanoma Tumor Infiltrating Lymphocytes", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CutaneousMelanomaTumorRegressionRange", - "@type": "rdfs:Class", - "rdfs:comment": "Description of the degree to which tumor cells are replaced by lymphocytic inflammation with or without dermal melanophages and fibrosis._Range; the difference between the lowest and highest numerical values.", - "rdfs:label": "CutaneousMelanomaTumorRegressionRange", - "rdfs:subClassOf": [ + "@id": "bts:RectalPerforation" + }, { - "@id": "bts:MelanomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:RectalStenosis" + }, { - "@id": "bts:Absent" + "@id": "bts:RectalUlcer" }, { - "@id": "bts:Presentinvolving75%ormore" + "@id": "bts:RecurrentLaryngealNervePalsy" }, { - "@id": "bts:Presentinvolvinglessthan75%" + "@id": "bts:RenalandUrinaryDisordersOther" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Cutaneous Melanoma Tumor Regression Range", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MelanomaSpecimenClarkLevelValue", - "@type": "rdfs:Class", - "rdfs:comment": "Definition of the Clark level or depth of involvement of a melanoma in the skin or a specimen.", - "rdfs:label": "MelanomaSpecimenClarkLevelValue", - "rdfs:subClassOf": [ + "@id": "bts:RenalCalculi" + }, { - "@id": "bts:MelanomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:RenalColic" + }, { - "@id": "bts:I" + "@id": "bts:RenalHemorrhage" }, { - "@id": "bts:II" + "@id": "bts:ReproductiveSystemandBreastDisordersOther" }, { - "@id": "bts:III" + "@id": "bts:RespiratoryFailure" }, { - "@id": "bts:IV" + "@id": "bts:Respiratory" }, { - "@id": "bts:V" + "@id": "bts:ThoracicandMediastinalDisordersOther" }, { - "@id": "bts:NoSourceDocumentation" + "@id": "bts:Restlessness" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Melanoma Specimen Clark Level Value", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CutaneousMelanomaSurgicalMargins", - "@type": "rdfs:Class", - "rdfs:comment": "Text term to indicate presence of tumor at resection margins", - "rdfs:label": "CutaneousMelanomaSurgicalMargins", - "rdfs:subClassOf": [ + "@id": "bts:RestrictiveCardiomyopathy" + }, { - "@id": "bts:MelanomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:RetinalDetachment" + }, { - "@id": "bts:Positive" + "@id": "bts:RetinalTear" }, { - "@id": "bts:Negative" + "@id": "bts:RetinalVascularDisorder" }, { - "@id": "bts:Unknown" + "@id": "bts:RetinoicAcidSyndrome" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Cutaneous Melanoma Surgical Margins", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MelanomaLesionSize", - "@type": "rdfs:Class", - "rdfs:comment": "Diameter of lesion determined on skin examination (pre-bx), in mm", - "rdfs:label": "MelanomaLesionSize", - "rdfs:subClassOf": [ + "@id": "bts:Retinopathy" + }, { - "@id": "bts:MelanomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Melanoma Lesion Size", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HistoryofAtypicalNevi", - "@type": "rdfs:Class", - "rdfs:comment": "Patient has a history of atypical nevi", - "rdfs:label": "HistoryofAtypicalNevi", - "rdfs:subClassOf": [ + "@id": "bts:RetroperitonealHemorrhage" + }, { - "@id": "bts:MelanomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:ReversiblePosteriorLeukoencephalopathySyndrome" + }, { - "@id": "bts:Yes(morethan50)" + "@id": "bts:RhinitisInfective" }, { - "@id": "bts:Yes(lessthan50)" + "@id": "bts:RightVentricularDysfunction" }, { - "@id": "bts:No" + "@id": "bts:SalivaryDuctInflammation" }, { - "@id": "bts:Unknown" + "@id": "bts:SalivaryGlandFistula" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "History of Atypical Nevi", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FitzpatrickSkinTone", - "@type": "rdfs:Class", - "rdfs:comment": "The Fitzpatrick classification of skin phototype", - "rdfs:label": "FitzpatrickSkinTone", - "rdfs:subClassOf": [ + "@id": "bts:SalivaryGlandInfection" + }, { - "@id": "bts:MelanomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:ScalpPain" + }, { - "@id": "bts:I" + "@id": "bts:ScleralDisorder" }, { - "@id": "bts:II" + "@id": "bts:Scoliosis" }, { - "@id": "bts:III" + "@id": "bts:ScrotalInfection" }, { - "@id": "bts:IV" + "@id": "bts:ScrotalPain" }, { - "@id": "bts:V" + "@id": "bts:Seizure" }, { - "@id": "bts:VI" + "@id": "bts:Sepsis" }, { - "@id": "bts:Unknown" + "@id": "bts:Seroma" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Fitzpatrick Skin Tone", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HistoryofChronicUVExposure", - "@type": "rdfs:Class", - "rdfs:comment": "History of chronic UV exposure", - "rdfs:label": "HistoryofChronicUVExposure", - "rdfs:subClassOf": [ + "@id": "bts:SerumAmylaseIncreased" + }, { - "@id": "bts:MelanomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:SerumSickness" + }, { - "@id": "bts:Outdooroccupational" + "@id": "bts:SickSinusSyndrome" }, { - "@id": "bts:Outdoorrecreational" + "@id": "bts:SinusBradycardia" }, { - "@id": "bts:Therapeutic" + "@id": "bts:SinusDisorder" }, { - "@id": "bts:None" + "@id": "bts:SinusPain" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "History of Chronic UV Exposure", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HistoryofBlisteringSunburn", - "@type": "rdfs:Class", - "rdfs:comment": "Patient has history of blistering sunburn", - "rdfs:label": "HistoryofBlisteringSunburn", - "rdfs:subClassOf": [ + "@id": "bts:SinusTachycardia" + }, { - "@id": "bts:MelanomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Sinusitis" + }, { - "@id": "bts:Yes" + "@id": "bts:SkinandSubcutaneousTissueDisordersOther" }, { - "@id": "bts:No" + "@id": "bts:SkinAtrophy" }, { - "@id": "bts:Unknown" + "@id": "bts:SkinHyperpigmentation" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "History of Blistering Sunburn", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HistoryofTanningBedUse", - "@type": "rdfs:Class", - "rdfs:comment": "History of tanning bed use of the patient", - "rdfs:label": "HistoryofTanningBedUse", - "rdfs:subClassOf": [ + "@id": "bts:SkinHypopigmentation" + }, { - "@id": "bts:MelanomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:SkinInduration" + }, { - "@id": "bts:Never" + "@id": "bts:SkinInfection" }, { - "@id": "bts:Lessthan10times" + "@id": "bts:SkinUlceration" }, { - "@id": "bts:10-50times" + "@id": "bts:SleepApnea" }, { - "@id": "bts:50-100times" + "@id": "bts:SmallIntestinalAnastomoticLeak" }, { - "@id": "bts:Morethan100times" + "@id": "bts:SmallIntestinalMucositis" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "History of Tanning Bed Use", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ImmediateFamilyHistoryMelanoma", - "@type": "rdfs:Class", - "rdfs:comment": "Text that describes the age at which the family member was diagnosed with melanoma skin cancer in relationship to their 50th birthday.", - "rdfs:label": "ImmediateFamilyHistoryMelanoma", - "rdfs:subClassOf": [ + "@id": "bts:SmallIntestinalObstruction" + }, { - "@id": "bts:MelanomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:SmallIntestinalPerforation" + }, { - "@id": "bts:Beforeage50" + "@id": "bts:SmallIntestinalStenosis" }, { - "@id": "bts:Notbeforeage50" + "@id": "bts:SmallIntestineInfection" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Immediate Family History Melanoma", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MelanomaBiopsyResectionSites", - "@type": "rdfs:Class", - "rdfs:comment": "Biopsy resection sites specific to melanoma (not covered in Tiers 1 and 2)", - "rdfs:label": "MelanomaBiopsyResectionSites", - "rdfs:subClassOf": [ + "@id": "bts:SmallIntestineUlcer" + }, { - "@id": "bts:MelanomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Sneezing" + }, { - "@id": "bts:Skinofscalp" + "@id": "bts:SocialCircumstancesOther" }, { - "@id": "bts:Skinofeyelid" + "@id": "bts:SoftTissueInfection" }, { - "@id": "bts:Skinofnose" + "@id": "bts:SoftTissueNecrosisLowerLimb" }, { - "@id": "bts:Skinoflip" + "@id": "bts:SoftTissueNecrosisUpperLimb" }, { - "@id": "bts:Skinofear" + "@id": "bts:Somnolence" }, { - "@id": "bts:Skinofneck" + "@id": "bts:SoreThroat" }, { - "@id": "bts:Skinofotherpartsofface" + "@id": "bts:Spasticity" }, { - "@id": "bts:Skinofchest" + "@id": "bts:SpermaticCordAnastomoticLeak" }, { - "@id": "bts:Skinofback" + "@id": "bts:SpermaticCordHemorrhage" }, { - "@id": "bts:Skinofabdomen" + "@id": "bts:SpermaticCordObstruction" }, { - "@id": "bts:Skinoftrunk-other" + "@id": "bts:SpinalFracture" }, { - "@id": "bts:Skinofbreast" + "@id": "bts:SpleenDisorder" }, { - "@id": "bts:Skinofupperlimbandshoulder" + "@id": "bts:SplenicInfection" }, { - "@id": "bts:Skinofpalm" + "@id": "bts:StenosisofGastrointestinalStoma" }, { - "@id": "bts:Skinoflowerlimbandhip" + "@id": "bts:Stevens-JohnsonSyndrome" }, { - 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"@id": "bts:NestingMelanoma" + "@id": "bts:TesticularPain" }, { - "@id": "bts:PagetoidSpread" + "@id": "bts:ThromboembolicEvent" }, { - "@id": "bts:VascularProliferation" + "@id": "bts:ThromboticThrombocytopenicPurpura" }, { - "@id": "bts:Other" + "@id": "bts:Tinnitus" }, { - "@id": "bts:Unknown" + "@id": "bts:ToothDevelopmentDisorder" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Cutaneous Melanoma Additional Findings", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:DaystoBirth", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date from a person's date of birth represented as a calculated negative number of days. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoBirth", - "rdfs:subClassOf": [ + "@id": "bts:ToothDiscoloration" + }, { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Birth", - "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:CountryofResidence", - "@type": "rdfs:Class", - "rdfs:comment": "Country of Residence at enrollment", - "rdfs:label": "CountryofResidence", - "rdfs:subClassOf": [ + "@id": "bts:ToothInfection" + }, { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Toothache" + }, { - "@id": "bts:Afghanistan" + "@id": "bts:ToxicEpidermalNecrolysis" }, { - "@id": "bts:Albania" + "@id": "bts:TrachealFistula" }, { - "@id": "bts:Algeria" + "@id": "bts:TrachealHemorrhage" }, { - "@id": "bts:Andorra" + "@id": "bts:TrachealMucositis" }, { - "@id": "bts:Angola" + "@id": "bts:TrachealObstruction" }, { - "@id": "bts:Anguilla" + "@id": "bts:TrachealStenosis" }, { - "@id": "bts:AntiguaandBarbuda" + "@id": "bts:Tracheitis" }, { - "@id": "bts:Argentina" + "@id": "bts:TracheostomySiteBleeding" }, { - "@id": "bts:Armenia" + "@id": "bts:TransientIschemicAttacks" }, { - "@id": "bts:Aruba" + "@id": "bts:TreatmentRelatedSecondaryMalignancy" }, { - "@id": "bts:Australia" + "@id": "bts:Tremor" }, { - "@id": "bts:Austria" + "@id": "bts:TricuspidValveDisease" }, { - "@id": "bts:Azerbaijan" + "@id": "bts:TrigeminalNerveDisorder" }, { - "@id": "bts:Bahamas" + "@id": "bts:Trismus" }, { - "@id": "bts:Bahrain" + "@id": "bts:TumorLysisSyndrome" }, { - "@id": "bts:Bangladesh" + "@id": "bts:TumorPain" }, { - "@id": "bts:Barbados" + "@id": "bts:Typhlitis" }, { - "@id": "bts:Belarus" + "@id": "bts:UnequalLimbLength" }, { - "@id": "bts:Belgium" + "@id": "bts:UnintendedPregnancy" }, { - "@id": "bts:Belize" + "@id": "bts:UpperGastrointestinalHemorrhage" }, { - "@id": "bts:Benin" + "@id": "bts:UpperRespiratoryInfection" }, { - "@id": "bts:Bermuda" + "@id": "bts:UretericAnastomoticLeak" }, { - "@id": "bts:Bhutan" + "@id": "bts:UrethralAnastomoticLeak" }, { - "@id": "bts:Bolivia" + "@id": "bts:UrethralInfection" }, { - "@id": "bts:BosniaandHerzegovina" + "@id": "bts:UrinaryFistula" }, { - "@id": "bts:Botswana" + "@id": "bts:UrinaryFrequency" }, { - "@id": "bts:Brazil" + "@id": "bts:UrinaryIncontinence" }, { - "@id": "bts:Brunei" + "@id": "bts:UrinaryRetention" }, { - "@id": "bts:Bulgaria" + "@id": "bts:UrinaryTractInfection" }, { - "@id": "bts:BurkinaFaso" + "@id": "bts:UrinaryTractObstruction" }, { - "@id": "bts:Burundi" + "@id": "bts:UrinaryTractPain" }, { - "@id": "bts:Cambodia" + "@id": "bts:UrinaryUrgency" }, { - "@id": "bts:Cameroon" + "@id": "bts:UrineDiscoloration" }, { - "@id": "bts:Canada" + "@id": "bts:UrineOutputDecreased" }, { - "@id": "bts:CapeVerde" + "@id": "bts:UrostomyLeak" }, { - "@id": "bts:CaymanIslands" + "@id": "bts:UrostomyObstruction" }, { - "@id": "bts:CentralAfricanRepublic" + "@id": "bts:UrostomySiteBleeding" }, { - "@id": "bts:Chad" + "@id": "bts:UrostomyStenosis" }, { - "@id": "bts:Chile" + "@id": "bts:Urticaria" }, { - "@id": "bts:China" + "@id": "bts:UterineAnastomoticLeak" }, { - "@id": "bts:Colombia" + "@id": "bts:UterineFistula" }, { - "@id": "bts:Comoros" + "@id": "bts:UterineHemorrhage" }, { - "@id": "bts:Congo" + "@id": "bts:UterineInfection" }, { - "@id": "bts:CookIslands" + "@id": "bts:UterineObstruction" }, { - "@id": "bts:CostaRica" + "@id": "bts:UterinePain" }, { - "@id": "bts:Coted'Ivoire" + "@id": "bts:UterinePerforation" }, { - "@id": "bts:Croatia" + "@id": "bts:Uveitis" }, { - "@id": "bts:Cuba" + "@id": "bts:VaginalAnastomoticLeak" }, { - "@id": "bts:Curacao" + "@id": "bts:VaginalDischarge" }, { - "@id": "bts:Cyprus" + "@id": "bts:VaginalDryness" }, { - "@id": "bts:CzechRepublic(Czechia)" + "@id": "bts:VaginalFistula" }, { - "@id": "bts:DemocraticRepublicoftheCongo" + "@id": "bts:VaginalHemorrhage" }, { - "@id": "bts:Denmark" + "@id": "bts:VaginalInfection" }, { - "@id": "bts:Djibouti" + "@id": "bts:VaginalInflammation" }, { - "@id": "bts:Dominica" + "@id": "bts:VaginalObstruction" }, { - "@id": "bts:DominicanRepublic" + "@id": "bts:VaginalPain" }, { - "@id": "bts:Ecuador" + "@id": "bts:VaginalPerforation" }, { - "@id": "bts:Egypt" + "@id": "bts:VaginalStricture" }, { - "@id": "bts:ElSalvador" + "@id": "bts:Vaginismus" }, { - "@id": "bts:EquatorialGuinea" + "@id": "bts:VagusNerveDisorder" }, { - "@id": "bts:Eritrea" + "@id": "bts:VasDeferensAnastomoticLeak" }, { - "@id": "bts:Estonia" + "@id": "bts:VascularAccessComplication" }, { - "@id": "bts:Eswatini" + "@id": "bts:VascularDisordersOther" }, { - "@id": "bts:Ethiopia" + "@id": "bts:Vasculitis" }, { - "@id": "bts:FalklandIslands(Malvinas)" + "@id": "bts:VasovagalReaction" }, { - "@id": "bts:FaroeIslands" + "@id": "bts:VenousInjury" }, { - "@id": "bts:FederatedStatesofMicronesia" + "@id": "bts:VentricularArrhythmia" }, { - "@id": "bts:Fiji" + "@id": "bts:VentricularFibrillation" }, { - "@id": "bts:Finland" + "@id": "bts:VentricularTachycardia" }, { - "@id": "bts:France" + "@id": "bts:Vertigo" }, { - "@id": "bts:FrenchGuiana" + "@id": "bts:VestibularDisorder" }, { - "@id": "bts:FrenchPolynesia" + "@id": "bts:Virilization" }, { - "@id": "bts:Gabon" + "@id": "bts:VisceralArterialIschemia" }, { - "@id": "bts:Gambia" + "@id": "bts:VitalCapacityAbnormal" }, { - "@id": "bts:Georgia" + "@id": "bts:VitreousHemorrhage" }, { - "@id": "bts:Germany" + "@id": "bts:VoiceAlteration" }, { - "@id": "bts:Ghana" + "@id": "bts:Vomiting" }, { - "@id": "bts:Gibraltar" + "@id": "bts:VulvalInfection" }, { - "@id": "bts:Greece" + "@id": "bts:WateringEyes" }, { - "@id": "bts:Greenland" + "@id": "bts:WeightGain" }, { - "@id": "bts:Grenada" + "@id": "bts:WeightLoss" }, { - "@id": "bts:Guadeloupe" + "@id": "bts:Wheezing" }, { - "@id": "bts:Guam" + "@id": "bts:WhiteBloodCellDecreased" }, { - "@id": "bts:Guatemala" + "@id": "bts:Wolff-Parkinson-WhiteSyndrome" }, { - "@id": "bts:Guernsey" + "@id": "bts:WoundComplication" }, { - "@id": "bts:Guinea" + "@id": "bts:WoundDehiscence" }, { - "@id": "bts:Guinea-Bissau" + "@id": "bts:WoundInfection" }, { - "@id": "bts:Guyana" + "@id": "bts:WristFracture" + } + ], + "sms:displayName": "Adverse Event", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BarrettsEsophagusGobletCellsPresent", + "@type": "rdfs:Class", + "rdfs:comment": "Presence or absennce of Barretts esophagus goblet cells.", + "rdfs:label": "BarrettsEsophagusGobletCellsPresent", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" }, { - "@id": "bts:Haiti" + "@id": "bts:No" + } + ], + "sms:displayName": "Barretts Esophagus Goblet Cells Present", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BMI", + "@type": "rdfs:Class", + "rdfs:comment": "A calculated numerical quantity that represents an individual's weight to height ratio.", + "rdfs:label": "BMI", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "BMI", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CauseofResponse", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the suspected cause or reason for the patient disease response.", + "rdfs:label": "CauseofResponse", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Cause of Response", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Comorbidity", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe a comorbidity disease, which coexists with the patient's malignant disease.", + "rdfs:label": "Comorbidity", + "rdfs:subClassOf": [ + { + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:AcuteRenalFailure" }, { - "@id": "bts:HolySee" + "@id": "bts:Adenocarcinoma" }, { - "@id": "bts:Honduras" + "@id": "bts:AdrenocorticalInsufficiency" }, { - "@id": "bts:HongKong" + "@id": "bts:AdenomatousPolyposisColi" }, { - "@id": "bts:Hungary" + "@id": "bts:Allergies" }, { - "@id": "bts:Iceland" + "@id": "bts:Alpha-1Antitrypsin" }, { - "@id": "bts:India" + "@id": "bts:Anemia" }, { - "@id": "bts:Indonesia" + "@id": "bts:Anxiety" }, { - "@id": "bts:Iran" + "@id": "bts:Arrhythmia" }, { - "@id": "bts:Iraq" + "@id": "bts:Arthritis" }, { - "@id": "bts:Ireland" + "@id": "bts:Asthma" }, { - "@id": "bts:IsleofMan" + "@id": "bts:AtrialFibrillation" }, { - "@id": "bts:Israel" + "@id": "bts:AvascularNecrosis" }, { - "@id": "bts:Italy" + "@id": "bts:Barrett'sEsophagus" }, { - "@id": "bts:Jamaica" + "@id": "bts:BasalCellCarcinoma" }, { - "@id": "bts:Japan" + "@id": "bts:Beckwith-Wiedemann" }, { - "@id": "bts:Jersey" + "@id": "bts:Behcet'sDisease" }, { - "@id": "bts:Jordan" + "@id": "bts:BiliaryDisorder" }, { - "@id": "bts:Kazakhstan" + "@id": "bts:BloodClots" }, { - "@id": "bts:Kenya" + "@id": "bts:BoneFracture(s)" }, { - "@id": "bts:Kiribati" + "@id": "bts:Bronchitis" }, { - "@id": "bts:Kosovo" + "@id": "bts:CalciumChannelBlockers" }, { - "@id": "bts:Kuwait" + "@id": "bts:Cancer" }, { - "@id": "bts:Kyrgyzstan" + "@id": "bts:Cataracts" }, { - "@id": "bts:Laos" + "@id": "bts:CeliacDisease" }, { - "@id": "bts:Latvia" + "@id": "bts:Cirrhosis" }, { - "@id": "bts:Lebanon" + "@id": "bts:UnknownEtiology" }, { - "@id": "bts:Lesotho" + "@id": "bts:CerebrovascularDisease" }, { - "@id": "bts:Liberia" + "@id": "bts:Cholelithiasis" }, { - "@id": "bts:Libya" + "@id": "bts:ChronicRenalFailure" }, { - "@id": "bts:Liechtenstein" + "@id": "bts:ColonPolyps" }, { - "@id": "bts:Lithuania" + "@id": "bts:CommonVariableImmunodeficiency" }, { - "@id": "bts:Luxembourg" + "@id": "bts:CongestiveHeartFailure(CHF)" }, { - "@id": "bts:Macau" + "@id": "bts:ConnectiveTissueDisorder" }, { - "@id": "bts:Madagascar" + "@id": "bts:COPD" }, { - "@id": "bts:Malawi" + "@id": "bts:CoronaryArteryDisease" }, { - "@id": "bts:Malaysia" + "@id": "bts:Crohn'sDisease" }, { - "@id": "bts:Maldives" + "@id": "bts:CryptogenicOrganizingPneumonia" }, { - "@id": "bts:Mali" + "@id": "bts:DeepVeinThrombosis/Thromboembolism" }, { - "@id": "bts:Malta" + "@id": "bts:Denys-DrashSyndrome" }, { - "@id": "bts:MarshallIslands" + "@id": "bts:Depression" }, { - "@id": "bts:Martinique" + "@id": "bts:Diabetes" }, { - "@id": "bts:Mauritania" + "@id": "bts:TypeII" }, { - "@id": "bts:Mauritius" + "@id": "bts:DiabeticNeuropathy" }, { - "@id": "bts:Mayotte" + "@id": "bts:DietControlledDiabetes" }, { - "@id": "bts:Mexico" + "@id": "bts:Diverticulitis" }, { - "@id": "bts:Moldova" + "@id": "bts:DVT/PE" }, { - "@id": "bts:Monaco" + "@id": "bts:Dyslipidemia" }, { - "@id": "bts:Mongolia" + "@id": "bts:Epilepsy" }, { - "@id": "bts:Montenegro" + "@id": "bts:Eczema" }, { - "@id": "bts:Montserrat" + "@id": "bts:Epstein-BarrVirus" }, { - "@id": "bts:Morocco" + "@id": "bts:FamilialAdenomatousPolyposis" }, { - "@id": "bts:Mozambique" + "@id": "bts:FanconiAnemia" }, { - "@id": "bts:Myanmar" + "@id": "bts:Fibrosis" }, { - "@id": "bts:Namibia" + "@id": "bts:GastroesophagealRefluxDisease" }, { - "@id": "bts:Nauru" + "@id": "bts:GERD" }, { - "@id": "bts:Nepal" + "@id": "bts:Glaucoma" }, { - "@id": "bts:Netherlands" + "@id": "bts:GlycogenStorageDisease" }, { - "@id": "bts:NewCaledonia" + "@id": "bts:Gout" }, { - "@id": "bts:NewZealand" + "@id": "bts:GonadalDysfunction" }, { - "@id": "bts:Nicaragua" + "@id": "bts:GorlinSyndrome" }, { - "@id": "bts:Niger" + "@id": "bts:H.pyloriInfection" }, { - "@id": "bts:Nigeria" + "@id": "bts:Hashimoto'sThyroiditis" }, { - "@id": "bts:Niue" + "@id": "bts:Headache" }, { - "@id": "bts:NorthKorea" + "@id": "bts:HeartDisease" }, { - "@id": "bts:NorthMacedonia" + "@id": "bts:Hemihypertrophy" }, { - "@id": "bts:NorthernMarianaIslands" + "@id": "bts:HemorrhagicCystitis" }, { - "@id": "bts:Norway" + "@id": "bts:Hepatitis" }, { - "@id": "bts:Oman" + "@id": "bts:HepatitisAInfection" }, { - "@id": "bts:Pakistan" + "@id": "bts:HepatitisBInfection" }, { - "@id": "bts:Palau" + "@id": "bts:HepatitisCInfection" }, { - "@id": "bts:Panama" + "@id": "bts:ChronicHepatitis" }, { - "@id": "bts:PapuaNewGuinea" + "@id": "bts:HereditaryNon-polyposisColonCancer" }, { - "@id": "bts:Paraguay" + "@id": "bts:Herpes" }, { - "@id": "bts:Peru" + "@id": "bts:HighGradeLiverDysplasticNodule" }, { - "@id": "bts:Philippines" + "@id": "bts:HIV/AIDS" }, { - "@id": "bts:Poland" + "@id": "bts:HumanPapillomavirusInfection" }, { - "@id": "bts:Portugal" + "@id": "bts:HUS/TTP" }, { - "@id": "bts:PuertoRico" + "@id": "bts:Hypercholesterolemia" }, { - "@id": "bts:Qatar" + "@id": "bts:Hypercalcemia" }, { - "@id": "bts:Reunion" + "@id": "bts:Hyperglycemia" }, { - "@id": "bts:Romania" + "@id": "bts:Hyperlipidemia" }, { - "@id": "bts:Russia" + "@id": "bts:Hypertension" }, { - "@id": "bts:Rwanda" + "@id": "bts:Hypospadias" }, { - "@id": "bts:SaintHelenaAscensionandTristandaCunha" + "@id": "bts:Hypothyroidism" }, { - "@id": "bts:SaintKittsandNevis" + "@id": "bts:InflammatoryBowelDisease" }, { - "@id": "bts:SaintLucia" + "@id": "bts:InsulinControlledDiabetes" }, { - "@id": "bts:SaintPierreandMiquelon" + "@id": "bts:InterstitialPneumontisorARDS" }, { - "@id": "bts:SaintVincentandtheGrenadines" + "@id": "bts:IntraductalPapillaryMucinousNeoplasm" }, { - "@id": "bts:Samoa" + "@id": "bts:IronOverload" }, { - "@id": "bts:SanMarino" + "@id": "bts:IschemicHeartDisease" }, { - "@id": "bts:SaoTomeandPrincipe" + "@id": "bts:ITP" }, { - "@id": "bts:SaudiArabia" + "@id": "bts:JointReplacement" }, { - "@id": "bts:Senegal" + "@id": "bts:KidneyDisease" }, { - "@id": "bts:Serbia" + "@id": "bts:LiverCirrhosis(LiverDisease)" }, { - "@id": "bts:Seychelles" + "@id": "bts:LiverToxicity(Non-Infectious)" }, { - "@id": "bts:SierraLeone" + "@id": "bts:Li-FraumeniSyndrome" }, { - "@id": "bts:Singapore" + "@id": "bts:LowGradeLiverDysplasticNodule" }, { - "@id": "bts:Slovakia" + "@id": "bts:Lupus" }, { - "@id": "bts:Slovenia" + "@id": "bts:LynchSyndrome" }, { - "@id": "bts:SolomonIslands" + "@id": "bts:MAI" }, { - "@id": "bts:Somalia" + "@id": "bts:MyastheniaGravis" }, { - "@id": "bts:SouthAfrica" + "@id": "bts:MyocardialInfarction" }, { - "@id": "bts:SouthKorea" + "@id": "bts:NeuroendocrineTumor" }, { - "@id": "bts:SouthSudan" + "@id": "bts:NonalcoholicSteatohepatitis" }, { - "@id": "bts:Spain" + "@id": "bts:Obesity" }, { - "@id": "bts:SriLanka" + "@id": "bts:Organtransplant(site)" }, { - "@id": "bts:StateofPalestine" + "@id": "bts:Osteoarthritis" }, { - "@id": "bts:Sudan" + "@id": "bts:OsteoporosisorOsteopenia" }, { - "@id": "bts:Suriname" + "@id": "bts:Other" }, { - "@id": "bts:Svalbard&JanMayenIslands" + "@id": "bts:OtherCancerWithin5Years" }, { - "@id": "bts:Sweden" + "@id": "bts:OtherNonmalignantSystemicDisease" }, { - "@id": "bts:Switzerland" + "@id": "bts:OtherPulmonaryComplications" }, { - "@id": "bts:Syria" + "@id": "bts:Pancreatitis" }, { - "@id": "bts:Taiwan" + "@id": "bts:Pain(Various)" }, { - "@id": "bts:Tajikistan" + "@id": "bts:PepticUlcer(Ulcer)" }, { - "@id": "bts:Tanzania" + "@id": "bts:PeripheralNeuropathy" }, { - "@id": "bts:Thailand" + "@id": "bts:PeripheralVascularDisease" }, { - "@id": "bts:Timor-Leste" + "@id": "bts:Peutz-JeghersDisease" }, { - "@id": "bts:Togo" + "@id": "bts:PregnancyinPatientorPartner" }, { - "@id": "bts:Tokelau" + "@id": "bts:PrimarySclerosingCholangitis" }, { - "@id": "bts:Tonga" + "@id": "bts:Psoriasis" }, { - "@id": "bts:TrinidadandTobago" + "@id": "bts:PulmonaryFibrosis" }, { - "@id": "bts:Tunisia" + "@id": "bts:PulmonaryHemorrhage" }, { - "@id": "bts:Turkey" + "@id": "bts:RenalFailure(RequiringDialysis)" }, { - "@id": "bts:Turkmenistan" + "@id": "bts:RenalDialysis" }, { - "@id": "bts:Tuvalu" + "@id": "bts:RenalInsufficiency" }, { - "@id": "bts:Uganda" + "@id": "bts:RheumatologicDisease" }, { - "@id": "bts:Ukraine" + "@id": "bts:RheumatoidArthritis" }, { - "@id": "bts:UnitedArabEmirates" + "@id": "bts:Rubinstein-TaybiSyndrome" }, { - "@id": "bts:UnitedKingdom" + "@id": "bts:Sarcoidosis" }, { - "@id": "bts:UnitedStates" + "@id": "bts:Seizure" }, { - "@id": "bts:Uruguay" + "@id": "bts:Sleepapnea" }, { - "@id": "bts:Uzbekistan" + "@id": "bts:Smoking" }, { - "@id": "bts:Vanuatu" + "@id": "bts:Steatosis" }, { - "@id": "bts:Venezuela" + "@id": "bts:Stroke" }, { - "@id": "bts:Vietnam" + "@id": "bts:TransientIschemicAttack" }, { - "@id": "bts:VirginIslandsBritish" + "@id": "bts:Tuberculosis" }, { - "@id": "bts:VirginIslandsU.S." + "@id": "bts:TurcotSyndrome" }, { - "@id": "bts:WallisandFutuna" + "@id": "bts:Tyrosinemia" }, { - "@id": "bts:WesternSahara" + "@id": "bts:UlcerativeColitis" }, { - "@id": "bts:Yemen" + "@id": "bts:WagrSyndrome" }, { - "@id": "bts:Zambia" + "@id": "bts:Unknown" }, { - "@id": "bts:Zimbabwe" + "@id": "bts:NotReported" } ], - "sms:displayName": "Country of Residence", + "sms:displayName": "Comorbidity", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AgeIsObfuscated", + "@id": "bts:ComorbidityMethodofDiagnosis", "@type": "rdfs:Class", - "rdfs:comment": "The age of the patient has been modified for compliance reasons. The actual age differs from what is reported. Other date intervals for this patient may also be modified.", - "rdfs:label": "AgeIsObfuscated", + "rdfs:comment": "The text term used to describe the method used to diagnose the patient's comorbidity disease.", + "rdfs:label": "ComorbidityMethodofDiagnosis", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -19606,58 +23424,71 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:True" + "@id": "bts:Histology" }, { - "@id": "bts:False" + "@id": "bts:Pathology" + }, + { + "@id": "bts:Radiology" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Age Is Obfuscated", + "sms:displayName": "Comorbidity Method of Diagnosis", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:YearOfBirth", + "@id": "bts:DaystoAdverseEvent", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the calendar year in which an individual was born.", - "rdfs:label": "YearOfBirth", + "rdfs:comment": "Number of days between the date used for index and the date of the patient's adverse event. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoAdverseEvent", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Year Of Birth", + "sms:displayName": "Days to Adverse Event", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:OccupationDurationYears", + "@id": "bts:DaystoComorbidity", "@type": "rdfs:Class", - "rdfs:comment": "The number of years a patient worked in a specific occupation.", - "rdfs:label": "OccupationDurationYears", + "rdfs:comment": "Number of days between the date used for index and the date the patient was diagnosed with a comorbidity. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoComorbidity", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Occupation Duration Years", + "sms:displayName": "Days to Comorbidity", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:PrematureAtBirth", + "@id": "bts:DiabetesTreatmentType", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was premature (less than 37 weeks gestation) at birth.", - "rdfs:label": "PrematureAtBirth", + "rdfs:comment": "Text term used to describe the types of treatment used to manage diabetes.", + "rdfs:label": "DiabetesTreatmentType", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -19665,10 +23496,31 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Alpha-GlucosidaseInhibitor" }, { - "@id": "bts:No" + "@id": "bts:Biguanide" + }, + { + "@id": "bts:Diet" + }, + { + "@id": "bts:InjectedInsulin" + }, + { + "@id": "bts:Insulin" + }, + { + "@id": "bts:OralHypoglycemic" + }, + { + "@id": "bts:Sulfonylurea" + }, + { + "@id": "bts:Thiazolidinedione" + }, + { + "@id": "bts:Other" }, { "@id": "bts:Unknown" @@ -19677,35 +23529,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Premature At Birth", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:WeeksGestationatBirth", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the number of weeks starting from the approximate date of the biological mother's last menstrual period and ending with the birth of the patient.", - "rdfs:label": "WeeksGestationatBirth", - "rdfs:subClassOf": [ - { - "@id": "bts:Demographics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Weeks Gestation at Birth", + "sms:displayName": "Diabetes Treatment Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RelativewithCancerHistory", + "@id": "bts:DiseaseResponse", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether any of the patient's relatives have a history of cancer.", - "rdfs:label": "RelativewithCancerHistory", + "rdfs:comment": "Code assigned to describe the patient's response or outcome to the disease.", + "rdfs:label": "DiseaseResponse", "rdfs:subClassOf": [ { - "@id": "bts:FamilyHistory" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -19713,10 +23548,97 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes-CancerHistoryRelative" + "@id": "bts:AJ-AdjuvantTherapy" }, { - "@id": "bts:None" + "@id": "bts:BED-BiochemicalEvidenceofDisease" + }, + { + "@id": "bts:CPD-ClinicalProgression" + }, + { + "@id": "bts:CR-CompleteResponse" + }, + { + "@id": "bts:CRU-CompleteResponseUnconfirmed" + }, + { + "@id": "bts:DU-DiseaseUnchanged" + }, + { + "@id": "bts:IMR-Immunoresponse" + }, + { + "@id": "bts:IPD-Immunoprogression" + }, + { + "@id": "bts:MR-Minimal/Marginalresponse" + }, + { + "@id": "bts:MX-MixedResponse" + }, + { + "@id": "bts:Non-CR/Non-PD-Non-CR/Non-PD" + }, + { + "@id": "bts:NPB-NoPalliativeBenefit" + }, + { + "@id": "bts:NR-NoResponse" + }, + { + "@id": "bts:PA-PalliativeTherapy" + }, + { + "@id": "bts:PB-PalliativeBenefit" + }, + { + "@id": "bts:PD-ProgressiveDisease" + }, + { + "@id": "bts:PDM-PersistentDistantMetastasis" + }, + { + "@id": "bts:PLD-PersistentLocoregionalDisease" + }, + { + "@id": "bts:PPD-Pseudoprogression" + }, + { + "@id": "bts:PR-PartialResponse" + }, + { + "@id": "bts:PSR-Pseudoresponse" + }, + { + "@id": "bts:RD-ResponsiveDisease" + }, + { + "@id": "bts:RP-Response" + }, + { + "@id": "bts:RPD-RadiographicProgressiveDisease" + }, + { + "@id": "bts:SCR-StringentCompleteResponse" + }, + { + "@id": "bts:SD-StableDisease" + }, + { + "@id": "bts:SPD-SurgicalProgression" + }, + { + "@id": "bts:TE-TooEarly" + }, + { + "@id": "bts:TF-TumorFree" + }, + { + "@id": "bts:VGPR-VeryGoodPartialResponse" + }, + { + "@id": "bts:WT-WithTumor" }, { "@id": "bts:Unknown" @@ -19725,46 +23647,35 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Relative with Cancer History", + "sms:displayName": "Disease Response", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SmokingExposure", + "@id": "bts:DLCORefPredictivePercent", "@type": "rdfs:Class", - "rdfs:comment": "Indicate if individual has smoking exposure", - "rdfs:label": "SmokingExposure", + "rdfs:comment": "The value, as a percentage of predicted lung volume, measuring the amount of carbon monoxide detected in a patient's lungs.", + "rdfs:label": "DLCORefPredictivePercent", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes-SmokingExposure" - }, - { - "@id": "bts:No-SmokingExposure" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Smoking Exposure", - "sms:required": "sms:true", + "sms:displayName": "DLCO Ref Predictive Percent", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AlcoholExposure", + "@id": "bts:ECOGPerformanceStatus", "@type": "rdfs:Class", - "rdfs:comment": "Indicate if individual has alcohol exposure", - "rdfs:label": "AlcoholExposure", + "rdfs:comment": "The ECOG functional performance status of the patient/participant.", + "rdfs:label": "ECOGPerformanceStatus", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -19772,38 +23683,40 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes-AlcoholExposure" + "@id": "bts:\"0\"" }, { - "@id": "bts:No-AlcoholExposure" + "@id": "bts:\"1\"" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Alcohol Exposure", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:AsbestosExposure", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was exposed to asbestos.", - "rdfs:label": "AsbestosExposure", - "rdfs:subClassOf": [ + "@id": "bts:\"2\"" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:\"3\"" + }, { - "@id": "bts:Yes" + "@id": "bts:\"4\"" }, { - "@id": "bts:No" + "@id": "bts:\"5\"" + }, + { + "@id": "bts:\"0.0\"" + }, + { + "@id": "bts:\"1.0\"" + }, + { + "@id": "bts:\"2.0\"" + }, + { + "@id": "bts:\"3.0\"" + }, + { + "@id": "bts:\"4.0\"" + }, + { + "@id": "bts:\"5.0\"" }, { "@id": "bts:Unknown" @@ -19812,105 +23725,103 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Asbestos Exposure", + "sms:displayName": "ECOG Performance Status", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CoalDustExposure", + "@id": "bts:FEV1FVCPostBronchPercent", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposed to fine powder derived by the crushing of coal.", - "rdfs:label": "CoalDustExposure", + "rdfs:comment": "Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) post-bronchodilator.", + "rdfs:label": "FEV1FVCPostBronchPercent", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Coal Dust Exposure", + "sms:displayName": "FEV1 FVC Post Bronch Percent", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:EnvironmentalTobaccoSmokeExposure", + "@id": "bts:FEV1FVCPreBronchPercent", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposed to smoke that is emitted from burning tobacco, including cigarettes, pipes, and cigars. This includes tobacco smoke exhaled by smokers.", - "rdfs:label": "EnvironmentalTobaccoSmokeExposure", + "rdfs:comment": "Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) pre-bronchodilator.", + "rdfs:label": "FEV1FVCPreBronchPercent", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, + "sms:displayName": "FEV 1 FVC Pre Bronch Percent", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:FEV1RefPostBronchPercent", + "@type": "rdfs:Class", + "rdfs:comment": "The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second post-bronchodilator.", + "rdfs:label": "FEV1RefPostBronchPercent", + "rdfs:subClassOf": [ { - "@id": "bts:Unknown" + "@id": "bts:FollowUp" } ], - "sms:displayName": "Environmental Tobacco Smoke Exposure", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "FEV1 Ref Post Bronch Percent", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RadonExposure", + "@id": "bts:FEV1RefPreBronchPercent", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was exposed to radon.", - "rdfs:label": "RadonExposure", + "rdfs:comment": "The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second pre-bronchodilator.", + "rdfs:label": "FEV1RefPreBronchPercent", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, + "sms:displayName": "FEV1 Ref Pre Bronch Percent", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Height", + "@type": "rdfs:Class", + "rdfs:comment": "The height of the patient in centimeters.", + "rdfs:label": "Height", + "rdfs:subClassOf": [ { - "@id": "bts:NotReported" + "@id": "bts:FollowUp" } ], - "sms:displayName": "Radon Exposure", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Height", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RespirableCrystallineSilicaExposure", + "@id": "bts:HepatitisSustainedVirologicalResponse", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposured to respirable crystalline silica, a widespread, naturally occurring, crystalline metal oxide that consists of different forms including quartz, cristobalite, tridymite, tripoli, ganister, chert and novaculite.", - "rdfs:label": "RespirableCrystallineSilicaExposure", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.", + "rdfs:label": "HepatitisSustainedVirologicalResponse", "rdfs:subClassOf": [ { - "@id": "bts:Exposure" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { @@ -19925,17 +23836,20 @@ }, { "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Respirable Crystalline Silica Exposure", + "sms:displayName": "Hepatitis Sustained Virological Response", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AdverseEvent", + "@id": "bts:HPVPositiveType", "@type": "rdfs:Class", - "rdfs:comment": "Text that represents the Common Terminology Criteria for Adverse Events low level term name for an adverse event.", - "rdfs:label": "AdverseEvent", + "rdfs:comment": "Text classification to represent the strain or type of human papillomavirus identified in an individual.", + "rdfs:label": "HPVPositiveType", "rdfs:subClassOf": [ { "@id": "bts:FollowUp" @@ -19946,2403 +23860,3263 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:AbdominalDistension" - }, - { - "@id": "bts:AbdominalInfection" - }, - { - "@id": "bts:AbdominalPain" - }, - { - "@id": "bts:AbdominalSoftTissueNecrosis" - }, - { - "@id": "bts:AbducensNerveDisorder" - }, - { - "@id": "bts:AccessoryNerveDisorder" - }, - { - "@id": "bts:Acidosis" - }, - { - "@id": "bts:AcousticNerveDisorderNOS" - }, - { - "@id": "bts:ActivatedPartialThromboplastinTimeProlonged" - }, - { - "@id": "bts:AcuteCoronarySyndrome" - }, - { - "@id": "bts:AcuteKidneyInjury" - }, - { - "@id": "bts:AdrenalInsufficiency" - }, - { - "@id": "bts:AdultRespiratoryDistressSyndrome" - }, - { - "@id": "bts:Agitation" - }, - { - "@id": "bts:Akathisia" - }, - { - "@id": "bts:AlanineAminotransferaseIncreased" - }, - { - "@id": "bts:AlcoholIntolerance" - }, - { - "@id": "bts:AlkalinePhosphataseIncreased" - }, - { - "@id": "bts:Alkalosis" - }, - { - "@id": "bts:AllergicReaction" - }, - { - "@id": "bts:AllergicRhinitis" - }, - { - "@id": "bts:Alopecia" - }, - { - "@id": "bts:Amnesia" + "@id": "bts:\"16\"" }, { - "@id": "bts:AnalFistula" + "@id": "bts:\"18\"" }, { - "@id": "bts:AnalHemorrhage" + "@id": "bts:\"26\"" }, { - "@id": "bts:AnalMucositis" + "@id": "bts:\"31\"" }, { - "@id": "bts:AnalNecrosis" + "@id": "bts:\"33\"" }, { - "@id": "bts:AnalPain" + "@id": "bts:\"35\"" }, { - "@id": "bts:AnalStenosis" + "@id": "bts:\"39\"" }, { - "@id": "bts:AnalUlcer" + "@id": "bts:\"45\"" }, { - "@id": "bts:Anaphylaxis" + "@id": "bts:\"51\"" }, { - "@id": "bts:Anemia" + "@id": "bts:\"52\"" }, { - "@id": "bts:AnkleFracture" + "@id": "bts:\"53\"" }, { - "@id": "bts:AnorectalInfection" + "@id": "bts:\"56\"" }, { - "@id": "bts:Anorexia" + "@id": "bts:\"58\"" }, { - "@id": "bts:Anorgasmia" + "@id": "bts:\"59\"" }, { - "@id": "bts:Anxiety" + "@id": "bts:\"63\"" }, { - "@id": "bts:AorticInjury" + "@id": "bts:\"66\"" }, { - "@id": "bts:AorticValveDisease" + "@id": "bts:\"68\"" }, { - "@id": "bts:Aphonia" + "@id": "bts:\"70\"" }, { - "@id": "bts:Apnea" + "@id": "bts:\"73\"" }, { - "@id": "bts:Appendicitis" + "@id": "bts:\"82\"" }, { - "@id": "bts:AppendicitisPerforated" + "@id": "bts:Other" }, { - "@id": "bts:Arachnoiditis" + "@id": "bts:Unknown" }, { - "@id": "bts:ArterialInjury" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "HPV Positive Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:KarnofskyPerformanceStatus", + "@type": "rdfs:Class", + "rdfs:comment": "Text term used to describe the classification used of the functional capabilities of a person.", + "rdfs:label": "KarnofskyPerformanceStatus", + "rdfs:subClassOf": [ { - "@id": "bts:ArteritisInfective" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Arthralgia" + "@id": "bts:\"0\"" }, { - "@id": "bts:Arthritis" + "@id": "bts:\"10\"" }, { - "@id": "bts:Ascites" + "@id": "bts:\"20\"" }, { - "@id": "bts:AspartateAminotransferaseIncreased" + "@id": "bts:\"30\"" }, { - "@id": "bts:Aspiration" + "@id": "bts:\"40\"" }, { - "@id": "bts:Asystole" + "@id": "bts:\"50\"" }, { - "@id": "bts:Ataxia" + "@id": "bts:\"60\"" }, { - "@id": "bts:Atelectasis" + "@id": "bts:\"70\"" }, { - "@id": "bts:AtrialFibrillation" + "@id": "bts:\"80\"" }, { - "@id": "bts:AtrialFlutter" + "@id": "bts:\"90\"" }, { - "@id": "bts:AtrioventricularBlockComplete" + "@id": "bts:\"100\"" }, { - "@id": "bts:AtrioventricularBlockFirstDegree" + "@id": "bts:Unknown" }, { - "@id": "bts:AutoimmuneDisorder" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Karnofsky Performance Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MenopauseStatus", + "@type": "rdfs:Class", + "rdfs:comment": "Text term used to describe the patient's menopause status.", + "rdfs:label": "MenopauseStatus", + "rdfs:subClassOf": [ { - "@id": "bts:AvascularNecrosis" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Azoospermia" + "@id": "bts:Premenopausal" }, { - "@id": "bts:BackPain" + "@id": "bts:Perimenopausal" }, { - "@id": "bts:BileDuctStenosis" + "@id": "bts:Postmenopausal" }, { - "@id": "bts:BiliaryAnastomoticLeak" + "@id": "bts:Unknown" }, { - "@id": "bts:BiliaryFistula" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Menopause Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PancreatitisOnsetYear", + "@type": "rdfs:Class", + "rdfs:comment": "Date of onset of pancreatitis.", + "rdfs:label": "PancreatitisOnsetYear", + "rdfs:subClassOf": [ { - "@id": "bts:BiliaryTractInfection" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Pancreatitis Onset Year", + "sms:required": "sms:false", + "sms:validationRules": [ + "num" + ] + }, + { + "@id": "bts:RefluxTreatmentType", + "@type": "rdfs:Class", + "rdfs:comment": "Text term used to describe the types of treatment used to manage gastroesophageal reflux disease (GERD).", + "rdfs:label": "RefluxTreatmentType", + "rdfs:subClassOf": [ { - "@id": "bts:BladderAnastomoticLeak" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:BladderInfection" + "@id": "bts:Antacids" }, { - "@id": "bts:BladderPerforation" + "@id": "bts:H2Blockers" }, { - "@id": "bts:BladderSpasm" + "@id": "bts:MedicallyTreated" }, { - "@id": "bts:Bloating" + "@id": "bts:NoTreatment" }, { - "@id": "bts:BloodandLymphaticSystemDisordersOther" + "@id": "bts:NotApplicable" }, { - "@id": "bts:BloodAntidiureticHormoneAbnormal" + "@id": "bts:NotReported" }, { - "@id": "bts:BloodBilirubinIncreased" + "@id": "bts:ProtonPumpInhibitors" }, { - "@id": "bts:BloodCorticotrophinDecreased" + "@id": "bts:SurgicallyTreated" }, { - "@id": "bts:BloodGonadotrophinAbnormal" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Reflux Treatment Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:RiskFactor", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe a risk factor the patient had at the time of or prior to their diagnosis.", + "rdfs:label": "RiskFactor", + "rdfs:subClassOf": [ { - "@id": "bts:BloodProlactinAbnormal" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:BlurredVision" + "@id": "bts:AlcoholConsumption" }, { - "@id": "bts:BodyOdor" + "@id": "bts:AlcoholicLiverDisease" }, { - "@id": "bts:BoneInfection" + "@id": "bts:AllergyAnimalNOS" }, { - "@id": "bts:BoneMarrowHypocellular" + "@id": "bts:AllergyAnt" }, { - "@id": "bts:BonePain" + "@id": "bts:AllergyBee" }, { - "@id": "bts:BrachialPlexopathy" + "@id": "bts:AllergyCat" }, { - "@id": "bts:BreastAtrophy" + "@id": "bts:AllergyDairyorLactose" }, { - "@id": "bts:BreastInfection" + "@id": "bts:AllergyDog" }, { - "@id": "bts:BreastPain" + "@id": "bts:AllergyEggs" }, { - "@id": "bts:BronchialFistula" + "@id": "bts:AllergyFoodNOS" }, { - "@id": "bts:BronchialInfection" + "@id": "bts:AllergyFruit" }, { - "@id": "bts:BronchialObstruction" + "@id": "bts:AllergyMeat" }, { - "@id": "bts:BronchialStricture" + "@id": "bts:AllergyMoldorDust" }, { - "@id": "bts:BronchopleuralFistula" + "@id": "bts:AllergyNuts" }, { - "@id": "bts:BronchopulmonaryHemorrhage" + "@id": "bts:AllergyProcessedFoods" }, { - "@id": "bts:Bronchospasm" + "@id": "bts:AllergySeafood" }, { - "@id": "bts:Bruising" + "@id": "bts:AllergyWasp" }, { - "@id": "bts:BullousDermatitis" + "@id": "bts:Alpha-1AntitrypsinDeficiency" }, { - "@id": "bts:Burn" + "@id": "bts:AutoimmuneAtrophicChronicGastritis" }, { - "@id": "bts:ButtockPain" + "@id": "bts:Barrett'sEsophagus" }, { - "@id": "bts:CapillaryLeakSyndrome" + "@id": "bts:Beckwith-Wiedemann" }, { - "@id": "bts:CarbonMonoxideDiffusingCapacityDecreased" + "@id": "bts:Behcet'sDisease" }, { - "@id": "bts:CardiacArrest" + "@id": "bts:Cancer" }, { - "@id": "bts:CardiacDisordersOther" + "@id": "bts:Cholelithiasis" }, { - "@id": "bts:CardiacTroponinIIncreased" + "@id": "bts:ChronicHepatitis" }, { - "@id": "bts:CardiacTroponinTIncreased" + "@id": "bts:Cirrhosis" }, { - "@id": "bts:Cataract" + "@id": "bts:ColonPolyps" }, { - "@id": "bts:CatheterRelatedInfection" + "@id": "bts:Commonvariableimmunedeficiency(CVID)" }, { - "@id": "bts:CD4LymphocytesDecreased" + "@id": "bts:Denys-DrashSyndrome" }, { - "@id": "bts:CecalHemorrhage" + "@id": "bts:DiabetesNOS" }, { - "@id": "bts:CecalInfection" + "@id": "bts:DiabetesTypeI" }, { - "@id": "bts:CentralNervousSystemNecrosis" + "@id": "bts:DiabetesTypeII" }, { - "@id": "bts:CerebrospinalFluidLeakage" + "@id": "bts:Diet" }, { - "@id": "bts:CervicitisInfection" + "@id": "bts:Diverticulitis" }, { - "@id": "bts:Cheilitis" + "@id": "bts:Endometriosis" }, { - "@id": "bts:ChestPainCardiac" + "@id": "bts:Endosalpingiosis" }, { - "@id": "bts:ChestWallPain" + "@id": "bts:Eczema" }, { - "@id": "bts:Chills" + "@id": "bts:Epstein-BarrVirus" }, { - "@id": "bts:Cholecystitis" + "@id": "bts:FamilialAdenomatousPolyposis" }, { - "@id": "bts:CholesterolHigh" + "@id": "bts:FanconiAnemia" }, { - "@id": "bts:ChronicKidneyDisease" + "@id": "bts:Fibrosis" }, { - "@id": "bts:Chylothorax" + "@id": "bts:GastricPolyp(s)" }, { - "@id": "bts:CognitiveDisturbance" + "@id": "bts:Gilbert'sSyndrome" }, { - "@id": "bts:Colitis" + "@id": "bts:GorlinSyndrome" }, { - "@id": "bts:ColonicFistula" + "@id": "bts:Hashimoto'sThyroiditis" }, { - "@id": "bts:ColonicHemorrhage" + "@id": "bts:HayFever" }, { - "@id": "bts:ColonicObstruction" + "@id": "bts:Headache" }, { - "@id": "bts:ColonicPerforation" + "@id": "bts:HelicobacterPylori-AssociatedGastritis" }, { - "@id": "bts:ColonicStenosis" + "@id": "bts:HematologicDisorderNOS" }, { - "@id": "bts:ColonicUlcer" + "@id": "bts:Hemihypertrophy" }, { - "@id": "bts:ConcentrationImpairment" + "@id": "bts:Hemochromatosis" }, { - "@id": "bts:ConductionDisorder" + "@id": "bts:HepaticEncephalopathy" }, { - "@id": "bts:Confusion" + "@id": "bts:HepatitisBInfection" }, { - "@id": "bts:Congenital" + "@id": "bts:HepatitisCInfection" }, { - "@id": "bts:FamilialandGeneticDisordersOther" + "@id": "bts:HepatitisNOS" }, { - "@id": "bts:Conjunctivitis" + "@id": "bts:HighGradeDysplasia" }, { - "@id": "bts:ConjunctivitisInfective" + "@id": "bts:HIV" }, { - "@id": "bts:Constipation" + "@id": "bts:HumanPapillomavirusInfection" }, { - "@id": "bts:ConstrictivePericarditis" + "@id": "bts:Hypospadias" }, { - "@id": "bts:CornealInfection" + "@id": "bts:IntestinalMetaplasia" }, { - "@id": "bts:CornealUlcer" + "@id": "bts:IronOverload" }, { - "@id": "bts:Cough" + "@id": "bts:Li-FraumeniSyndrome" }, { - "@id": "bts:CPKIncreased" + "@id": "bts:LowGradeDysplasia" }, { - "@id": "bts:CranialNerveInfection" + "@id": "bts:LymphocyticThyroiditis" }, { - "@id": "bts:CreatinineIncreased" + "@id": "bts:LynchSyndrome" }, { - "@id": "bts:Cushingoid" + "@id": "bts:MyastheniaGravis" }, { - "@id": "bts:CystitisNoninfective" + "@id": "bts:NonalcoholicFattyLiverDisease" }, { - "@id": "bts:CytokineReleaseSyndrome" + "@id": "bts:NonalcoholicSteatohepatitis" }, { - "@id": "bts:DeathNeonatal" + "@id": "bts:Obesity" }, { - "@id": "bts:DeathNOS" + "@id": "bts:OralContraceptives" }, { - "@id": "bts:Dehydration" + "@id": "bts:Pancreatitis" }, { - "@id": "bts:DelayedOrgasm" + "@id": "bts:ParasiticDiseaseofBiliaryTract" }, { - "@id": "bts:DelayedPuberty" + "@id": "bts:PrimarySclerosingCholangitis" }, { - "@id": "bts:Delirium" + "@id": "bts:RecurrentPyogenicCholangitis" }, { - "@id": "bts:Delusions" + "@id": "bts:RefluxDisease" }, { - "@id": "bts:DentalCaries" + "@id": "bts:RheumatoidArthritis" }, { - "@id": "bts:DepressedLevelofConsciousness" + "@id": "bts:Rubinstein-TaybiSyndrome" }, { - "@id": "bts:Depression" + "@id": "bts:Sarcoidosis" }, { - "@id": "bts:DermatitisRadiation" + "@id": "bts:Seizure" }, { - "@id": "bts:DeviceRelatedInfection" + "@id": "bts:SensoryChanges" }, { - "@id": "bts:Diarrhea" + "@id": "bts:Seroustubalintraepithelialcarcinoma(STIC)" }, { - "@id": "bts:DisseminatedIntravascularCoagulation" + "@id": "bts:Steatosis" }, { - "@id": "bts:Dizziness" + "@id": "bts:Tattoo" }, { - "@id": "bts:DryEye" + "@id": "bts:ThyroidNodularHyperplasia" }, { - "@id": "bts:DryMouth" + "@id": "bts:TobaccoNOS" }, { - "@id": "bts:DrySkin" + "@id": "bts:TobaccoSmokeless" }, { - "@id": "bts:DuodenalFistula" + "@id": "bts:TobaccoSmoking" }, { - "@id": "bts:DuodenalHemorrhage" + "@id": "bts:TurcotSyndrome" }, { - "@id": "bts:DuodenalInfection" + "@id": "bts:UndescendedTestis" }, { - "@id": "bts:DuodenalObstruction" + "@id": "bts:VisionChanges" }, { - "@id": "bts:DuodenalPerforation" + "@id": "bts:WagrSyndrome" }, { - "@id": "bts:DuodenalStenosis" + "@id": "bts:Unknown" }, { - "@id": "bts:DuodenalUlcer" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Risk Factor", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:RiskFactorTreatment", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.", + "rdfs:label": "RiskFactorTreatment", + "rdfs:subClassOf": [ { - "@id": "bts:Dysarthria" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Dysesthesia" + "@id": "bts:Yes" }, { - "@id": "bts:Dysgeusia" + "@id": "bts:No" }, { - "@id": "bts:Dysmenorrhea" + "@id": "bts:Unknown" }, { - "@id": "bts:Dyspareunia" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Risk Factor Treatment", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ViralHepatitisSerologies", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that describes the kind of serological laboratory test used to determine the patient's hepatitus status.", + "rdfs:label": "ViralHepatitisSerologies", + "rdfs:subClassOf": [ { - "@id": "bts:Dyspepsia" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Dysphagia" + "@id": "bts:HBVCoreAntibody" }, { - "@id": "bts:Dysphasia" + "@id": "bts:HBVDNA" }, { - "@id": "bts:Dyspnea" + "@id": "bts:HBVGenotype" }, { - "@id": "bts:EarandLabyrinthDisordersOther" + "@id": "bts:HBVSurfaceAntibody" }, { - "@id": "bts:EarPain" + "@id": "bts:HCVGenotype" }, { - "@id": "bts:EdemaCerebral" + "@id": "bts:HepatitisBSurfaceAntigen" }, { - "@id": "bts:EdemaFace" + "@id": "bts:HepatitisCAntibody" }, { - "@id": "bts:EdemaLimbs" + "@id": "bts:HepatitisCVirusRNA" }, { - "@id": "bts:EdemaTrunk" + "@id": "bts:Unknown" }, { - "@id": "bts:EjaculationDisorder" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Viral Hepatitis Serologies", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Weight", + "@type": "rdfs:Class", + "rdfs:comment": "The weight of the patient measured in kilograms.", + "rdfs:label": "Weight", + "rdfs:subClassOf": [ { - "@id": "bts:EjectionFractionDecreased" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Weight", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AdverseEventGrade", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.", + "rdfs:label": "AdverseEventGrade", + "rdfs:subClassOf": [ { - 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If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoImaging", + "rdfs:subClassOf": [ { - "@id": "bts:FacialNerveDisorder" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Days to Imaging", + "sms:required": "sms:false", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:EvidenceofRecurrenceType", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the type of evidence used to determine whether the patient's disease recurred", + "rdfs:label": "EvidenceofRecurrenceType", + "rdfs:subClassOf": [ { - "@id": "bts:FacialPain" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Fall" + "@id": "bts:BiopsywithHistologicConfirmation" }, { - "@id": "bts:FallopianTubeAnastomoticLeak" + "@id": "bts:ConvincingImageSource" }, { - "@id": "bts:FallopianTubeObstruction" - 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"@id": "bts:IntraoperativeReproductiveTractInjury" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofupperlimbandshoulder" }, { - "@id": "bts:IntraoperativeRespiratoryInjury" + "@id": "bts:ConnectivesubcutaneousandothersofttissuesNOS" }, { - "@id": "bts:IntraoperativeSkinInjury" + "@id": "bts:CorneaNOS" }, { - "@id": "bts:IntraoperativeSplenicInjury" + "@id": "bts:Corpusuteri" }, { - "@id": "bts:IntraoperativeUrinaryInjury" + "@id": "bts:Cortexofadrenalgland" }, { - "@id": "bts:IntraoperativeVenousInjury" + "@id": "bts:CranialnerveNOS" }, { - "@id": "bts:InvestigationsOther" + "@id": "bts:Craniopharyngealduct" }, { - "@id": "bts:IronOverload" + "@id": "bts:Descendedtestis" }, { - "@id": "bts:IrregularMenstruation" + "@id": "bts:Descendingcolon" }, { - "@id": "bts:Irritability" + "@id": "bts:Domeofbladder" }, { - "@id": "bts:IschemiaCerebrovascular" + "@id": "bts:DorsalsurfaceoftongueNOS" }, { - "@id": "bts:IVthNerveDisorder" + "@id": "bts:Duodenum" }, { - "@id": "bts:JejunalFistula" + "@id": "bts:Endocervix" }, { - 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"@id": "bts:LargeIntestinalAnastomoticLeak" + "@id": "bts:FloorofmouthNOS" }, { - "@id": "bts:LaryngealEdema" + "@id": "bts:Frontallobe" }, { - "@id": "bts:LaryngealFistula" + "@id": "bts:Frontalsinus" }, { - "@id": "bts:LaryngealHemorrhage" + "@id": "bts:Fundusofstomach" }, { - "@id": "bts:LaryngealInflammation" + "@id": "bts:Fundusuteri" }, { - "@id": "bts:LaryngealMucositis" + "@id": "bts:Gallbladder" }, { - "@id": "bts:LaryngealObstruction" + "@id": "bts:Gastricantrum" }, { - "@id": "bts:LaryngealStenosis" + "@id": "bts:GastrointestinaltractNOS" }, { - "@id": "bts:Laryngitis" + "@id": "bts:Glanspenis" }, { - "@id": "bts:LaryngopharyngealDysesthesia" + "@id": "bts:Glottis" }, { - "@id": "bts:Laryngospasm" + "@id": "bts:GreatercurvatureofstomachNOS" }, { - "@id": "bts:LeftVentricularSystolicDysfunction" + "@id": "bts:GumNOS" }, { - "@id": "bts:Lethargy" + "@id": "bts:Hardpalate" }, { - "@id": "bts:LeukemiaSecondarytoOncologyChemotherapy" + "@id": "bts:Headofpancreas" }, { - "@id": "bts:Leukocytosis" + "@id": "bts:HeadfaceorneckNOS" }, { - "@id": "bts:Leukoencephalopathy" + "@id": "bts:Heart" }, { - "@id": "bts:LibidoDecreased" + "@id": "bts:HematopoieticsystemNOS" }, { - "@id": "bts:LibidoIncreased" + "@id": "bts:Hepaticflexureofcolon" }, { - "@id": "bts:LipInfection" + "@id": "bts:Hypopharyngealaspectofaryepiglotticfold" }, { - "@id": "bts:LipPain" + "@id": "bts:HypopharynxNOS" }, { - "@id": "bts:LipaseIncreased" + "@id": "bts:Ileum" }, { - "@id": "bts:Lipohypertrophy" + "@id": "bts:Ill-definedsiteswithinrespiratorysystem" }, { - "@id": "bts:LocalizedEdema" + "@id": "bts:IntestinaltractNOS" }, { - "@id": "bts:Lordosis" + "@id": "bts:Intra-abdominallymphnodes" }, { - "@id": "bts:LowerGastrointestinalHemorrhage" + "@id": "bts:Intrahepaticbileduct" }, { - "@id": "bts:LungInfection" + "@id": "bts:Intrathoraciclymphnodes" }, { - "@id": "bts:LymphGlandInfection" + "@id": "bts:IsletsofLangerhans" }, { - "@id": "bts:LymphLeakage" + "@id": "bts:Isthmusuteri" }, { - "@id": "bts:LymphNodePain" + "@id": "bts:Jejunum" }, { - "@id": "bts:Lymphedema" + "@id": "bts:KidneyNOS" }, { - "@id": "bts:Lymphocele" + "@id": "bts:Labiummajus" }, { - "@id": "bts:LymphocyteCountDecreased" + "@id": "bts:Labiumminus" }, { - "@id": "bts:LymphocyteCountIncreased" + "@id": "bts:Lacrimalgland" }, { - "@id": "bts:Malabsorption" + "@id": "bts:Laryngealcartilage" }, { - "@id": "bts:Malaise" + "@id": "bts:LarynxNOS" }, { - "@id": "bts:Mania" + "@id": "bts:Lateralfloorofmouth" }, { - "@id": "bts:MediastinalHemorrhage" + "@id": "bts:Lateralwallofbladder" }, { - "@id": "bts:MediastinalInfection" + "@id": "bts:Lateralwallofnasopharynx" }, { - "@id": "bts:MemoryImpairment" + "@id": "bts:Lateralwalloforopharynx" }, { - "@id": "bts:Meningismus" + "@id": "bts:LessercurvatureofstomachNOS" }, { - "@id": "bts:Meningitis" + "@id": "bts:Lingualtonsil" }, { - "@id": "bts:Menopause" + "@id": "bts:LipNOS" }, { - "@id": "bts:Menorrhagia" + "@id": "bts:Liver" }, { - "@id": "bts:MetabolismandNutritionDisordersOther" + "@id": "bts:Longbonesoflowerlimbandassociatedjoints" }, { - "@id": "bts:MiddleEarInflammation" + "@id": "bts:Longbonesofupperlimbscapulaandassociatedjoints" }, { - "@id": "bts:MitralValveDisease" + "@id": "bts:Lowergum" }, { - "@id": "bts:Mobitz(Type)IIAtrioventricularBlock" + "@id": "bts:LowerlimbNOS" }, { - "@id": "bts:MobitzTypeI" + "@id": "bts:Lowerlobelung" }, { - "@id": "bts:MovementsInvoluntary" + "@id": "bts:Lowerthirdofesophagus" }, { - "@id": "bts:MucosalInfection" + "@id": "bts:Lower-innerquadrantofbreast" }, { - "@id": "bts:MucositisOral" + "@id": "bts:Lower-outerquadrantofbreast" }, { - "@id": "bts:Multi-OrganFailure" + "@id": "bts:LungNOS" }, { - "@id": "bts:MuscleWeaknessLeft-Sided" + "@id": "bts:LymphnodeNOS" }, { - "@id": "bts:MuscleWeaknessLowerLimb" + "@id": "bts:Lymphnodesofaxillaorarm" }, { - "@id": "bts:MuscleWeaknessRight-Sided" + "@id": "bts:Lymphnodesofheadfaceandneck" }, { - "@id": "bts:MuscleWeaknessTrunk" + "@id": "bts:Lymphnodesofinguinalregionorleg" }, { - "@id": "bts:MuscleWeaknessUpperLimb" + "@id": "bts:Lymphnodesofmultipleregions" }, { - "@id": "bts:MusculoskeletalandConnectiveTissueDisordersOther" + "@id": "bts:Mainbronchus" }, { - "@id": "bts:MusculoskeletalDeformity" + "@id": "bts:MajorsalivaryglandNOS" }, { - "@id": "bts:Myalgia" + "@id": "bts:MalegenitalorgansNOS" }, { - "@id": "bts:Myelitis" + "@id": "bts:Mandible" }, { - "@id": "bts:MyelodysplasticSyndrome" + "@id": "bts:Maxillarysinus" }, { - "@id": "bts:MyocardialInfarction" + "@id": "bts:Meckeldiverticulum" }, { - "@id": "bts:Myocarditis" + "@id": "bts:MediastinumNOS" }, { - "@id": "bts:Myositis" + "@id": "bts:Medullaofadrenalgland" }, { - "@id": "bts:NailDiscoloration" + "@id": "bts:MeningesNOS" }, { - "@id": "bts:NailInfection" + "@id": "bts:Middleear" }, { - "@id": "bts:NailLoss" + "@id": "bts:Middlelobelung" }, { - "@id": "bts:NailRidging" + "@id": "bts:Middlethirdofesophagus" }, { - "@id": "bts:NasalCongestion" + "@id": "bts:MouthNOS" }, { - "@id": "bts:Nausea" + "@id": "bts:MucosaoflipNOS" }, { - "@id": "bts:NeckEdema" + "@id": "bts:Mucosaoflowerlip" }, { - "@id": "bts:NeckPain" + "@id": "bts:Mucosaofupperlip" }, { - "@id": "bts:NeckSoftTissueNecrosis" + "@id": "bts:Myometrium" }, { - "@id": "bts:NeoplasmsBenign" + "@id": "bts:Nasalcavity" }, { - "@id": "bts:MalignantandUnspecified(InclCystsandPolyps)Other" + "@id": "bts:NasopharynxNOS" }, { - "@id": "bts:NervousSystemDisordersOther" + "@id": "bts:NervoussystemNOS" }, { - "@id": "bts:Neuralgia" + "@id": "bts:Nipple" }, { - "@id": "bts:NeutrophilCountDecreased" + "@id": "bts:Occipitallobe" }, { - "@id": "bts:NightBlindness" + "@id": "bts:Olfactorynerve" }, { - "@id": "bts:NippleDeformity" + "@id": "bts:Opticnerve" }, { - "@id": "bts:Non-CardiacChestPain" + "@id": "bts:OrbitNOS" }, { - "@id": "bts:Nystagmus" + "@id": "bts:OropharynxNOS" }, { - "@id": "bts:Obesity" + "@id": "bts:Otherill-definedsites" }, { - "@id": "bts:ObstructionGastric" + "@id": "bts:Otherspecifiedpartsoffemalegenitalorgans" }, { - "@id": "bts:OculomotorNerveDisorder" + "@id": "bts:Otherspecifiedpartsofmalegenitalorgans" }, { - "@id": "bts:OlfactoryNerveDisorder" + "@id": "bts:Otherspecifiedpartsofpancreas" }, { - "@id": "bts:Oligospermia" + "@id": "bts:Ovary" }, { - "@id": "bts:OpticNerveDisorder" + "@id": "bts:Overlappinglesionofaccessorysinuses" }, { - "@id": "bts:OralCavityFistula" + "@id": "bts:Overlappinglesionofbladder" }, { - "@id": "bts:OralDysesthesia" + "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilage" }, { - "@id": "bts:OralHemorrhage" + "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilageoflimbs" }, { - "@id": "bts:OralPain" + "@id": "bts:Overlappinglesionofbrain" }, { - "@id": "bts:OsteonecrosisofJaw" + "@id": "bts:Overlappinglesionofbrainandcentralnervoussystem" }, { - "@id": "bts:Osteoporosis" + "@id": "bts:Overlappinglesionofbreast" }, { - "@id": "bts:OtitisExterna" + "@id": "bts:Overlappinglesionofcervixuteri" }, { - "@id": "bts:OtitisMedia" + "@id": "bts:Overlappinglesionofcolon" }, { - "@id": "bts:OvarianHemorrhage" + "@id": "bts:Overlappinglesionofconnectivesubcutaneousandothersofttissues" }, { - "@id": "bts:OvarianInfection" + "@id": "bts:Overlappinglesionofcorpusuteri" }, { - "@id": "bts:OvarianRupture" + "@id": "bts:Overlappinglesionofdigestivesystem" }, { - "@id": "bts:OvulationPain" + "@id": "bts:Overlappinglesionofendocrineglandsandrelatedstructures" }, { - "@id": "bts:Pain" + "@id": "bts:Overlappinglesionofesophagus" }, { - "@id": "bts:PaininExtremity" + "@id": "bts:Overlappinglesionofeyeandadnexa" }, { - "@id": "bts:PainofSkin" + "@id": "bts:Overlappinglesionoffemalegenitalorgans" }, { - "@id": "bts:Palmar-PlantarErythrodysesthesiaSyndrome" + "@id": "bts:Overlappinglesionoffloorofmouth" }, { - "@id": "bts:Palpitations" + "@id": "bts:Overlappinglesionofheartmediastinumandpleura" }, { - "@id": "bts:PancreasInfection" + "@id": "bts:Overlappinglesionofhypopharynx" }, { - "@id": "bts:PancreaticAnastomoticLeak" + "@id": "bts:Overlappinglesionofill-definedsites" }, { - "@id": "bts:PancreaticDuctStenosis" + "@id": "bts:Overlappinglesionoflarynx" }, { - "@id": "bts:PancreaticEnzymesDecreased" + "@id": "bts:Overlappinglesionoflip" }, { - "@id": "bts:PancreaticFistula" + "@id": "bts:Overlappinglesionofliporalcavityandpharynx" }, { - "@id": "bts:PancreaticHemorrhage" + "@id": "bts:Overlappinglesionoflung" }, { - "@id": "bts:PancreaticNecrosis" + "@id": "bts:Overlappinglesionofmajorsalivaryglands" }, { - "@id": "bts:Pancreatitis" + "@id": "bts:Overlappinglesionofmalegenitalorgans" }, { - "@id": "bts:Papilledema" + "@id": "bts:Overlappinglesionofnasopharynx" }, { - "@id": "bts:PapulopustularRash" + "@id": "bts:Overlappinglesionofotherandunspecifiedpartsofmouth" }, { - "@id": "bts:Paresthesia" + "@id": "bts:Overlappinglesionofpalate" }, { - "@id": "bts:Paronychia" + "@id": "bts:Overlappinglesionofpancreas" }, { - "@id": "bts:ParoxysmalAtrialTachycardia" + "@id": "bts:Overlappinglesionofpenis" }, { - "@id": "bts:PelvicFloorMuscleWeakness" + "@id": "bts:Overlappinglesionofperipheralnervesandautonomicnervoussystem" }, { - "@id": "bts:PelvicInfection" + "@id": "bts:Overlappinglesionofrectumanusandanalcanal" }, { - "@id": "bts:PelvicPain" + "@id": "bts:Overlappinglesionofrespiratorysystemandintrathoracicorgans" }, { - "@id": "bts:PelvicSoftTissueNecrosis" + "@id": "bts:Overlappinglesionofretroperitoneumandperitoneum" }, { - "@id": "bts:PenileInfection" + "@id": "bts:Overlappinglesionofskin" }, { - "@id": "bts:PenilePain" + "@id": "bts:Overlappinglesionofsmallintestine" }, { - "@id": "bts:PerforationBileDuct" + "@id": "bts:Overlappinglesionofstomach" }, { - "@id": "bts:PericardialEffusion" + "@id": "bts:Overlappinglesionoftongue" }, { - "@id": "bts:PericardialTamponade" + "@id": "bts:Overlappinglesionoftonsil" }, { - "@id": "bts:Pericarditis" + "@id": "bts:Overlappinglesionofurinaryorgans" }, { - "@id": "bts:PerinealPain" + "@id": "bts:Overlappinglesionofvulva" }, { - "@id": "bts:PeriodontalDisease" + "@id": "bts:Overlappinglesionsoforopharynx" }, { - "@id": "bts:PeriorbitalEdema" + "@id": "bts:PalateNOS" }, { - "@id": "bts:PeriorbitalInfection" + "@id": "bts:PancreasNOS" }, { - "@id": "bts:PeripheralIschemia" + "@id": "bts:Pancreaticduct" }, { - "@id": "bts:PeripheralMotorNeuropathy" + "@id": "bts:Parametrium" }, { - "@id": "bts:PeripheralNerveInfection" + "@id": "bts:Parathyroidgland" }, { - "@id": "bts:PeripheralSensoryNeuropathy" + "@id": "bts:Paraurethralgland" }, { - "@id": "bts:PeritonealInfection" + "@id": "bts:Parietallobe" }, { - "@id": "bts:PeritonealNecrosis" + "@id": "bts:Parotidgland" }, { - "@id": "bts:PersonalityChange" + "@id": "bts:Pelvicbonessacrumcoccyxandassociatedjoints" }, { - "@id": "bts:PhantomPain" + "@id": "bts:Pelviclymphnodes" }, { - "@id": "bts:PharyngealAnastomoticLeak" + "@id": "bts:PelvisNOS" }, { - "@id": "bts:PharyngealFistula" + "@id": "bts:PenisNOS" }, { - "@id": "bts:PharyngealHemorrhage" + "@id": "bts:Peripheralnervesandautonomicnervoussystemofabdomen" }, { - "@id": "bts:PharyngealMucositis" + "@id": "bts:Peripheralnervesandautonomicnervoussystemofheadfaceandneck" }, { - "@id": "bts:PharyngealNecrosis" + "@id": "bts:Peripheralnervesandautonomicnervoussystemoflowerlimbandhip" }, { - "@id": "bts:PharyngealStenosis" + "@id": "bts:Peripheralnervesandautonomicnervoussystemofpelvis" }, { - "@id": "bts:Pharyngitis" + "@id": "bts:Peripheralnervesandautonomicnervoussystemofthorax" }, { - "@id": "bts:PharyngolaryngealPain" + "@id": "bts:PeripheralnervesandautonomicnervoussystemoftrunkNOS" }, { - "@id": "bts:Phlebitis" + "@id": "bts:Peripheralnervesandautonomicnervoussystemofupperlimbandshoulder" }, { - "@id": "bts:PhlebitisInfective" + "@id": "bts:PeritoneumNOS" }, { - "@id": "bts:Photophobia" + "@id": "bts:PharynxNOS" }, { - "@id": "bts:Photosensitivity" + "@id": "bts:Pinealgland" }, { - "@id": "bts:PlateletCountDecreased" + "@id": "bts:Pituitarygland" }, { - "@id": "bts:PleuralEffusion" + "@id": "bts:Placenta" }, { - "@id": "bts:PleuralHemorrhage" + "@id": "bts:PleuraNOS" }, { - "@id": "bts:PleuralInfection" + "@id": "bts:Postcricoidregion" }, { - "@id": "bts:PleuriticPain" + "@id": "bts:Posteriormediastinum" }, { - "@id": "bts:Pneumonitis" + "@id": "bts:Posteriorwallofbladder" }, { - "@id": "bts:Pneumothorax" + "@id": "bts:Posteriorwallofhypopharynx" }, { - "@id": "bts:PortalHypertension" + "@id": "bts:Posteriorwallofnasopharynx" }, { - "@id": "bts:PortalVeinThrombosis" + "@id": "bts:Posteriorwalloforopharynx" }, { - "@id": "bts:PostnasalDrip" + "@id": "bts:Prepuce" }, { - "@id": "bts:PostoperativeHemorrhage" + "@id": "bts:Prostategland" }, { - "@id": "bts:PostoperativeThoracicProcedureComplication" + "@id": "bts:Pylorus" }, { - "@id": "bts:PrecociousPuberty" + "@id": "bts:Pyriformsinus" }, { - "@id": "bts:Pregnancy" + "@id": "bts:Rectosigmoidjunction" }, { - "@id": "bts:PuerperiumandPerinatalConditionsOther" + "@id": "bts:RectumNOS" }, { - "@id": "bts:PrematureDelivery" + "@id": "bts:Renalpelvis" }, { - "@id": "bts:PrematureMenopause" + "@id": "bts:ReticuloendothelialsystemNOS" }, { - "@id": "bts:Presyncope" + "@id": "bts:Retina" }, { - "@id": "bts:Proctitis" + "@id": "bts:Retromolararea" }, { - "@id": "bts:ProductiveCough" + "@id": "bts:Retroperitoneum" }, { - "@id": "bts:ProlapseofIntestinalStoma" + "@id": "bts:Ribsternumclavicleandassociatedjoints" }, { - "@id": "bts:ProlapseofUrostomy" + "@id": "bts:Roundligament" }, { - "@id": "bts:ProstateInfection" + "@id": "bts:ScrotumNOS" }, { - "@id": "bts:ProstaticHemorrhage" + "@id": "bts:Shortbonesoflowerlimbandassociatedjoints" }, { - "@id": "bts:ProstaticObstruction" + "@id": "bts:Shortbonesofupperlimbandassociatedjoints" }, { - "@id": "bts:ProstaticPain" + "@id": "bts:Sigmoidcolon" }, { - "@id": "bts:Proteinuria" + "@id": "bts:SkinoflipNOS" }, { - "@id": "bts:Pruritus" + "@id": "bts:Skinoflowerlimbandhip" }, { - "@id": "bts:PsychiatricDisordersOther" + "@id": "bts:Skinofotherandunspecifiedpartsofface" }, { - "@id": "bts:Psychosis" + "@id": "bts:Skinofscalpandneck" }, { - "@id": "bts:PulmonaryEdema" + "@id": "bts:Skinoftrunk" }, { - "@id": "bts:PulmonaryFibrosis" + "@id": "bts:Skinofupperlimbandshoulder" }, { - "@id": "bts:PulmonaryFistula" + "@id": "bts:SkinNOS" }, { - "@id": "bts:PulmonaryHypertension" + "@id": "bts:SmallintestineNOS" }, { - "@id": "bts:PulmonaryValveDisease" + "@id": "bts:SoftpalateNOS" }, { - "@id": "bts:Purpura" + "@id": "bts:Specifiedpartsofperitoneum" }, { - "@id": "bts:PyramidalTractSyndrome" + "@id": "bts:Spermaticcord" }, { - "@id": "bts:RadiationRecallReaction(Dermatologic)" + "@id": "bts:Sphenoidsinus" }, { - "@id": "bts:Radiculitis" + "@id": "bts:Spinalcord" }, { - "@id": "bts:RashAcneiform" + "@id": "bts:Spinalmeninges" }, { - "@id": "bts:RashMaculo-Papular" + "@id": "bts:Spleen" }, { - "@id": "bts:RashPustular" + "@id": "bts:Splenicflexureofcolon" }, { - "@id": "bts:RectalAnastomoticLeak" + "@id": "bts:StomachNOS" }, { - "@id": "bts:RectalFistula" + "@id": "bts:Subglottis" }, { - "@id": "bts:RectalHemorrhage" + "@id": "bts:Sublingualgland" }, { - "@id": "bts:RectalMucositis" + "@id": "bts:Submandibulargland" }, { - "@id": "bts:RectalNecrosis" + "@id": "bts:Superiorwallofnasopharynx" }, { - "@id": "bts:RectalObstruction" + "@id": "bts:Supraglottis" }, { - "@id": "bts:RectalPain" + "@id": "bts:Tailofpancreas" }, { - "@id": "bts:RectalPerforation" + "@id": "bts:Temporallobe" }, { - "@id": "bts:RectalStenosis" + "@id": "bts:TestisNOS" }, { - "@id": "bts:RectalUlcer" + "@id": "bts:Thoracicesophagus" }, { - "@id": "bts:RecurrentLaryngealNervePalsy" + "@id": "bts:ThoraxNOS" }, { - "@id": "bts:RenalandUrinaryDisordersOther" + "@id": "bts:Thymus" }, { - "@id": "bts:RenalCalculi" + "@id": "bts:Thyroidgland" }, { - "@id": "bts:RenalColic" + "@id": "bts:TongueNOS" }, { - "@id": "bts:RenalHemorrhage" + "@id": "bts:TonsilNOS" }, { - "@id": "bts:ReproductiveSystemandBreastDisordersOther" + "@id": "bts:Tonsillarfossa" }, { - "@id": "bts:RespiratoryFailure" + "@id": "bts:Tonsillarpillar" }, { - "@id": "bts:Respiratory" + "@id": "bts:Trachea" }, { - "@id": "bts:ThoracicandMediastinalDisordersOther" + "@id": "bts:Transversecolon" }, { - "@id": "bts:Restlessness" + "@id": "bts:Trigoneofbladder" }, { - "@id": "bts:RestrictiveCardiomyopathy" + "@id": "bts:Undescendedtestis" }, { - "@id": "bts:RetinalDetachment" + "@id": "bts:Unknownprimarysite" }, { - "@id": "bts:RetinalTear" + "@id": "bts:Uppergum" }, { - "@id": "bts:RetinalVascularDisorder" + "@id": "bts:UpperlimbNOS" }, { - "@id": "bts:RetinoicAcidSyndrome" + "@id": "bts:Upperlobelung" }, { - "@id": "bts:Retinopathy" + "@id": "bts:UpperrespiratorytractNOS" }, { - "@id": "bts:RetroperitonealHemorrhage" + "@id": "bts:Upperthirdofesophagus" }, { - 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If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoTreatmentStart", + "rdfs:subClassOf": [ + { + "@id": "bts:Therapy" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Days to Treatment Start", + "sms:required": "sms:false", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:InitialDiseaseStatus", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the status of the patient's malignancy when the treatment began.", + "rdfs:label": "InitialDiseaseStatus", + "rdfs:subClassOf": [ + { + "@id": "bts:Therapy" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:InitialDiagnosis" }, { - "@id": "bts:SkinHyperpigmentation" + "@id": "bts:ProgressiveDisease" }, { - "@id": "bts:SkinHypopigmentation" + "@id": "bts:RecurrentDisease" }, { - "@id": "bts:SkinInduration" + "@id": "bts:ResidualDisease" }, { - "@id": "bts:SkinInfection" + "@id": "bts:Unknown" }, { - "@id": "bts:SkinUlceration" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Initial Disease Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:RegimenorLineofTherapy", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the regimen or line of therapy.", + "rdfs:label": "RegimenorLineofTherapy", + "rdfs:subClassOf": [ + { + "@id": "bts:Therapy" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Regimen or Line of Therapy", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TherapeuticAgents", + "@type": "rdfs:Class", + "rdfs:comment": "Text identification of the individual agent(s) used as part of a treatment regimen.", + "rdfs:label": "TherapeuticAgents", + "rdfs:subClassOf": [ + { + "@id": "bts:Therapy" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Therapeutic Agents", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TreatmentIntentType", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to identify the reason for the administration of a treatment regimen. 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"@id": "bts:UpperGastrointestinalHemorrhage" + "@id": "bts:Biopsy" }, { - "@id": "bts:UpperRespiratoryInfection" + "@id": "bts:BloodDraw" }, { - "@id": "bts:UretericAnastomoticLeak" + "@id": "bts:BoneMarrowAspirate" }, { - "@id": "bts:UrethralAnastomoticLeak" + "@id": "bts:CoreBiopsy" }, { - "@id": "bts:UrethralInfection" + "@id": "bts:Cytology" }, { - "@id": "bts:UrinaryFistula" + "@id": "bts:Cystoscopy" }, { - "@id": "bts:UrinaryFrequency" + "@id": "bts:Debulking" }, { - "@id": "bts:UrinaryIncontinence" + "@id": "bts:DiagnosticImaging" }, { - "@id": "bts:UrinaryRetention" + "@id": "bts:DilationandCurettageProcedure" }, { - "@id": "bts:UrinaryTractInfection" + "@id": "bts:Enucleation" }, { - "@id": "bts:UrinaryTractObstruction" + "@id": "bts:ExcisionalBiopsy" }, { - "@id": "bts:UrinaryTractPain" + "@id": "bts:FineNeedleAspiration" }, { - "@id": "bts:UrinaryUrgency" + "@id": "bts:IncisionalBiopsy" }, { - "@id": "bts:UrineDiscoloration" + "@id": "bts:Laparoscopy" }, { - "@id": "bts:UrineOutputDecreased" + "@id": "bts:Laparotomy" }, { - "@id": "bts:UrostomyLeak" + "@id": "bts:Other" }, { - "@id": "bts:UrostomyObstruction" + "@id": "bts:PapSmear" }, { - "@id": "bts:UrostomySiteBleeding" + "@id": "bts:PhysicalExam" }, { - "@id": "bts:UrostomyStenosis" + "@id": "bts:PathologicReview" }, { - "@id": "bts:Urticaria" + "@id": "bts:SurgicalResection" }, { - "@id": "bts:UterineAnastomoticLeak" + "@id": "bts:Thoracentesis" }, { - "@id": "bts:UterineFistula" + "@id": "bts:UltrasoundGuidedBiopsy" }, { - "@id": "bts:UterineHemorrhage" + "@id": "bts:Unknown" }, { - "@id": "bts:UterineInfection" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Method of Diagnosis", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PriorMalignancy", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe the patient's history of prior cancer diagnosis.", + "rdfs:label": "PriorMalignancy", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" }, { - "@id": "bts:UterineObstruction" + "@id": "bts:No" }, { - "@id": "bts:UterinePain" + "@id": "bts:Unknown" }, { - "@id": "bts:UterinePerforation" + "@id": "bts:NotReported" }, { - "@id": "bts:Uveitis" + "@id": "bts:NotAllowedToCollect" + } + ], + "sms:displayName": "Prior Malignancy", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PriorTreatment", + "@type": "rdfs:Class", + "rdfs:comment": "A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received before the body specimen was collected.", + "rdfs:label": "PriorTreatment", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" }, { - "@id": "bts:VaginalAnastomoticLeak" + "@id": "bts:No" }, { - "@id": "bts:VaginalDischarge" + "@id": "bts:Unknown" }, { - "@id": "bts:VaginalDryness" + "@id": "bts:NotReported" }, { - "@id": "bts:VaginalFistula" + "@id": "bts:NotAllowedToCollect" + } + ], + "sms:displayName": "Prior Treatment", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MetastasisatDiagnosis", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the extent of metastatic disease present at diagnosis.", + "rdfs:label": "MetastasisatDiagnosis", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:DistantMetastasis" }, { - "@id": "bts:VaginalHemorrhage" + "@id": "bts:MetastasisNOS" }, { - "@id": "bts:VaginalInfection" + "@id": "bts:NoMetastasis" }, { - "@id": "bts:VaginalInflammation" + "@id": "bts:RegionalMetastasis" }, { - "@id": "bts:VaginalObstruction" + "@id": "bts:Unknown" }, { - "@id": "bts:VaginalPain" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Metastasis at Diagnosis", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MetastasisatDiagnosisSite", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to identify an anatomic site in which metastatic disease involvement is found.", + "rdfs:label": "MetastasisatDiagnosisSite", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Abdomen" }, { - "@id": "bts:VaginalPerforation" + "@id": "bts:AdrenalGland" }, { - "@id": "bts:VaginalStricture" + "@id": "bts:Ascites" }, { - "@id": "bts:Vaginismus" + "@id": "bts:Bone" }, { - "@id": "bts:VagusNerveDisorder" + "@id": "bts:BoneMarrow" }, { - "@id": "bts:VasDeferensAnastomoticLeak" + "@id": "bts:Brain" }, { - "@id": "bts:VascularAccessComplication" + "@id": "bts:CerebrospinalFluid" }, { - "@id": "bts:VascularDisordersOther" + "@id": "bts:CentralNervousSystem" }, { - "@id": "bts:Vasculitis" + "@id": "bts:Colon" }, { - "@id": "bts:VasovagalReaction" + "@id": "bts:DistantNodes" }, { - "@id": "bts:VenousInjury" + "@id": "bts:DistantOrgan" }, { - "@id": "bts:VentricularArrhythmia" + "@id": "bts:Groin" }, { - "@id": "bts:VentricularFibrillation" + "@id": "bts:Kidney" }, { - "@id": "bts:VentricularTachycardia" + "@id": "bts:Liver" }, { - "@id": "bts:Vertigo" + "@id": "bts:Lung" }, { - "@id": "bts:VestibularDisorder" + "@id": "bts:LymphNode" }, { - "@id": "bts:Virilization" + "@id": "bts:Axillary" }, { - "@id": "bts:VisceralArterialIschemia" + "@id": "bts:Inguinal" }, { - "@id": "bts:VitalCapacityAbnormal" + "@id": "bts:LymphNodeNOS" }, { - "@id": "bts:VitreousHemorrhage" + "@id": "bts:Mediastinum" }, { - "@id": "bts:VoiceAlteration" + "@id": "bts:Omentum" }, { - "@id": "bts:Vomiting" + "@id": "bts:Ovary" }, { - "@id": "bts:VulvalInfection" + "@id": "bts:Pelvis" }, { - "@id": "bts:WateringEyes" + "@id": "bts:PeritonealCavity" }, { - "@id": "bts:WeightGain" + "@id": "bts:Peritoneum" }, { - "@id": "bts:WeightLoss" + "@id": "bts:Pleura" }, { - "@id": "bts:Wheezing" + "@id": "bts:Scalp" }, { - "@id": "bts:WhiteBloodCellDecreased" + "@id": "bts:Skin" }, { - "@id": "bts:Wolff-Parkinson-WhiteSyndrome" + "@id": "bts:SmallIntestine" }, { - "@id": "bts:WoundComplication" + "@id": "bts:SoftTissue" }, { - "@id": "bts:WoundDehiscence" + "@id": "bts:SpinalCord" }, { - "@id": "bts:WoundInfection" + "@id": "bts:Unknown" }, { - "@id": "bts:WristFracture" + "@id": "bts:NotReported" } ], - "sms:displayName": "Adverse Event", + "sms:displayName": "Metastasis at Diagnosis Site", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BarrettsEsophagusGobletCellsPresent", + "@id": "bts:FirstSymptomPriortoDiagnosis", "@type": "rdfs:Class", - "rdfs:comment": "Presence or absennce of Barretts esophagus goblet cells.", - "rdfs:label": "BarrettsEsophagusGobletCellsPresent", + "rdfs:comment": "Text term used to describe the patient's first symptom experienced prior to diagnosis and thought to be related to the disease.", + "rdfs:label": "FirstSymptomPriortoDiagnosis", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -22350,58 +27124,81 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:AlteredMentalStatus" }, { - "@id": "bts:No" + "@id": "bts:Headaches" + }, + { + "@id": "bts:MotororMovementChanges" + }, + { + "@id": "bts:Seizures" + }, + { + "@id": "bts:SensoryChanges" + }, + { + "@id": "bts:VisualChanges" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Barretts Esophagus Goblet Cells Present", + "sms:displayName": "First Symptom Prior to Diagnosis", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BMI", + "@id": "bts:DaystoDiagnosis", "@type": "rdfs:Class", - "rdfs:comment": "A calculated numerical quantity that represents an individual's weight to height ratio.", - "rdfs:label": "BMI", + "rdfs:comment": "Number of days between the date used for index and the date the patient was diagnosed with the malignant disease. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoDiagnosis", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "BMI", + "sms:displayName": "Days to Diagnosis", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:CauseofResponse", + "@id": "bts:PercentTumorInvasion", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the suspected cause or reason for the patient disease response.", - "rdfs:label": "CauseofResponse", + "rdfs:comment": "The percentage of tumor cells spread locally in a malignant neoplasm through infiltration or destruction of adjacent tissue.", + "rdfs:label": "PercentTumorInvasion", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cause of Response", + "sms:displayName": "Percent Tumor Invasion", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Comorbidity", + "@id": "bts:ResidualDisease", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a comorbidity disease, which coexists with the patient's malignant disease.", - "rdfs:label": "Comorbidity", + "rdfs:comment": "Text terms to describe the status of a tissue margin following surgical resection.", + "rdfs:label": "ResidualDisease", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" + }, + { + "@id": "bts:InitialDiseaseStatus" } ], "schema:isPartOf": { @@ -22409,430 +27206,761 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:AcuteRenalFailure" + "@id": "bts:R0" }, { - "@id": "bts:Adenocarcinoma" + "@id": "bts:R1" }, { - "@id": "bts:AdrenocorticalInsufficiency" + "@id": "bts:R2" }, { - "@id": "bts:AdenomatousPolyposisColi" + "@id": "bts:RX" }, { - "@id": "bts:Allergies" + "@id": "bts:Unknown" }, { - "@id": "bts:Alpha-1Antitrypsin" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Residual Disease", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SynchronousMalignancy", + "@type": "rdfs:Class", + "rdfs:comment": "A yes/no/unknown indicator used to describe whether the patient had an additional malignant diagnosis at the same time the tumor used for sequencing was diagnosed. If both tumors were sequenced, both tumors would have synchronous malignancies.", + "rdfs:label": "SynchronousMalignancy", + "rdfs:subClassOf": [ { - "@id": "bts:Anemia" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Anxiety" + "@id": "bts:Yes" }, { - "@id": "bts:Arrhythmia" + "@id": "bts:No" }, { - "@id": "bts:Arthritis" + "@id": "bts:Unknown" }, { - "@id": "bts:Asthma" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Synchronous Malignancy", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TumorConfinedtoOrganofOrigin", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the tumor is confined to the organ where it originated and did not spread to a proximal or distant location within the body.", + "rdfs:label": "TumorConfinedtoOrganofOrigin", + "rdfs:subClassOf": [ { - "@id": "bts:AtrialFibrillation" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:AvascularNecrosis" + "@id": "bts:Yes" }, { - "@id": "bts:Barrett'sEsophagus" + "@id": "bts:No" }, { - "@id": "bts:BasalCellCarcinoma" + "@id": "bts:Unknown" }, { - "@id": "bts:Beckwith-Wiedemann" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Tumor Confined to Organ of Origin", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TumorFocality", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe whether the patient's disease originated in a single location or multiple locations.", + "rdfs:label": "TumorFocality", + "rdfs:subClassOf": [ { - "@id": "bts:Behcet'sDisease" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:BiliaryDisorder" + "@id": "bts:Multifocal" }, { - "@id": "bts:BloodClots" + "@id": "bts:Unifocal" }, { - "@id": "bts:BoneFracture(s)" + "@id": "bts:Unknown" }, { - "@id": "bts:Bronchitis" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Tumor Focality", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:GrossTumorWeight", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value used to describe the gross pathologic tumor weight, measured in grams.", + "rdfs:label": "GrossTumorWeight", + "rdfs:subClassOf": [ { - "@id": "bts:CalciumChannelBlockers" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Gross Tumor Weight", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreslowThickness", + "@type": "rdfs:Class", + "rdfs:comment": "The number that describes the distance, in millimeters, between the upper layer of the epidermis and the deepest point of tumor penetration.", + "rdfs:label": "BreslowThickness", + "rdfs:subClassOf": [ { - "@id": "bts:Cancer" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Breslow Thickness", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:VascularInvasionPresent", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no indicator to ask if large vessel or venous invasion was detected by surgery or presence in a tumor specimen.", + "rdfs:label": "VascularInvasionPresent", + "rdfs:subClassOf": [ { - "@id": "bts:Cataracts" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:CeliacDisease" + "@id": "bts:Yes-VascularInvasionPresent" }, { - "@id": "bts:Cirrhosis" + "@id": "bts:No" }, { - "@id": "bts:UnknownEtiology" + "@id": "bts:Unknown" }, { - "@id": "bts:CerebrovascularDisease" + "@id": "bts:NotReported" }, { - "@id": "bts:Cholelithiasis" - }, + "@id": "bts:NotAllowedToCollect" + } + ], + "sms:displayName": "Vascular Invasion Present", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:VascularInvasionType", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that represents the type of vascular tumor invasion.", + "rdfs:label": "VascularInvasionType", + "rdfs:subClassOf": [ { - "@id": "bts:ChronicRenalFailure" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:ColonPolyps" + "@id": "bts:Extramural" }, { - "@id": "bts:CommonVariableImmunodeficiency" + "@id": "bts:Intramural" }, { - "@id": "bts:CongestiveHeartFailure(CHF)" + "@id": "bts:Macro" }, { - "@id": "bts:ConnectiveTissueDisorder" + "@id": "bts:Micro" }, { - "@id": "bts:COPD" + "@id": "bts:NoVascularInvasion" }, { - "@id": "bts:CoronaryArteryDisease" + "@id": "bts:Unknown" }, { - "@id": "bts:Crohn'sDisease" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Vascular Invasion Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AnaplasiaPresent", + "@type": "rdfs:Class", + "rdfs:comment": "Yes/no/unknown/Not Reported indicator used to describe whether anaplasia was present at the time of diagnosis.", + "rdfs:label": "AnaplasiaPresent", + "rdfs:subClassOf": [ { - "@id": "bts:CryptogenicOrganizingPneumonia" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:DeepVeinThrombosis/Thromboembolism" + "@id": "bts:Yes-AnaplasiaPresent" }, { - "@id": "bts:Denys-DrashSyndrome" + "@id": "bts:No" }, { - "@id": "bts:Depression" + "@id": "bts:Unknown" }, { - "@id": "bts:Diabetes" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Anaplasia Present", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AnaplasiaPresentType", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the morphologic findings indicating the presence of a malignant cellular infiltrate characterized by the presence of large pleomorphic cells, necrosis, and high mitotic activity in a tissue sample.", + "rdfs:label": "AnaplasiaPresentType", + "rdfs:subClassOf": [ { - "@id": "bts:TypeII" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:DiabeticNeuropathy" + "@id": "bts:Absent" }, { - "@id": "bts:DietControlledDiabetes" + "@id": "bts:Diffuse" }, { - "@id": "bts:Diverticulitis" + "@id": "bts:Equivocal" }, { - "@id": "bts:DVT/PE" + "@id": "bts:Focal" }, { - "@id": "bts:Dyslipidemia" + "@id": "bts:Present" }, { - "@id": "bts:Epilepsy" + "@id": "bts:Sclerosis" }, { - "@id": "bts:Eczema" + "@id": "bts:Unknown" }, { - "@id": "bts:Epstein-BarrVirus" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Anaplasia Present Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Laterality", + "@type": "rdfs:Class", + "rdfs:comment": "For tumors in paired organs, designates the side on which the cancer originates.", + "rdfs:label": "Laterality", + "rdfs:subClassOf": [ { - "@id": "bts:FamilialAdenomatousPolyposis" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:FanconiAnemia" + "@id": "bts:Bilateral" }, { - "@id": "bts:Fibrosis" + "@id": "bts:Left" }, { - "@id": "bts:GastroesophagealRefluxDisease" + "@id": "bts:Midline" }, { - "@id": "bts:GERD" + "@id": "bts:Right" }, { - "@id": "bts:Glaucoma" + "@id": "bts:Unilateral" }, { - "@id": "bts:GlycogenStorageDisease" + "@id": "bts:Unknown" }, { - "@id": "bts:Gout" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Laterality", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PerineuralInvasionPresent", + "@type": "rdfs:Class", + "rdfs:comment": "A yes/no indicator to ask if perineural invasion or infiltration of tumor or cancer is present.", + "rdfs:label": "PerineuralInvasionPresent", + "rdfs:subClassOf": [ { - "@id": "bts:GonadalDysfunction" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:GorlinSyndrome" + "@id": "bts:Yes" }, { - "@id": "bts:H.pyloriInfection" + "@id": "bts:No" }, { - "@id": "bts:Hashimoto'sThyroiditis" + "@id": "bts:Unknown" }, { - "@id": "bts:Headache" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Perineural Invasion Present", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:LymphaticInvasionPresent", + "@type": "rdfs:Class", + "rdfs:comment": "A yes/no indicator to ask if small or thin-walled vessel invasion is present, indicating lymphatic involvement", + "rdfs:label": "LymphaticInvasionPresent", + "rdfs:subClassOf": [ { - "@id": "bts:HeartDisease" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Hemihypertrophy" + "@id": "bts:Yes" }, { - "@id": "bts:HemorrhagicCystitis" + "@id": "bts:No" }, { - "@id": "bts:Hepatitis" + "@id": "bts:Unknown" }, { - "@id": "bts:HepatitisAInfection" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Lymphatic Invasion Present", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:LymphNodesPositive", + "@type": "rdfs:Class", + "rdfs:comment": "The number of lymph nodes involved with disease as determined by pathologic examination.", + "rdfs:label": "LymphNodesPositive", + "rdfs:subClassOf": [ { - "@id": "bts:HepatitisBInfection" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Lymph Nodes Positive", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:LymphNodesTested", + "@type": "rdfs:Class", + "rdfs:comment": "The number of lymph nodes tested to determine whether lymph nodes were involved with disease as determined by a pathologic examination.", + "rdfs:label": "LymphNodesTested", + "rdfs:subClassOf": [ { - "@id": "bts:HepatitisCInfection" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Lymph Nodes Tested", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PeritonealFluidCytologicalStatus", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the malignant status of the peritoneal fluid determined by cytologic testing.", + "rdfs:label": "PeritonealFluidCytologicalStatus", + "rdfs:subClassOf": [ { - "@id": "bts:ChronicHepatitis" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:HereditaryNon-polyposisColonCancer" + "@id": "bts:Atypical" }, { - "@id": "bts:Herpes" + "@id": "bts:Malignant" }, { - "@id": "bts:HighGradeLiverDysplasticNodule" + "@id": "bts:Non-Malignant" }, { - "@id": "bts:HIV/AIDS" + "@id": "bts:Unsatisfactory" }, { - "@id": "bts:HumanPapillomavirusInfection" + "@id": "bts:Unknown" }, { - "@id": "bts:HUS/TTP" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Peritoneal Fluid Cytological Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ClassificationofTumor", + "@type": "rdfs:Class", + "rdfs:comment": "Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint.", + "rdfs:label": "ClassificationofTumor", + "rdfs:subClassOf": [ { - "@id": "bts:Hypercholesterolemia" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Hypercalcemia" + "@id": "bts:Primary" }, { - "@id": "bts:Hyperglycemia" + "@id": "bts:Metastasis" }, { - "@id": "bts:Hyperlipidemia" + "@id": "bts:Recurrence" }, { - "@id": "bts:Hypertension" + "@id": "bts:Other" }, { - "@id": "bts:Hypospadias" + "@id": "bts:Unknown" }, { - "@id": "bts:Hypothyroidism" + "@id": "bts:NotReported" }, { - "@id": "bts:InflammatoryBowelDisease" + "@id": "bts:NotAllowedToCollect" + } + ], + "sms:displayName": "Classification of Tumor", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BestOverallResponse", + "@type": "rdfs:Class", + "rdfs:comment": "The best improvement achieved throughout the entire course of protocol treatment.", + "rdfs:label": "BestOverallResponse", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:AJ-AdjuvantTherapy" }, { - "@id": "bts:InsulinControlledDiabetes" + "@id": "bts:CPD-ClinicalProgression" }, { - "@id": "bts:InterstitialPneumontisorARDS" + "@id": "bts:CR-CompleteResponse" }, { - "@id": "bts:IntraductalPapillaryMucinousNeoplasm" + "@id": "bts:CRU-CompleteResponseUnconfirmed" }, { - "@id": "bts:IronOverload" + "@id": "bts:DU-DiseaseUnchanged" }, { - "@id": "bts:IschemicHeartDisease" + "@id": "bts:IMR-Immunoresponse" }, { - "@id": "bts:ITP" + "@id": "bts:IPD-Immunoprogression" }, { - "@id": "bts:JointReplacement" + "@id": "bts:MR-Minimal/MarginalResponse" }, { - "@id": "bts:KidneyDisease" + "@id": "bts:MX-MixedResponse" }, { - "@id": "bts:LiverCirrhosis(LiverDisease)" + "@id": "bts:Non-CR/Non-PD-Non-CR/Non-PD" }, { - "@id": "bts:LiverToxicity(Non-Infectious)" + "@id": "bts:NPB-NoPalliativeBenefit" }, { - "@id": "bts:Li-FraumeniSyndrome" + "@id": "bts:NR-NoResponse" }, { - "@id": "bts:LowGradeLiverDysplasticNodule" + "@id": "bts:PA-PalliativeTherapy" }, { - "@id": "bts:Lupus" + "@id": "bts:PB-PalliativeBenefit" }, { - "@id": "bts:LynchSyndrome" + "@id": "bts:PD-ProgressiveDisease" }, { - "@id": "bts:MAI" + "@id": "bts:PPD-Pseudoprogression" }, { - "@id": "bts:MyastheniaGravis" + "@id": "bts:PR-PartialResponse" }, { - "@id": "bts:MyocardialInfarction" + "@id": "bts:PSR-Pseudoresponse" }, { - "@id": "bts:NeuroendocrineTumor" + "@id": "bts:RD-ResponsiveDisease" }, { - "@id": "bts:NonalcoholicSteatohepatitis" + "@id": "bts:RP-Response" }, { - "@id": "bts:Obesity" + "@id": "bts:RPD-RadiographicProgressiveDisease" }, { - "@id": "bts:Organtransplant(site)" + "@id": "bts:SCR-StringentCompleteResponse" }, { - "@id": "bts:Osteoarthritis" + "@id": "bts:SD-StableDisease" }, { - "@id": "bts:OsteoporosisorOsteopenia" + "@id": "bts:SPD-SurgicalProgression" }, { - "@id": "bts:Other" + "@id": "bts:TE-TooEarly" }, { - "@id": "bts:OtherCancerWithin5Years" + "@id": "bts:VGPR-VeryGoodPartialResponse" + } + ], + "sms:displayName": "Best Overall Response", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MitoticCount", + "@type": "rdfs:Class", + "rdfs:comment": "The number of mitoses identified under the microscope in tumors. The method of counting varies, according to the specific tumor examined. Usually, the mitotic count is determined based on the number of mitoses per high power field (40X) or 10 high power fields.", + "rdfs:label": "MitoticCount", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Mitotic Count", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AJCCClinicalM", + "@type": "rdfs:Class", + "rdfs:comment": "Extent of the distant metastasis for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.", + "rdfs:label": "AJCCClinicalM", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:M0" }, { - "@id": "bts:OtherNonmalignantSystemicDisease" + "@id": "bts:M1" }, { - "@id": "bts:OtherPulmonaryComplications" + "@id": "bts:M1a" }, { - "@id": "bts:Pancreatitis" + "@id": "bts:M1b" }, { - "@id": "bts:Pain(Various)" + "@id": "bts:M1c" }, { - "@id": "bts:PepticUlcer(Ulcer)" + "@id": "bts:MX" }, { - "@id": "bts:PeripheralNeuropathy" + "@id": "bts:CM0(i+)" }, { - "@id": "bts:PeripheralVascularDisease" + "@id": "bts:Unknown" }, { - "@id": "bts:Peutz-JeghersDisease" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "AJCC Clinical M", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AJCCClinicalN", + "@type": "rdfs:Class", + "rdfs:comment": "Extent of the regional lymph node involvement for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.", + "rdfs:label": "AJCCClinicalN", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:N0" }, { - "@id": "bts:PregnancyinPatientorPartner" + "@id": "bts:N0(i+)" }, { - "@id": "bts:PrimarySclerosingCholangitis" + "@id": "bts:N0(i-)" }, { - "@id": "bts:Psoriasis" + "@id": "bts:N0(mol+)" }, { - "@id": "bts:PulmonaryFibrosis" + "@id": "bts:N0(mol-)" }, { - "@id": "bts:PulmonaryHemorrhage" + "@id": "bts:N1" }, { - "@id": "bts:RenalFailure(RequiringDialysis)" + "@id": "bts:N1a" }, { - "@id": "bts:RenalDialysis" + "@id": "bts:N1b" }, { - "@id": "bts:RenalInsufficiency" + "@id": "bts:N1bI" }, { - "@id": "bts:RheumatologicDisease" + "@id": "bts:N1bII" }, { - "@id": "bts:RheumatoidArthritis" + "@id": "bts:N1bIII" }, { - "@id": "bts:Rubinstein-TaybiSyndrome" + "@id": "bts:N1bIV" }, { - "@id": "bts:Sarcoidosis" + "@id": "bts:N1c" }, { - "@id": "bts:Seizure" + "@id": "bts:N1mi" }, { - "@id": "bts:Sleepapnea" + "@id": "bts:N2" }, { - "@id": "bts:Smoking" + "@id": "bts:N2a" }, { - "@id": "bts:Steatosis" + "@id": "bts:N2b" }, { - "@id": "bts:Stroke" + "@id": "bts:N2c" }, { - "@id": "bts:TransientIschemicAttack" + "@id": "bts:N3" }, { - "@id": "bts:Tuberculosis" + "@id": "bts:N3a" }, { - "@id": "bts:TurcotSyndrome" + "@id": "bts:N3b" }, { - "@id": "bts:Tyrosinemia" + "@id": "bts:N3c" }, { - "@id": "bts:UlcerativeColitis" + "@id": "bts:N4" }, { - "@id": "bts:WagrSyndrome" + "@id": "bts:NX" }, { "@id": "bts:Unknown" @@ -22841,18 +27969,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Comorbidity", + "sms:displayName": "AJCC Clinical N", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ComorbidityMethodofDiagnosis", + "@id": "bts:AJCCClinicalStage", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the method used to diagnose the patient's comorbidity disease.", - "rdfs:label": "ComorbidityMethodofDiagnosis", + "rdfs:comment": "Stage group determined from clinical information on the tumor (T), regional node (N) and metastases (M) and by grouping cases with similar prognosis for cancer.", + "rdfs:label": "AJCCClinicalStage", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -22860,299 +27988,224 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Histology" + "@id": "bts:Stage0" }, { - "@id": "bts:Pathology" + "@id": "bts:Stage0a" }, { - "@id": "bts:Radiology" + "@id": "bts:Stage0is" }, { - "@id": "bts:Unknown" + "@id": "bts:StageI" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Comorbidity Method of Diagnosis", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:DaystoAdverseEvent", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date of the patient's adverse event. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoAdverseEvent", - "rdfs:subClassOf": [ - { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Adverse Event", - "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:DaystoComorbidity", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date the patient was diagnosed with a comorbidity. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoComorbidity", - "rdfs:subClassOf": [ + "@id": "bts:StageIA" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Comorbidity", - "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:DiabetesTreatmentType", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the types of treatment used to manage diabetes.", - "rdfs:label": "DiabetesTreatmentType", - "rdfs:subClassOf": [ + "@id": "bts:StageIA1" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:StageIA2" + }, { - "@id": "bts:Alpha-GlucosidaseInhibitor" + "@id": "bts:StageIB" }, { - "@id": "bts:Biguanide" + "@id": "bts:StageIB1" }, { - "@id": "bts:Diet" + "@id": "bts:StageIB2" }, { - "@id": "bts:InjectedInsulin" + "@id": "bts:StageIC" }, { - "@id": "bts:Insulin" + "@id": "bts:StageII" }, { - "@id": "bts:OralHypoglycemic" + "@id": "bts:StageIIA" }, { - "@id": "bts:Sulfonylurea" + "@id": "bts:StageIIA1" }, { - "@id": "bts:Thiazolidinedione" + "@id": "bts:StageIIA2" }, { - "@id": "bts:Other" + "@id": "bts:StageIIB" }, { - "@id": "bts:Unknown" + "@id": "bts:StageIIC" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Diabetes Treatment Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:DiseaseResponse", - "@type": "rdfs:Class", - "rdfs:comment": "Code assigned to describe the patient's response or outcome to the disease.", - "rdfs:label": "DiseaseResponse", - "rdfs:subClassOf": [ + "@id": "bts:StageIIC1" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:StageIII" + }, { - "@id": "bts:AJ-AdjuvantTherapy" + "@id": "bts:StageIIIA" }, { - "@id": "bts:BED-BiochemicalEvidenceofDisease" + "@id": "bts:StageIIIB" }, { - "@id": "bts:CPD-ClinicalProgression" + "@id": "bts:StageIIIC" }, { - "@id": "bts:CR-CompleteResponse" + "@id": "bts:StageIIIC1" }, { - "@id": "bts:CRU-CompleteResponseUnconfirmed" + "@id": "bts:StageIIIC2" }, { - "@id": "bts:DU-DiseaseUnchanged" + "@id": "bts:StageIS" }, { - "@id": "bts:IMR-Immunoresponse" + "@id": "bts:StageIV" }, { - "@id": "bts:IPD-Immunoprogression" + "@id": "bts:StageIVA" }, { - "@id": "bts:MR-Minimal/Marginalresponse" + "@id": "bts:StageIVB" }, { - "@id": "bts:MX-MixedResponse" + "@id": "bts:StageIVC" }, { - "@id": "bts:Non-CR/Non-PD-Non-CR/Non-PD" + "@id": "bts:StageTis" }, { - "@id": "bts:NPB-NoPalliativeBenefit" + "@id": "bts:StageX" }, { - "@id": "bts:NR-NoResponse" + "@id": "bts:Unknown" }, { - "@id": "bts:PA-PalliativeTherapy" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "AJCC Clinical Stage", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AJCCClinicalT", + "@type": "rdfs:Class", + "rdfs:comment": "Extent of the primary cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.", + "rdfs:label": "AJCCClinicalT", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:T0" }, { - "@id": "bts:PB-PalliativeBenefit" + "@id": "bts:T1" }, { - "@id": "bts:PD-ProgressiveDisease" + "@id": "bts:T1a" }, { - "@id": "bts:PDM-PersistentDistantMetastasis" + "@id": "bts:T1a1" }, { - "@id": "bts:PLD-PersistentLocoregionalDisease" + "@id": "bts:T1a2" }, { - "@id": "bts:PPD-Pseudoprogression" + "@id": "bts:T1b" }, { - "@id": "bts:PR-PartialResponse" + "@id": "bts:T1b1" }, { - "@id": "bts:PSR-Pseudoresponse" + "@id": "bts:T1b2" }, { - "@id": "bts:RD-ResponsiveDisease" + "@id": "bts:T1c" }, { - "@id": "bts:RP-Response" + "@id": "bts:T1mi" }, { - "@id": "bts:RPD-RadiographicProgressiveDisease" + "@id": "bts:T2" }, { - "@id": "bts:SCR-StringentCompleteResponse" + "@id": "bts:T2a" }, { - "@id": "bts:SD-StableDisease" + "@id": "bts:T2a1" }, { - "@id": "bts:SPD-SurgicalProgression" + "@id": "bts:T2a2" }, { - "@id": "bts:TE-TooEarly" + "@id": "bts:T2b" }, { - "@id": "bts:TF-TumorFree" + "@id": "bts:T2c" }, { - "@id": "bts:VGPR-VeryGoodPartialResponse" + "@id": "bts:T2d" }, { - "@id": "bts:WT-WithTumor" + "@id": "bts:T3" }, { - "@id": "bts:Unknown" + "@id": "bts:T3a" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Disease Response", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:DLCORefPredictivePercent", - "@type": "rdfs:Class", - "rdfs:comment": "The value, as a percentage of predicted lung volume, measuring the amount of carbon monoxide detected in a patient's lungs.", - "rdfs:label": "DLCORefPredictivePercent", - "rdfs:subClassOf": [ + "@id": "bts:T3b" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "DLCO Ref Predictive Percent", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ECOGPerformanceStatus", - "@type": "rdfs:Class", - "rdfs:comment": "The ECOG functional performance status of the patient/participant.", - "rdfs:label": "ECOGPerformanceStatus", - "rdfs:subClassOf": [ + "@id": "bts:T3c" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:T3d" + }, { - "@id": "bts:\"0\"" + "@id": "bts:T4" }, { - "@id": "bts:\"1\"" + "@id": "bts:T4a" }, { - "@id": "bts:\"2\"" + "@id": "bts:T4b" }, { - "@id": "bts:\"3\"" + "@id": "bts:T4c" }, { - "@id": "bts:\"4\"" + "@id": "bts:T4d" }, { - "@id": "bts:\"5\"" + "@id": "bts:T4e" }, { - "@id": "bts:\"0.0\"" + "@id": "bts:TX" }, { - "@id": "bts:\"1.0\"" + "@id": "bts:Ta" }, { - "@id": "bts:\"2.0\"" + "@id": "bts:Tis" }, { - "@id": "bts:\"3.0\"" + "@id": "bts:Tis(DCIS)" }, { - "@id": "bts:\"4.0\"" + "@id": "bts:Tis(LCIS)" }, { - "@id": "bts:\"5.0\"" + "@id": "bts:Tis(Paget's)" }, { "@id": "bts:Unknown" @@ -23161,114 +28214,44 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "ECOG Performance Status", + "sms:displayName": "AJCC Clinical T", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FEV1FVCPostBronchPercent", + "@id": "bts:AJCCPathologicM", "@type": "rdfs:Class", - "rdfs:comment": "Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) post-bronchodilator.", - "rdfs:label": "FEV1FVCPostBronchPercent", + "rdfs:comment": "Code to represent the defined absence or presence of distant spread or metastases (M) to locations via vascular channels or lymphatics beyond the regional lymph nodes, using criteria established by the American Joint Committee on Cancer (AJCC).", + "rdfs:label": "AJCCPathologicM", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "FEV1 FVC Post Bronch Percent", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FEV1FVCPreBronchPercent", - "@type": "rdfs:Class", - "rdfs:comment": "Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) pre-bronchodilator.", - "rdfs:label": "FEV1FVCPreBronchPercent", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "FEV 1 FVC Pre Bronch Percent", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FEV1RefPostBronchPercent", - "@type": "rdfs:Class", - "rdfs:comment": "The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second post-bronchodilator.", - "rdfs:label": "FEV1RefPostBronchPercent", - "rdfs:subClassOf": [ + "@id": "bts:M0" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "FEV1 Ref Post Bronch Percent", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FEV1RefPreBronchPercent", - "@type": "rdfs:Class", - "rdfs:comment": "The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second pre-bronchodilator.", - "rdfs:label": "FEV1RefPreBronchPercent", - "rdfs:subClassOf": [ + "@id": "bts:M1" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "FEV1 Ref Pre Bronch Percent", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Height", - "@type": "rdfs:Class", - "rdfs:comment": "The height of the patient in centimeters.", - "rdfs:label": "Height", - "rdfs:subClassOf": [ + "@id": "bts:M1a" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Height", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HepatitisSustainedVirologicalResponse", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.", - "rdfs:label": "HepatitisSustainedVirologicalResponse", - "rdfs:subClassOf": [ + "@id": "bts:M1b" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:M1c" + }, { - "@id": "bts:Yes" + "@id": "bts:MX" }, { - "@id": "bts:No" + "@id": "bts:CM0(i+)" }, { "@id": "bts:Unknown" @@ -23277,18 +28260,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Hepatitis Sustained Virological Response", + "sms:displayName": "AJCC Pathologic M", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HPVPositiveType", + "@id": "bts:AJCCPathologicN", "@type": "rdfs:Class", - "rdfs:comment": "Text classification to represent the strain or type of human papillomavirus identified in an individual.", - "rdfs:label": "HPVPositiveType", + "rdfs:comment": "The codes that represent the stage of cancer based on the nodes present (N stage) according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.", + "rdfs:label": "AJCCPathologicN", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -23296,67 +28279,76 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:\"16\"" + "@id": "bts:N0" }, { - "@id": "bts:\"18\"" + "@id": "bts:N0(i+)" }, { - "@id": "bts:\"26\"" + "@id": "bts:N0(i-)" }, { - "@id": "bts:\"31\"" + "@id": "bts:N0(mol+)" }, { - "@id": "bts:\"33\"" + "@id": "bts:N0(mol-)" }, { - "@id": "bts:\"35\"" + "@id": "bts:N1" }, { - "@id": "bts:\"39\"" + "@id": "bts:N1a" }, { - "@id": "bts:\"45\"" + "@id": "bts:N1b" }, { - "@id": "bts:\"51\"" + "@id": "bts:N1bI" }, { - "@id": "bts:\"52\"" + "@id": "bts:N1bII" }, { - "@id": "bts:\"53\"" + "@id": "bts:N1bIII" }, { - "@id": "bts:\"56\"" + "@id": "bts:N1bIV" }, { - "@id": "bts:\"58\"" + "@id": "bts:N1c" }, { - "@id": "bts:\"59\"" + "@id": "bts:N1mi" }, { - "@id": "bts:\"63\"" + "@id": "bts:N2" }, { - "@id": "bts:\"66\"" + "@id": "bts:N2a" }, { - "@id": "bts:\"68\"" + "@id": "bts:N2b" }, { - "@id": "bts:\"70\"" + "@id": "bts:N2c" }, { - "@id": "bts:\"73\"" + "@id": "bts:N3" }, { - "@id": "bts:\"82\"" + "@id": "bts:N3a" }, { - "@id": "bts:Other" + "@id": "bts:N3b" + }, + { + "@id": "bts:N3c" + }, + { + "@id": "bts:N4" + }, + { + "@id": "bts:NX" }, { "@id": "bts:Unknown" @@ -23365,18 +28357,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "HPV Positive Type", + "sms:displayName": "AJCC Pathologic N", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:KarnofskyPerformanceStatus", + "@id": "bts:AJCCPathologicStage", "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the classification used of the functional capabilities of a person.", - "rdfs:label": "KarnofskyPerformanceStatus", + "rdfs:comment": "The extent of a cancer, especially whether the disease has spread from the original site to other parts of the body based on AJCC staging criteria.", + "rdfs:label": "AJCCPathologicStage", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -23384,156 +28376,117 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:\"0\"" + "@id": "bts:Stage0" }, { - "@id": "bts:\"10\"" + "@id": "bts:Stage0a" }, { - "@id": "bts:\"20\"" + "@id": "bts:Stage0is" }, { - "@id": "bts:\"30\"" + "@id": "bts:StageI" }, { - "@id": "bts:\"40\"" + "@id": "bts:StageIA" }, { - "@id": "bts:\"50\"" + "@id": "bts:StageIA1" }, { - "@id": "bts:\"60\"" + "@id": "bts:StageIA2" }, { - "@id": "bts:\"70\"" + "@id": "bts:StageIB" }, { - "@id": "bts:\"80\"" + "@id": "bts:StageIB1" }, { - "@id": "bts:\"90\"" + "@id": "bts:StageIB2" }, { - "@id": "bts:\"100\"" + "@id": "bts:StageIC" }, { - "@id": "bts:Unknown" + "@id": "bts:StageII" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Karnofsky Performance Status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MenopauseStatus", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the patient's menopause status.", - "rdfs:label": "MenopauseStatus", - "rdfs:subClassOf": [ + "@id": "bts:StageIIA" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:StageIIA1" + }, { - "@id": "bts:Premenopausal" + "@id": "bts:StageIIA2" }, { - "@id": "bts:Perimenopausal" + "@id": "bts:StageIIB" }, { - "@id": "bts:Postmenopausal" + "@id": "bts:StageIIC" }, { - "@id": "bts:Unknown" + "@id": "bts:StageIIC1" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Menopause Status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PancreatitisOnsetYear", - "@type": "rdfs:Class", - "rdfs:comment": "Date of onset of pancreatitis.", - "rdfs:label": "PancreatitisOnsetYear", - "rdfs:subClassOf": [ + "@id": "bts:StageIII" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Pancreatitis Onset Year", - "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] - }, - { - "@id": "bts:RefluxTreatmentType", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the types of treatment used to manage gastroesophageal reflux disease (GERD).", - "rdfs:label": "RefluxTreatmentType", - "rdfs:subClassOf": [ + "@id": "bts:StageIIIA" + }, { - "@id": "bts:FollowUp" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:StageIIIB" + }, { - "@id": "bts:Antacids" + "@id": "bts:StageIIIC" }, { - "@id": "bts:H2Blockers" + "@id": "bts:StageIIIC1" }, { - "@id": "bts:MedicallyTreated" + "@id": "bts:StageIIIC2" }, { - "@id": "bts:NoTreatment" + "@id": "bts:StageIS" }, { - "@id": "bts:NotApplicable" + "@id": "bts:StageIV" }, { - "@id": "bts:NotReported" + "@id": "bts:StageIVA" }, { - "@id": "bts:ProtonPumpInhibitors" + "@id": "bts:StageIVB" }, { - "@id": "bts:SurgicallyTreated" + "@id": "bts:StageIVC" + }, + { + "@id": "bts:StageTis" + }, + { + "@id": "bts:StageX" }, { "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Reflux Treatment Type", + "sms:displayName": "AJCC Pathologic Stage", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RiskFactor", + "@id": "bts:AJCCPathologicT", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a risk factor the patient had at the time of or prior to their diagnosis.", - "rdfs:label": "RiskFactor", + "rdfs:comment": "Code of pathological T (primary tumor) to define the size or contiguous extension of the primary tumor (T), using staging criteria from the American Joint Committee on Cancer (AJCC).", + "rdfs:label": "AJCCPathologicT", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -23541,277 +28494,495 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:AlcoholConsumption" + "@id": "bts:T0" }, { - "@id": "bts:AlcoholicLiverDisease" + "@id": "bts:T1" }, { - "@id": "bts:AllergyAnimalNOS" + "@id": "bts:T1a" }, { - "@id": "bts:AllergyAnt" + "@id": "bts:T1a1" }, { - "@id": "bts:AllergyBee" + "@id": "bts:T1a2" }, { - "@id": "bts:AllergyCat" + "@id": "bts:T1b" }, { - "@id": "bts:AllergyDairyorLactose" + "@id": "bts:T1b1" }, { - "@id": "bts:AllergyDog" + "@id": "bts:T1b2" }, { - "@id": "bts:AllergyEggs" + "@id": "bts:T1c" }, { - "@id": "bts:AllergyFoodNOS" + "@id": "bts:T1mi" }, { - "@id": "bts:AllergyFruit" + "@id": "bts:T2" }, { - "@id": "bts:AllergyMeat" + "@id": "bts:T2a" }, { - "@id": "bts:AllergyMoldorDust" + "@id": "bts:T2a1" }, { - "@id": "bts:AllergyNuts" + "@id": "bts:T2a2" }, { - "@id": "bts:AllergyProcessedFoods" + "@id": "bts:T2b" }, { - "@id": "bts:AllergySeafood" + "@id": "bts:T2c" }, { - "@id": "bts:AllergyWasp" + "@id": "bts:T2d" }, { - "@id": "bts:Alpha-1AntitrypsinDeficiency" + "@id": "bts:T3" }, { - "@id": "bts:AutoimmuneAtrophicChronicGastritis" + "@id": "bts:T3a" }, { - "@id": "bts:Barrett'sEsophagus" + "@id": "bts:T3b" }, { - "@id": "bts:Beckwith-Wiedemann" + "@id": "bts:T3c" }, { - "@id": "bts:Behcet'sDisease" + "@id": "bts:T3d" }, { - "@id": "bts:Cancer" + "@id": "bts:T4" }, { - "@id": "bts:Cholelithiasis" + "@id": "bts:T4a" }, { - "@id": "bts:ChronicHepatitis" + "@id": "bts:T4b" }, { - "@id": "bts:Cirrhosis" + "@id": "bts:T4c" }, { - "@id": "bts:ColonPolyps" + "@id": "bts:T4d" }, { - "@id": "bts:Commonvariableimmunedeficiency(CVID)" + "@id": "bts:T4e" }, { - "@id": "bts:Denys-DrashSyndrome" + "@id": "bts:TX" }, { - "@id": "bts:DiabetesNOS" + "@id": "bts:Ta" }, { - "@id": "bts:DiabetesTypeI" + "@id": "bts:Tis" }, { - "@id": "bts:DiabetesTypeII" + "@id": "bts:Tis(DCIS)" }, { - "@id": "bts:Diet" + "@id": "bts:Tis(LCIS)" }, { - "@id": "bts:Diverticulitis" + "@id": "bts:Tis(Paget's)" }, { - "@id": "bts:Endometriosis" + "@id": "bts:Unknown" }, { - "@id": "bts:Endosalpingiosis" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "AJCC Pathologic T", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AJCCStagingSystemEdition", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the version or edition of the American Joint Committee on Cancer Staging Handbooks, a publication by the group formed for the purpose of developing a system of staging for cancer that is acceptable to the American medical profession and is compatible with other accepted classifications.", + "rdfs:label": "AJCCStagingSystemEdition", + "rdfs:subClassOf": [ { - "@id": "bts:Eczema" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Epstein-BarrVirus" + "@id": "bts:1st" }, { - "@id": "bts:FamilialAdenomatousPolyposis" + "@id": "bts:2nd" }, { - "@id": "bts:FanconiAnemia" + "@id": "bts:3rd" }, { - "@id": "bts:Fibrosis" + "@id": "bts:4th" }, { - "@id": "bts:GastricPolyp(s)" + "@id": "bts:5th" }, { - "@id": "bts:Gilbert'sSyndrome" + "@id": "bts:6th" }, { - "@id": "bts:GorlinSyndrome" + "@id": "bts:7th" }, { - "@id": "bts:Hashimoto'sThyroiditis" + "@id": "bts:8th" }, { - "@id": "bts:HayFever" + "@id": "bts:Unknown" }, { - "@id": "bts:Headache" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "AJCC Staging System Edition", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CogNeuroblastomaRiskGroup", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that represents the categorization of patients on the basis of prognostic factors per a system developed by Children's Oncology Group (COG). Risk level is used to assign treatment intensity.", + "rdfs:label": "CogNeuroblastomaRiskGroup", + "rdfs:subClassOf": [ { - "@id": "bts:HelicobacterPylori-AssociatedGastritis" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:HematologicDisorderNOS" + "@id": "bts:HighRisk" }, { - "@id": "bts:Hemihypertrophy" + "@id": "bts:IntermediateRisk" }, { - "@id": "bts:Hemochromatosis" + "@id": "bts:LowRisk" }, { - "@id": "bts:HepaticEncephalopathy" + "@id": "bts:Unknown" }, { - "@id": "bts:HepatitisBInfection" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Cog Neuroblastoma Risk Group", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CogRhabdomyosarcomaRiskGroup", + "@type": "rdfs:Class", + "rdfs:comment": "Text term used to describe the classification of rhabdomyosarcoma, as defined by the Children's Oncology Group (COG).", + "rdfs:label": "CogRhabdomyosarcomaRiskGroup", + "rdfs:subClassOf": [ { - "@id": "bts:HepatitisCInfection" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:HepatitisNOS" + "@id": "bts:HighRisk" }, { - "@id": "bts:HighGradeDysplasia" + "@id": "bts:IntermediateRisk" }, { - "@id": "bts:HIV" + "@id": "bts:LowRisk" }, { - "@id": "bts:HumanPapillomavirusInfection" + "@id": "bts:Unknown" }, { - "@id": "bts:Hypospadias" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Cog Rhabdomyosarcoma Risk Group", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:GleasonGradeGroup", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the overall grouping of grades defined by the Gleason grading classification, which is used to determine the aggressiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.", + "rdfs:label": "GleasonGradeGroup", + "rdfs:subClassOf": [ { - "@id": "bts:IntestinalMetaplasia" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:IronOverload" + "@id": "bts:Group1" }, { - "@id": "bts:Li-FraumeniSyndrome" + "@id": "bts:Group2" }, { - "@id": "bts:LowGradeDysplasia" + "@id": "bts:Group3" }, { - "@id": "bts:LymphocyticThyroiditis" + "@id": "bts:Group4" }, { - "@id": "bts:LynchSyndrome" - }, + "@id": "bts:Group5" + } + ], + "sms:displayName": "Gleason Grade Group", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:GleasonGradeTertiary", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the tertiary pattern as described by the Gleason Grading System.", + "rdfs:label": "GleasonGradeTertiary", + "rdfs:subClassOf": [ { - "@id": "bts:MyastheniaGravis" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:NonalcoholicFattyLiverDisease" + "@id": "bts:Pattern4" }, { - "@id": "bts:NonalcoholicSteatohepatitis" - }, + "@id": "bts:Pattern5" + } + ], + "sms:displayName": "Gleason Grade Tertiary", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:GleasonPatternsPercent", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value that represents the percentage of Patterns 4 and 5, which is used when the Gleason score is greater than 7 to predict prognosis.", + "rdfs:label": "GleasonPatternsPercent", + "rdfs:subClassOf": [ { - "@id": "bts:Obesity" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Gleason Patterns Percent", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:GreatestTumorDimension", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value that represents the measurement of the widest portion of the tumor in centimeters.", + "rdfs:label": "GreatestTumorDimension", + "rdfs:subClassOf": [ { - "@id": "bts:OralContraceptives" + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Greatest Tumor Dimension", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:IGCCCGStage", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the International Germ Cell Cancer Collaborative Group (IGCCCG), a grouping used to further classify metastatic testicular tumors.", + "rdfs:label": "IGCCCGStage", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:GoodPrognosis" }, { - "@id": "bts:Pancreatitis" + "@id": "bts:IntermediatePrognosis" }, { - "@id": "bts:ParasiticDiseaseofBiliaryTract" + "@id": "bts:PoorPrognosis" }, { - "@id": "bts:PrimarySclerosingCholangitis" + "@id": "bts:Unknown" }, { - "@id": "bts:RecurrentPyogenicCholangitis" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "IGCCCG Stage", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:INPCGrade", + "@type": "rdfs:Class", + "rdfs:comment": "Text term used to describe the classification of neuroblastic differentiation within neuroblastoma tumors, as defined by the International Neuroblastoma Pathology Classification (INPC).", + "rdfs:label": "INPCGrade", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Differentiating" }, { - "@id": "bts:RefluxDisease" + "@id": "bts:PoorlyDifferentiated" }, { - "@id": "bts:RheumatoidArthritis" + "@id": "bts:Undifferentiated" }, { - "@id": "bts:Rubinstein-TaybiSyndrome" + "@id": "bts:Unknown" }, { - "@id": "bts:Sarcoidosis" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "INPC Grade", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:INPCHistologicGroup", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the classification of neuroblastomas distinguishing between favorable and unfavorable histologic groups. The histologic score, defined by the International Neuroblastoma Pathology Classification (INPC), is based on age, mitosis-karyorrhexis index (MKI), stromal content and degree of tumor cell differentiation.", + "rdfs:label": "INPCHistologicGroup", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Favorable" }, { - "@id": "bts:Seizure" + "@id": "bts:Unfavorable" }, { - "@id": "bts:SensoryChanges" + "@id": "bts:Unknown" }, { - "@id": "bts:Seroustubalintraepithelialcarcinoma(STIC)" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "INPC Histologic Group", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:INRGStage", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the staging classification of neuroblastic tumors, as defined by the International Neuroblastoma Risk Group (INRG).", + "rdfs:label": "INRGStage", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:L1" }, { - "@id": "bts:Steatosis" + "@id": "bts:L2" }, { - "@id": "bts:Tattoo" + "@id": "bts:M" }, { - "@id": "bts:ThyroidNodularHyperplasia" + "@id": "bts:Ms" }, { - "@id": "bts:TobaccoNOS" + "@id": "bts:Unknown" }, { - "@id": "bts:TobaccoSmokeless" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "INRG Stage", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:INSSStage", + "@type": "rdfs:Class", + "rdfs:comment": "Text term used to describe the staging classification of neuroblastic tumors, as defined by the International Neuroblastoma Staging System (INSS).", + "rdfs:label": "INSSStage", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Stage1" }, { - "@id": "bts:TobaccoSmoking" + "@id": "bts:Stage2A" }, { - "@id": "bts:TurcotSyndrome" + "@id": "bts:Stage2B" }, { - "@id": "bts:UndescendedTestis" + "@id": "bts:Stage3" }, { - "@id": "bts:VisionChanges" + "@id": "bts:Stage4" }, { - "@id": "bts:WagrSyndrome" + "@id": "bts:Stage4S" }, { "@id": "bts:Unknown" @@ -23820,18 +28991,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Risk Factor", + "sms:displayName": "INSS Stage", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RiskFactorTreatment", + "@id": "bts:InternationalPrognosticIndex", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.", - "rdfs:label": "RiskFactorTreatment", + "rdfs:comment": "The text term used to describe the International Prognostic Index, which classifies the prognosis of patients with aggressive non-Hodgkin's lymphoma.", + "rdfs:label": "InternationalPrognosticIndex", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -23839,30 +29010,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:LowRisk" }, { - "@id": "bts:No" + "@id": "bts:Low-IntermediateRisk" }, { - "@id": "bts:Unknown" + "@id": "bts:High-IntermediateRisk" }, { - "@id": "bts:NotReported" + "@id": "bts:HighRisk" } ], - "sms:displayName": "Risk Factor Treatment", + "sms:displayName": "International Prognostic Index", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ViralHepatitisSerologies", + "@id": "bts:IRSGroup", "@type": "rdfs:Class", - "rdfs:comment": "Text term that describes the kind of serological laboratory test used to determine the patient's hepatitus status.", - "rdfs:label": "ViralHepatitisSerologies", + "rdfs:comment": "Text term used to describe the classification of rhabdomyosarcoma tumors, as defined by the Intergroup Rhabdomyosarcoma Study (IRS).", + "rdfs:label": "IRSGroup", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -23870,28 +29041,34 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:HBVCoreAntibody" + "@id": "bts:GroupI" }, { - "@id": "bts:HBVDNA" + "@id": "bts:GroupIa" }, { - "@id": "bts:HBVGenotype" + "@id": "bts:GroupIb" }, { - "@id": "bts:HBVSurfaceAntibody" + "@id": "bts:GroupII" }, { - "@id": "bts:HCVGenotype" + "@id": "bts:GroupIIa" }, { - "@id": "bts:HepatitisBSurfaceAntigen" + "@id": "bts:GroupIIc" }, { - "@id": "bts:HepatitisCAntibody" + "@id": "bts:GroupIII" }, { - "@id": "bts:HepatitisCVirusRNA" + "@id": "bts:GroupIIIa" + }, + { + "@id": "bts:GroupIIIb" + }, + { + "@id": "bts:GroupIV" }, { "@id": "bts:Unknown" @@ -23900,35 +29077,55 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Viral Hepatitis Serologies", + "sms:displayName": "IRS Group", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Weight", + "@id": "bts:IRSStage", "@type": "rdfs:Class", - "rdfs:comment": "The weight of the patient measured in kilograms.", - "rdfs:label": "Weight", + "rdfs:comment": "The text term used to describe the classification of rhabdomyosarcoma tumors, as defined by the Intergroup Rhabdomyosarcoma Study (IRS).", + "rdfs:label": "IRSStage", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Weight", + "schema:rangeIncludes": [ + { + "@id": "bts:1" + }, + { + "@id": "bts:2" + }, + { + "@id": "bts:3" + }, + { + "@id": "bts:4" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "IRS Stage", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AdverseEventGrade", + "@id": "bts:ISSStage", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.", - "rdfs:label": "AdverseEventGrade", + "rdfs:comment": "The multiple myeloma disease stage at diagnosis.", + "rdfs:label": "ISSStage", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -23936,33 +29133,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Grade1" + "@id": "bts:I" }, { - "@id": "bts:Grade2" + "@id": "bts:II" }, { - "@id": "bts:Grade3" + "@id": "bts:III" }, { - "@id": "bts:Grade4" + "@id": "bts:NotReported" }, { - "@id": "bts:Grade5" + "@id": "bts:Unknown" } ], - "sms:displayName": "Adverse Event Grade", + "sms:displayName": "ISS Stage", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AIDSRiskFactors", + "@id": "bts:LymphNodeInvolvedSite", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a risk factor of the acquired immunodeficiency syndrome (AIDS) that the patient either had at time time of the study or experienced in the past.", - "rdfs:label": "AIDSRiskFactors", + "rdfs:comment": "The text term used to describe the anatomic site of lymph node involvement.", + "rdfs:label": "LymphNodeInvolvedSite", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -23970,109 +29167,147 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Candidiasis" + "@id": "bts:Axillary" }, { - "@id": "bts:Coccidioidomycosis" + "@id": "bts:Cervical" }, { - "@id": "bts:Cryptococcosis" + "@id": "bts:Epitrochlear" }, { - "@id": "bts:Cytomegalovirus" + "@id": "bts:Femoral" }, { - "@id": "bts:Encephalopathy" + "@id": "bts:Hilar" }, { - "@id": "bts:HerpesSimplexVirus" + "@id": "bts:Iliac-common" }, { - "@id": "bts:Histoplasmosis" + "@id": "bts:Iliac-external" }, { - "@id": "bts:Isosporiasis" + "@id": "bts:Iliac" }, { - "@id": "bts:MycobacteriumaviumComplex" + "@id": "bts:NOS" }, { - "@id": "bts:Mycobacteriumtuberculosis" + "@id": "bts:Inguinal" }, { - "@id": "bts:Mycobacterium" + "@id": "bts:Mediastinal" }, { - "@id": "bts:NOS" + "@id": "bts:Mesenteric" }, { - "@id": "bts:Nocardiosis" + "@id": "bts:None" }, { - "@id": "bts:PneumocystisPneumonia" + "@id": "bts:Occipital" }, { - "@id": "bts:Pneumonia" + "@id": "bts:Paraaortic" }, { - "@id": "bts:ProgressiveMultifocalLeukoencephalopathy" + "@id": "bts:Parotid" }, { - "@id": "bts:SalmonellaSepticemia" + "@id": "bts:Popliteal" }, { - "@id": "bts:Toxoplasmosis" + "@id": "bts:Retroperitoneal" }, { - "@id": "bts:WastingSyndrome" + "@id": "bts:Splenic" + }, + { + "@id": "bts:Submandibular" + }, + { + "@id": "bts:Supraclavicular" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "AIDS Risk Factors", + "sms:displayName": "Lymph Node Involved Site", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BodySurfaceArea", + "@id": "bts:MarginDistance", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to represent the 2-dimensional extent of the body surface relating height to weight.", - "rdfs:label": "BodySurfaceArea", + "rdfs:comment": "Numeric value (in centimeters) that represents the distance between the tumor and the surgical margin.", + "rdfs:label": "MarginDistance", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Body Surface Area", + "sms:displayName": "Margin Distance", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CD4Count", + "@id": "bts:MarginsInvolvedSite", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the outcome of the procedure to determine the amount of the CD4 expressing cells in a sample.", - "rdfs:label": "CD4Count", + "rdfs:comment": "The text term used to describe the anatomic sites that were involved in the survival margins.", + "rdfs:label": "MarginsInvolvedSite", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "CD4 Count", + "schema:rangeIncludes": [ + { + "@id": "bts:GerotaFascia" + }, + { + "@id": "bts:Parenchyma" + }, + { + "@id": "bts:PerinephricFat" + }, + { + "@id": "bts:Renal" + }, + { + "@id": "bts:RenalCapsule" + }, + { + "@id": "bts:RenalSinus" + }, + { + "@id": "bts:RenalVein" + }, + { + "@id": "bts:Ureter" + } + ], + "sms:displayName": "Margins Involved Site", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CDCHIVRiskFactors", + "@id": "bts:MedulloblastomaMolecularClassification", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a risk factor for human immunodeficiency virus, as described by the Center for Disease Control.", - "rdfs:label": "CDCHIVRiskFactors", + "rdfs:comment": "The text term used to describe the classification of medulloblastoma tumors based on molecular features.", + "rdfs:label": "MedulloblastomaMolecularClassification", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -24080,22 +29315,16 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Hemophiliac" - }, - { - "@id": "bts:HeterosexualContact" - }, - { - "@id": "bts:HomosexualContact" + "@id": "bts:NotDetermined" }, { - "@id": "bts:IntravenousDrugUser" + "@id": "bts:Non-WNT/non-SHHActivated" }, { - "@id": "bts:None" + "@id": "bts:SHH-Activated" }, { - "@id": "bts:TransfusionRecipient" + "@id": "bts:WNT-Activated" }, { "@id": "bts:Unknown" @@ -24104,37 +29333,49 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "CDC HIV Risk Factors", + "sms:displayName": "Medulloblastoma Molecular Classification", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DaystoImaging", + "@id": "bts:MicropapillaryFeatures", "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date the imaging or scan was performed on the patient. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoImaging", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether micropapillary features were determined to be present.", + "rdfs:label": "MicropapillaryFeatures", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Days to Imaging", + "schema:rangeIncludes": [ + { + "@id": "bts:Absent" + }, + { + "@id": "bts:Present" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Micropapillary Features", "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "sms:validationRules": [] }, { - "@id": "bts:EvidenceofRecurrenceType", + "@id": "bts:MitosisKaryorrhexisIndex", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the type of evidence used to determine whether the patient's disease recurred", - "rdfs:label": "EvidenceofRecurrenceType", + "rdfs:comment": "Text term that represents the component of the International Neuroblastoma Pathology Classification (INPC) for mitosis-karyorrhexis index (MKI).", + "rdfs:label": "MitosisKaryorrhexisIndex", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -24142,27 +29383,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:BiopsywithHistologicConfirmation" + "@id": "bts:High" }, { - "@id": "bts:ConvincingImageSource" + "@id": "bts:Intermediate" }, { - "@id": "bts:PositiveBiomarkers" + "@id": "bts:Low" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Evidence of Recurrence Type", + "sms:displayName": "Mitosis Karyorrhexis Index", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HAARTTreatmentIndicator", + "@id": "bts:NonNodalRegionalDisease", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to indicate whether the patient received Highly Active Antiretroviral Therapy (HAART).", - "rdfs:label": "HAARTTreatmentIndicator", + "rdfs:comment": "The text term used to describe whether the patient had non-nodal regional disease.", + "rdfs:label": "NonNodalRegionalDisease", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -24170,10 +29417,13 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Absent" }, { - "@id": "bts:No" + "@id": "bts:Indeterminate" + }, + { + "@id": "bts:Present" }, { "@id": "bts:Unknown" @@ -24182,35 +29432,49 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "HAART Treatment Indicator", + "sms:displayName": "Non Nodal Regional Disease", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HIVViralLoad", + "@id": "bts:NonNodalTumorDeposits", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the concentration of an analyte or aliquot extracted from the sample or sample portion, measured in milligrams per milliliter.", - "rdfs:label": "HIVViralLoad", + "rdfs:comment": "The yes/no/unknown indicator used to describe the presence of tumor deposits in the pericolic or perirectal fat or in adjacent mesentery away from the leading edge of the tumor.", + "rdfs:label": "NonNodalTumorDeposits", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HIV Viral Load", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Non Nodal Tumor Deposits", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HormonalContraceptiveUse", + "@id": "bts:OvarianSpecimenStatus", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to indicate whether the patient used hormonal contraceptives.", - "rdfs:label": "HormonalContraceptiveUse", + "rdfs:comment": "The text term used to describe the physical condition of the involved ovary.", + "rdfs:label": "OvarianSpecimenStatus", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -24218,13 +29482,13 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CurrentUser" + "@id": "bts:OvarianCapsuleIntact" }, { - "@id": "bts:FormerUser" + "@id": "bts:OvarianCapsuleRuptured" }, { - "@id": "bts:NeverUsed" + "@id": "bts:OvarianCapsuleFragmented" }, { "@id": "bts:Unknown" @@ -24233,18 +29497,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Hormonal Contraceptive Use", + "sms:displayName": "Ovarian Specimen Status", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HysterectomyMarginsInvolved", + "@id": "bts:OvarianSurfaceInvolvement", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to indicate whether the patient's disease was determined to be involved based on the surgical margins of the hysterectomy.", - "rdfs:label": "HysterectomyMarginsInvolved", + "rdfs:comment": "The text term that describes whether the surface tissue (outer boundary) of the ovary shows evidence of involvement or presence of cancer.", + "rdfs:label": "OvarianSurfaceInvolvement", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -24252,19 +29516,13 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Bladder" - }, - { - "@id": "bts:MacroscopicParametrium" - }, - { - "@id": "bts:MicroscopicParametrium" + "@id": "bts:Absent" }, { - "@id": "bts:None" + "@id": "bts:Present" }, { - "@id": "bts:Vagina" + "@id": "bts:Indeterminate" }, { "@id": "bts:Unknown" @@ -24273,18 +29531,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Hysterectomy Margins Involved", + "sms:displayName": "Ovarian Surface Involvement", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HysterectomyType", + "@id": "bts:PregnantatDiagnosis", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the type of hysterectomy the patient had.", - "rdfs:label": "HysterectomyType", + "rdfs:comment": "The text term used to indicate whether the patient was pregnant at the time they were diagnosed.", + "rdfs:label": "PregnantatDiagnosis", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -24292,16 +29550,10 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:HysterectomyNOS" - }, - { - "@id": "bts:Notperformed" - }, - { - "@id": "bts:RadicalHysterectomy" + "@id": "bts:Yes" }, { - "@id": "bts:SimpleHysterectomy" + "@id": "bts:No" }, { "@id": "bts:Unknown" @@ -24310,18 +29562,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Hysterectomy Type", + "sms:displayName": "Pregnant at Diagnosis", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ImagingResult", + "@id": "bts:PrimaryGleasonGrade", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the result of the imaging or scan performed on the patient.", - "rdfs:label": "ImagingResult", + "rdfs:comment": "The text term used to describe the primary Gleason score, which describes the pattern of cells making up the largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.", + "rdfs:label": "PrimaryGleasonGrade", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -24329,36 +29581,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Positive" - }, - { - "@id": "bts:Indeterminate" + "@id": "bts:Pattern1" }, { - "@id": "bts:Negative" + "@id": "bts:Pattern2" }, { - "@id": "bts:NotPerformed" + "@id": "bts:Pattern3" }, { - "@id": "bts:Unknown" + "@id": "bts:Pattern4" }, { - "@id": "bts:NotReported" + "@id": "bts:Pattern5" } ], - "sms:displayName": "Imaging Result", + "sms:displayName": "Primary Gleason Grade", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ImagingType", + "@id": "bts:SecondaryGleasonGrade", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the type of imaging or scan performed on the patient.", - "rdfs:label": "ImagingType", + "rdfs:comment": "The text term used to describe the secondary Gleason score, which describes the pattern of cells making up the second largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.", + "rdfs:label": "SecondaryGleasonGrade", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -24366,30 +29615,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:99mTcBoneScintigraphy" + "@id": "bts:Pattern1" }, { - "@id": "bts:CTScan" + "@id": "bts:Pattern2" }, { - "@id": "bts:MRI" + "@id": "bts:Pattern3" }, { - "@id": "bts:PET" + "@id": "bts:Pattern4" + }, + { + "@id": "bts:Pattern5" } ], - "sms:displayName": "Imaging Type", + "sms:displayName": "Secondary Gleason Grade", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ImmunosuppressiveTreatmentType", + "@id": "bts:SupratentorialLocalization", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the type of immunosuppresive treatment the patient received.", - "rdfs:label": "ImmunosuppressiveTreatmentType", + "rdfs:comment": "Text term to specify the location of the supratentorial tumor.", + "rdfs:label": "SupratentorialLocalization", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -24397,22 +29649,16 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Anti-TNFTherapy" - }, - { - "@id": "bts:Azathioprine" - }, - { - "@id": "bts:Cyclophosphamide" + "@id": "bts:CerebralCortex" }, { - "@id": "bts:Methotrexate" + "@id": "bts:DeepGray" }, { - "@id": "bts:None" + "@id": "bts:SpinalCord" }, { - "@id": "bts:Other" + "@id": "bts:WhiteMatter" }, { "@id": "bts:Unknown" @@ -24421,35 +29667,35 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Immunosuppressive Treatment Type", + "sms:displayName": "Supratentorial Localization", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NadirCD4Count", + "@id": "bts:TumorDepth", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the lowest point to which the CD4 count has dropped (nadir).", - "rdfs:label": "NadirCD4Count", + "rdfs:comment": "Numeric value that represents the depth of tumor invasion, measured in millimeters (mm).", + "rdfs:label": "TumorDepth", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Nadir CD4 Count", + "sms:displayName": "Tumor Depth", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PregnancyOutcome", + "@id": "bts:WHOCNSGrade", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the type of pregnancy the patient had", - "rdfs:label": "PregnancyOutcome", + "rdfs:comment": "WHO CNS Grade", + "rdfs:label": "WHOCNSGrade", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -24457,19 +29703,19 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:EctopicPregnancy" + "@id": "bts:GradeI" }, { - "@id": "bts:InducedAbortion" + "@id": "bts:GradeII" }, { - "@id": "bts:LiveBirth" + "@id": "bts:GradeIII" }, { - "@id": "bts:Miscarriage" + "@id": "bts:GradeIV" }, { - "@id": "bts:Stillbirth" + "@id": "bts:GradeNotAssigned" }, { "@id": "bts:Unknown" @@ -24478,52 +29724,72 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Pregnancy Outcome", + "sms:displayName": "WHO CNS Grade", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RecistTargetedRegionsNumber", + "@id": "bts:WHONTEGrade", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the number of baseline target lesions, as described by the Response Evaluation Criteria in Solid Tumours (RECIST) criteria", - "rdfs:label": "RecistTargetedRegionsNumber", + "rdfs:comment": "WHO NTE Grade", + "rdfs:label": "WHONTEGrade", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Recist Targeted Regions Number", + "schema:rangeIncludes": [ + { + "@id": "bts:G1" + }, + { + "@id": "bts:G2" + }, + { + "@id": "bts:G3" + }, + { + "@id": "bts:GX" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "WHO NTE Grade", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RecistTargetedRegionsSum", + "@id": "bts:AAChange", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the sum of baseline target lesions, as described by the Response Evaluation Criteria in Solid Tumours (RECIST) criteria.", - "rdfs:label": "RecistTargetedRegionsSum", + "rdfs:comment": "Alphanumeric value used to describe the amino acid change for a specific genetic variant. Example: R116Q. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "AAChange", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Recist Targeted Regions Sum", + "sms:displayName": "AA Change", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScanTracerUsed", + "@id": "bts:Antigen", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the type of tracer used during the imaging or scan of the patient.", - "rdfs:label": "ScanTracerUsed", + "rdfs:comment": "The text term used to describe an antigen included in molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "Antigen", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { @@ -24531,33 +29797,108 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Acetate" + "@id": "bts:BCL6" }, { - "@id": "bts:Axumin" + "@id": "bts:CA-125" }, { - "@id": "bts:Choline" + "@id": "bts:CA19-9" }, { - "@id": "bts:PSMA" + "@id": "bts:CCND1" }, { - "@id": "bts:SodiumFluoride" + "@id": "bts:CD10" + }, + { + "@id": "bts:CD117" + }, + { + "@id": "bts:CD138" + }, + { + "@id": "bts:CD14" + }, + { + "@id": "bts:CD15" + }, + { + "@id": "bts:CD19" + }, + { + "@id": "bts:CD20" + }, + { + "@id": "bts:CD22" + }, + { + "@id": "bts:CD23" + }, + { + "@id": "bts:CD25" + }, + { + "@id": "bts:CD3" + }, + { + "@id": "bts:CD30" + }, + { + "@id": "bts:CD33" + }, + { + "@id": "bts:CD34" + }, + { + "@id": "bts:CD45" + }, + { + "@id": "bts:CD5" + }, + { + "@id": "bts:CD56" + }, + { + "@id": "bts:CD7" + }, + { + "@id": "bts:CD79A" + }, + { + "@id": "bts:CEA" + }, + { + "@id": "bts:HLA-DR" + }, + { + "@id": "bts:Mesothelin" + }, + { + "@id": "bts:NSE" + }, + { + "@id": "bts:SquamousCellCarcinomaAntigen" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Scan Tracer Used", + "sms:displayName": "Antigen", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TreatmentorTherapy", + "@id": "bts:ClinicalBiospecimenType", "@type": "rdfs:Class", - "rdfs:comment": "A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received.", - "rdfs:label": "TreatmentorTherapy", + "rdfs:comment": "The text term used to describe the biological material used for testing, diagnostic, treatment or research purposes. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "ClinicalBiospecimenType", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { @@ -24565,10 +29906,70 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Blood" }, { - "@id": "bts:No" + "@id": "bts:BoneMarrow" + }, + { + "@id": "bts:BuccalMucosa" + }, + { + "@id": "bts:BuffyCoat" + }, + { + "@id": "bts:CerebrospinalFluid" + }, + { + "@id": "bts:ConnectiveTissue" + }, + { + "@id": "bts:EmbryonicFluid" + }, + { + "@id": "bts:EmbryonicTissue" + }, + { + "@id": "bts:Feces" + }, + { + "@id": "bts:Granulocyte" + }, + { + "@id": "bts:MuscleTissue" + }, + { + "@id": "bts:NerveTissue" + }, + { + "@id": "bts:PeritonealFluid" + }, + { + "@id": "bts:Plasma" + }, + { + "@id": "bts:PleuralFluid" + }, + { + "@id": "bts:Saliva" + }, + { + "@id": "bts:Serum" + }, + { + "@id": "bts:Skin" + }, + { + "@id": "bts:SoftTissue" + }, + { + "@id": "bts:TissueNOS" + }, + { + "@id": "bts:UninvolvedTissueNOS" + }, + { + "@id": "bts:Urine" }, { "@id": "bts:Unknown" @@ -24577,52 +29978,69 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Treatment or Therapy", + "sms:displayName": "Clinical Biospecimen Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TreatmentEffect", + "@id": "bts:BloodTestNormalRangeUpper", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the pathologic effect a treatment(s) had on the tumor.", - "rdfs:label": "TreatmentEffect", + "rdfs:comment": "Numeric value used to describe the upper limit of the normal range used to describe a healthy individual at the institution where the test was completed.", + "rdfs:label": "BloodTestNormalRangeUpper", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:CompleteNecrosis(NoViableTumor)" - }, - { - "@id": "bts:IncompleteNecrosis(ViableTumorPresent)" - }, - { - "@id": "bts:NoNecrosis" - }, + "sms:displayName": "Blood Test Normal Range Upper", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BloodTestNormalRangeLower", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value used to describe the lower limit of the normal range used to describe a healthy individual at the institution where the test was completed.", + "rdfs:label": "BloodTestNormalRangeLower", + "rdfs:subClassOf": [ { - "@id": "bts:Unknown" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Blood Test Normal Range Lower", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CellCount", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value used to describe the number of cells used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "CellCount", + "rdfs:subClassOf": [ { - "@id": "bts:NotReported" + "@id": "bts:MolecularTest" } ], - "sms:displayName": "Treatment Effect", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Cell Count", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TreatmentOutcome", + "@id": "bts:Chromosome", "@type": "rdfs:Class", - "rdfs:comment": "Text term that describes the patient's final outcome after the treatment was administered.", - "rdfs:label": "TreatmentOutcome", + "rdfs:comment": "The text term used to describe a chromosome targeted or included in molecular testing. If a specific genetic variant is being reported, this property can be used to capture the chromosome where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "Chromosome", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { @@ -24630,37 +30048,82 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CompleteResponse" + "@id": "bts:Chr1" }, { - "@id": "bts:MixedResponse" + "@id": "bts:Chr2" }, { - "@id": "bts:NoMeasurableDisease" + "@id": "bts:Chr3" }, { - "@id": "bts:NoResponse" + "@id": "bts:Chr4" }, { - "@id": "bts:PartialResponse" + "@id": "bts:Chr5" }, { - "@id": "bts:PersistentDisease" + "@id": "bts:Chr6" }, { - "@id": "bts:ProgressiveDisease" + "@id": "bts:Chr7" }, { - "@id": "bts:StableDisease" + "@id": "bts:Chr8" }, { - "@id": "bts:TreatmentOngoing" + "@id": "bts:Chr9" }, { - "@id": "bts:TreatmentStoppedDuetoToxicity" + "@id": "bts:Chr10" }, { - "@id": "bts:VeryGoodPartialResponse" + "@id": "bts:Chr11" + }, + { + "@id": "bts:Chr12" + }, + { + "@id": "bts:Chr13" + }, + { + "@id": "bts:Chr14" + }, + { + "@id": "bts:Chr15" + }, + { + "@id": "bts:Chr16" + }, + { + "@id": "bts:Chr17" + }, + { + "@id": "bts:Chr18" + }, + { + "@id": "bts:Chr19" + }, + { + "@id": "bts:Chr20" + }, + { + "@id": "bts:Chr21" + }, + { + "@id": "bts:Chr22" + }, + { + "@id": "bts:Chr23" + }, + { + "@id": "bts:ChrM" + }, + { + "@id": "bts:ChrX" + }, + { + "@id": "bts:ChrY" }, { "@id": "bts:Unknown" @@ -24669,37 +30132,94 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Treatment Outcome", + "sms:displayName": "Chromosome", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DaystoTreatmentEnd", + "@id": "bts:Clonality", "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date the treatment ended. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoTreatmentEnd", + "rdfs:comment": "The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "Clonality", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Days to Treatment End", + "schema:rangeIncludes": [ + { + "@id": "bts:Clonal" + }, + { + "@id": "bts:Non-clonal" + } + ], + "sms:displayName": "Clonality", "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "sms:validationRules": [] }, { - "@id": "bts:TreatmentAnatomicSite", + "@id": "bts:CopyNumber", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment", - "rdfs:label": "TreatmentAnatomicSite", + "rdfs:comment": "Numeric value used to describe the number of times a section of the genome is repeated or copied within an insertion, duplication or deletion variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "CopyNumber", "rdfs:subClassOf": [ { - "@id": "bts:FollowUp" + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Copy Number", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Cytoband", + "@type": "rdfs:Class", + "rdfs:comment": "Alphanumeric value used to describe the cytoband or chromosomal location targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the cytoband where the variant is located. Format: [chromosome][chromosome arm].[band+sub-bands]. Example: 17p13.1. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "Cytoband", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Cytoband", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Exon", + "@type": "rdfs:Class", + "rdfs:comment": "Exon number targeted or included in a molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the exon where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "Exon", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Exon", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HistoneFamily", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the family, or classification of a group of basic proteins found in chromatin, called histones.", + "rdfs:label": "HistoneFamily", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { @@ -24707,1302 +30227,1829 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:AbdomenNOS" + "@id": "bts:H1" }, { - "@id": "bts:Abdominalesophagus" + "@id": "bts:H2A" }, { - "@id": "bts:AccessorysinusNOS" + "@id": "bts:H2B" }, { - "@id": "bts:Acousticnerve" + "@id": "bts:H3" }, { - "@id": "bts:AdrenalglandNOS" + "@id": "bts:H4" }, { - "@id": "bts:AmpullaofVater" + "@id": "bts:Unknown" }, { - "@id": "bts:Analcanal" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Histone Family", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HistoneVariant", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.", + "rdfs:label": "HistoneVariant", + "rdfs:subClassOf": [ { - "@id": "bts:Anterior2/3oftongueNOS" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Anteriorfloorofmouth" + "@id": "bts:CENP-A" }, { - "@id": "bts:Anteriormediastinum" + "@id": "bts:H2A-Bbd" }, { - "@id": "bts:Anteriorsurfaceofepiglottis" + "@id": "bts:H2A.X" }, { - "@id": "bts:Anteriorwallofbladder" + "@id": "bts:H2A.Z" }, { - "@id": "bts:Anteriorwallofnasopharynx" + "@id": "bts:H2A.Z.1" }, { - "@id": "bts:AnusNOS" + "@id": "bts:H2A.Z.2" }, { - "@id": "bts:Aorticbodyandotherparaganglia" + "@id": "bts:H2A.Z.2.2" }, { - "@id": "bts:Appendix" + "@id": "bts:H3.1" }, { - "@id": "bts:Ascendingcolon" + "@id": "bts:H3.2" }, { - "@id": "bts:AutonomicnervoussystemNOS" + "@id": "bts:H3.3" }, { - "@id": "bts:Axillarytailofbreast" + "@id": "bts:H3.5" }, { - "@id": "bts:BaseoftongueNOS" + "@id": "bts:H3.X" }, { - "@id": "bts:Bladderneck" + "@id": "bts:H3.Y" }, { - "@id": "bts:BladderNOS" + "@id": "bts:H3t(H3.4)" }, { - "@id": "bts:Blood" + "@id": "bts:MH2A" }, { - "@id": "bts:Bodyofpancreas" + "@id": "bts:MH2A.1" }, { - "@id": "bts:Bodyofpenis" + "@id": "bts:MH2A.2" }, { - "@id": "bts:Bodyofstomach" + "@id": "bts:Unknown" }, { - "@id": "bts:Bonemarrow" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Histone Variant", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Intron", + "@type": "rdfs:Class", + "rdfs:comment": "Intron number targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the intron where that variant is located.", + "rdfs:label": "Intron", + "rdfs:subClassOf": [ { - "@id": "bts:BoneoflimbNOS" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Intron", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:LaboratoryTest", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the medical testing used to diagnose, treat or further understand a patient's disease.", + "rdfs:label": "LaboratoryTest", + "rdfs:subClassOf": [ { - "@id": "bts:BoneNOS" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Bonesofskullandfaceandassociatedjoints" + "@id": "bts:AbsoluteNeutrophil" }, { - "@id": "bts:Borderoftongue" + "@id": "bts:Albumin" }, { - "@id": "bts:Brainstem" + "@id": "bts:AlphaFetoprotein" }, { - "@id": "bts:BrainNOS" + "@id": "bts:B-cellgenotyping" }, { - "@id": "bts:Branchialcleft" + "@id": "bts:Basophil" }, { - "@id": "bts:BreastNOS" + "@id": "bts:Beta2Microglobulin" }, { - "@id": "bts:Broadligament" + "@id": "bts:BloodUreaNitrogen" }, { - "@id": "bts:CardiaNOS" + "@id": "bts:C-ReactiveProtein" }, { - "@id": "bts:Carotidbody" + "@id": "bts:Calcium" }, { - "@id": "bts:Caudaequina" + "@id": "bts:Cellularity" }, { - "@id": "bts:Cecum" + "@id": "bts:CirculatingTumorCells" }, { - "@id": "bts:Centralportionofbreast" + "@id": "bts:Creatinine" }, { - "@id": "bts:CerebellumNOS" + "@id": "bts:Eosinophil" }, { - "@id": "bts:Cerebralmeninges" + "@id": "bts:Epstein-BarrVirus" }, { - "@id": "bts:Cerebrum" + "@id": "bts:Glucose" }, { - "@id": "bts:Cervicalesophagus" + "@id": "bts:Hematocrit" }, { - "@id": "bts:Cervixuteri" + "@id": "bts:Hemoglobin" }, { - "@id": "bts:Choroid" + "@id": "bts:HPV-E6/E7" }, { - "@id": "bts:Ciliarybody" + "@id": "bts:HumanChorionicGonadotropin" }, { - "@id": "bts:Cloacogeniczone" + "@id": "bts:HumanPapillomavirus" }, { - "@id": "bts:ColonNOS" + "@id": "bts:ImmunoglobulinA" }, { - "@id": "bts:Commissureoflip" + "@id": "bts:ImmunoglobulinG" }, { - "@id": "bts:Conjunctiva" + "@id": "bts:ImmunoglobulinM" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofabdomen" + "@id": "bts:LactateDehydrogenase" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofheadfaceandneck" + "@id": "bts:Leukocytes" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesoflowerlimbandhip" + "@id": "bts:LuteinizingHormone" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofpelvis" + "@id": "bts:Lymphoblasts" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofthorax" + "@id": "bts:Lymphocytes" }, { - "@id": "bts:ConnectivesubcutaneousandothersofttissuesoftrunkNOS" + "@id": "bts:MProtein" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofupperlimbandshoulder" + "@id": "bts:Metamyelocytes" }, { - "@id": "bts:ConnectivesubcutaneousandothersofttissuesNOS" + "@id": "bts:Myeloblasts" }, { - "@id": "bts:CorneaNOS" + "@id": "bts:Myelocytes" }, { - "@id": "bts:Corpusuteri" + "@id": "bts:NeutrophilBands" }, { - "@id": "bts:Cortexofadrenalgland" + "@id": "bts:Platelets" }, { - "@id": "bts:CranialnerveNOS" + "@id": "bts:Prolymphocytes" }, { - "@id": "bts:Craniopharyngealduct" + "@id": "bts:Promonocytes" }, { - "@id": "bts:Descendedtestis" + "@id": "bts:Promyelocytes" }, { - "@id": "bts:Descendingcolon" + "@id": "bts:SegmentedNeutrophil" }, { - "@id": "bts:Domeofbladder" + "@id": "bts:SerumFreeImmunoglobulinLightChain" }, { - "@id": "bts:DorsalsurfaceoftongueNOS" + "@id": "bts:Kappa" }, { - "@id": "bts:Duodenum" + "@id": "bts:Lambda" }, { - "@id": "bts:Endocervix" + "@id": "bts:NOS" }, { - "@id": "bts:EndocrineglandNOS" + "@id": "bts:Testosterone" }, { - "@id": "bts:Endometrium" + "@id": "bts:TotalBilirubin" }, { - "@id": "bts:Epididymis" + "@id": "bts:TotalProtein" }, { - "@id": "bts:EsophagusNOS" + "@id": "bts:Unknown" }, { - "@id": "bts:Ethmoidsinus" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Laboratory Test", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:LociAbnormalCount", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value used to describe the number of loci determined to be abnormal.", + "rdfs:label": "LociAbnormalCount", + "rdfs:subClassOf": [ { - "@id": "bts:Exocervix" + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Loci Abnormal Count", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:LociCount", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value used to describe the number of loci tested.", + "rdfs:label": "LociCount", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Loci Count", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Locus", + "@type": "rdfs:Class", + "rdfs:comment": "Alphanumeric value used to describe the locus of a specific genetic variant. Example: NM_001126114.", + "rdfs:label": "Locus", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Locus", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MismatchRepairMutation", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the mutation included in molecular testing was known to have an affect on the mismatch repair process. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "MismatchRepairMutation", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" }, { - "@id": "bts:Externalear" + "@id": "bts:No" }, { - "@id": "bts:ExternallipNOS" + "@id": "bts:Unknown" }, { - "@id": "bts:Externallowerlip" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Mismatch Repair Mutation", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MolecularConsequence", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the molecular consequence of genetic variation. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "MolecularConsequence", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:3PrimeUTRVariant" }, { - "@id": "bts:Externalupperlip" + "@id": "bts:5PrimeUTRVariant" }, { - "@id": "bts:Extrahepaticbileduct" + "@id": "bts:CodingSequenceVariant" }, { - "@id": "bts:EyeNOS" + "@id": "bts:DownstreamGeneVariant" }, { - "@id": "bts:Eyelid" + "@id": "bts:FeatureElongation" }, { - "@id": "bts:Fallopiantube" + "@id": "bts:FeatureTruncation" }, { - "@id": "bts:FemalegenitaltractNOS" + "@id": "bts:FrameshiftVariant" }, { - "@id": "bts:FloorofmouthNOS" + "@id": "bts:IncompleteTerminalCodonVariant" }, { - "@id": "bts:Frontallobe" + "@id": "bts:InframeDeletion" }, { - "@id": "bts:Frontalsinus" + "@id": "bts:InframeInsertion" }, { - "@id": "bts:Fundusofstomach" + "@id": "bts:IntergenicVariant" }, { - "@id": "bts:Fundusuteri" + "@id": "bts:IntronVariant" }, { - "@id": "bts:Gallbladder" + "@id": "bts:MaturemiRNAVariant" }, { - "@id": "bts:Gastricantrum" + "@id": "bts:MissenseVariant" }, { - "@id": "bts:GastrointestinaltractNOS" + "@id": "bts:NMDTranscriptVariant" }, { - "@id": "bts:Glanspenis" + "@id": "bts:Non-codingTranscriptExonVariant" }, { - "@id": "bts:Glottis" + "@id": "bts:Non-codingTranscriptVariant" }, { - "@id": "bts:GreatercurvatureofstomachNOS" + "@id": "bts:ProteinAlteringVariant" }, { - "@id": "bts:GumNOS" + "@id": "bts:RegulatoryRegionAblation" }, { - "@id": "bts:Hardpalate" + "@id": "bts:RegulatoryRegionAmplification" }, { - "@id": "bts:Headofpancreas" + "@id": "bts:RegulatoryRegionVariant" }, { - "@id": "bts:HeadfaceorneckNOS" + "@id": "bts:SpliceAcceptorVariant" }, { - "@id": "bts:Heart" + "@id": "bts:SpliceDonorVariant" }, { - "@id": "bts:HematopoieticsystemNOS" + "@id": "bts:SpliceRegionVariant" }, { - "@id": "bts:Hepaticflexureofcolon" + "@id": "bts:StartLost" }, { - "@id": "bts:Hypopharyngealaspectofaryepiglotticfold" + "@id": "bts:StopGain" }, { - "@id": "bts:HypopharynxNOS" + "@id": "bts:StopLost" }, { - "@id": "bts:Ileum" + "@id": "bts:StopRetainedVariant" }, { - "@id": "bts:Ill-definedsiteswithinrespiratorysystem" + "@id": "bts:SynonymousVariant" }, { - "@id": "bts:IntestinaltractNOS" + "@id": "bts:TFBindingSiteVariant" }, { - "@id": "bts:Intra-abdominallymphnodes" + "@id": "bts:TFBSAblation" }, { - "@id": "bts:Intrahepaticbileduct" + "@id": "bts:TFBSAmplification" }, { - "@id": "bts:Intrathoraciclymphnodes" + "@id": "bts:TranscriptAblation" }, { - "@id": "bts:IsletsofLangerhans" + "@id": "bts:TranscriptAmplification" }, { - "@id": "bts:Isthmusuteri" - }, + "@id": "bts:UpstreamGeneVariant" + } + ], + "sms:displayName": "Molecular Consequence", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Pathogenicity", + "@type": "rdfs:Class", + "rdfs:comment": "The text used to describe a variant's level of involvement in the cause of the patient's disease according to the standards outlined by the American College of Medical Genetics and Genomics (ACMG).", + "rdfs:label": "Pathogenicity", + "rdfs:subClassOf": [ + { + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Jejunum" + "@id": "bts:Benign" }, { - "@id": "bts:KidneyNOS" + "@id": "bts:LikelyBenign" }, { - "@id": "bts:Labiummajus" + "@id": "bts:LikelyPathogenic" }, { - "@id": "bts:Labiumminus" + "@id": "bts:Pathogenic" }, { - "@id": "bts:Lacrimalgland" - }, + "@id": "bts:UncertainSignificance" + } + ], + "sms:displayName": "Pathogenicity", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Ploidy", + "@type": "rdfs:Class", + "rdfs:comment": "Text term used to describe the number of sets of homologous chromosomes.", + "rdfs:label": "Ploidy", + "rdfs:subClassOf": [ { - "@id": "bts:Laryngealcartilage" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:LarynxNOS" + "@id": "bts:Aneuploid" }, { - "@id": "bts:Lateralfloorofmouth" + "@id": "bts:Diploid" }, { - "@id": "bts:Lateralwallofbladder" + "@id": "bts:Hyperdiploid" }, { - "@id": "bts:Lateralwallofnasopharynx" + "@id": "bts:Hypodiploid" }, { - "@id": "bts:Lateralwalloforopharynx" + "@id": "bts:NearDiploid" }, { - "@id": "bts:LessercurvatureofstomachNOS" + "@id": "bts:Tetraploid" }, { - "@id": "bts:Lingualtonsil" + "@id": "bts:Unknown" }, { - "@id": "bts:LipNOS" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Ploidy", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SecondExon", + "@type": "rdfs:Class", + "rdfs:comment": "The second exon number involved in molecular variation. If a specific genetic variant is being reported, this property can be used to capture the second exon where that variant is located. This property is typically used for a translocation where two different locations are involved in the variation.", + "rdfs:label": "SecondExon", + "rdfs:subClassOf": [ { - "@id": "bts:Liver" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Second Exon", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SecondGeneSymbol", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe a secondary gene targeted or included in molecular analysis. For rearrangements, this is should represent the location of the variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "SecondGeneSymbol", + "rdfs:subClassOf": [ { - "@id": "bts:Longbonesoflowerlimbandassociatedjoints" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Second Gene Symbol", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SpecializedMolecularTest", + "@type": "rdfs:Class", + "rdfs:comment": "Text term used to describe a specific test that is not covered in the list of molecular analysis methods. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "SpecializedMolecularTest", + "rdfs:subClassOf": [ { - "@id": "bts:Longbonesofupperlimbscapulaandassociatedjoints" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Specialized Molecular Test", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TestAnalyteType", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the type of analyte used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "TestAnalyteType", + "rdfs:subClassOf": [ { - "@id": "bts:Lowergum" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:LowerlimbNOS" + "@id": "bts:DNA" }, { - "@id": "bts:Lowerlobelung" + "@id": "bts:MRNA" }, { - "@id": "bts:Lowerthirdofesophagus" + "@id": "bts:MiRNA" }, { - "@id": "bts:Lower-innerquadrantofbreast" + "@id": "bts:ProteinAnalyte" }, { - "@id": "bts:Lower-outerquadrantofbreast" + "@id": "bts:TotalRNA" }, { - "@id": "bts:LungNOS" + "@id": "bts:Unknown" }, { - "@id": "bts:LymphnodeNOS" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Test Analyte Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TestUnits", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the units of the test value for a molecular test. This property is used in conjunction with test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "TestUnits", + "rdfs:subClassOf": [ { - "@id": "bts:Lymphnodesofaxillaorarm" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Test Units", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TestValue", + "@type": "rdfs:Class", + "rdfs:comment": "The text term or numeric value used to describe a specific result of a molecular test. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here", + "rdfs:label": "TestValue", + "rdfs:subClassOf": [ { - "@id": "bts:Lymphnodesofheadfaceandneck" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Test Value", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Transcript", + "@type": "rdfs:Class", + "rdfs:comment": "Alphanumeric value used to describe the transcript of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "Transcript", + "rdfs:subClassOf": [ { - "@id": "bts:Lymphnodesofinguinalregionorleg" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Transcript", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:VariantOrigin", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the biological origin of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label": "VariantOrigin", + "rdfs:subClassOf": [ { - "@id": "bts:Lymphnodesofmultipleregions" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Mainbronchus" + "@id": "bts:Germline" }, { - "@id": "bts:MajorsalivaryglandNOS" + "@id": "bts:Somatic" }, { - "@id": "bts:MalegenitalorgansNOS" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Variant Origin", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:VariantType", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the type of genetic variation.", + "rdfs:label": "VariantType", + "rdfs:subClassOf": [ { - "@id": "bts:Mandible" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Maxillarysinus" + "@id": "bts:Alleles" }, { - "@id": "bts:Meckeldiverticulum" + "@id": "bts:Amplification" }, { - "@id": "bts:MediastinumNOS" + "@id": "bts:Chrimerism" }, { - "@id": "bts:Medullaofadrenalgland" + "@id": "bts:Conversion" }, { - "@id": "bts:MeningesNOS" + "@id": "bts:Deletion" }, { - "@id": "bts:Middleear" + "@id": "bts:Deletion-Insertion" }, { - "@id": "bts:Middlelobelung" + "@id": "bts:Duplication" }, { - "@id": "bts:Middlethirdofesophagus" + "@id": "bts:Extension" }, { - "@id": "bts:MouthNOS" + "@id": "bts:Gain" }, { - "@id": "bts:MucosaoflipNOS" + "@id": "bts:Hypermethylation" }, { - "@id": "bts:Mucosaoflowerlip" + "@id": "bts:Insertion" }, { - "@id": "bts:Mucosaofupperlip" + "@id": "bts:Inversion" }, { - "@id": "bts:Myometrium" + "@id": "bts:Loss" }, { - "@id": "bts:Nasalcavity" + "@id": "bts:Methylation" }, { - "@id": "bts:NasopharynxNOS" + "@id": "bts:Mosaicism" }, { - "@id": "bts:NervoussystemNOS" + "@id": "bts:Other" }, { - "@id": "bts:Nipple" + "@id": "bts:PartialMethylation" }, { - "@id": "bts:Occipitallobe" + "@id": "bts:Rearrangement" }, { - "@id": "bts:Olfactorynerve" + "@id": "bts:RepeatedSequences" }, { - "@id": "bts:Opticnerve" + "@id": "bts:Splice" }, { - "@id": "bts:OrbitNOS" + "@id": "bts:Substitution" }, { - "@id": "bts:OropharynxNOS" + "@id": "bts:Translocation" }, { - "@id": "bts:Otherill-definedsites" + "@id": "bts:Unknown" }, { - "@id": "bts:Otherspecifiedpartsoffemalegenitalorgans" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Variant Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Zygosity", + "@type": "rdfs:Class", + "rdfs:comment": "The text term used to describe the zygosity of a specific genetic variant.", + "rdfs:label": "Zygosity", + "rdfs:subClassOf": [ { - "@id": "bts:Otherspecifiedpartsofmalegenitalorgans" - }, + "@id": "bts:MolecularTest" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Otherspecifiedpartsofpancreas" + "@id": "bts:Heterozygous" }, { - "@id": "bts:Ovary" + "@id": "bts:Hemizygous" }, { - "@id": "bts:Overlappinglesionofaccessorysinuses" + "@id": "bts:Homozygous" }, { - "@id": "bts:Overlappinglesionofbladder" + "@id": "bts:Nullizygous" }, { - "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilage" + "@id": "bts:Unknown" }, { - "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilageoflimbs" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Zygosity", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SourceHTANBiospecimenID", + "@type": "rdfs:Class", + "rdfs:comment": "This is the HTAN ID that may have been assigned to the biospecimen at the site of biospecimen origin (e.g. BU).", + "rdfs:label": "SourceHTANBiospecimenID", + "rdfs:subClassOf": [ { - "@id": "bts:Overlappinglesionofbrain" - }, + "@id": "bts:Biosample" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Source HTAN Biospecimen ID", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CollectionDaysfromIndex", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days from the research participant's index date that the biospecimen was obtained. If not applicable please enter 'Not Applicable'", + "rdfs:label": "CollectionDaysfromIndex", + "rdfs:subClassOf": [ { - "@id": "bts:Overlappinglesionofbrainandcentralnervoussystem" - }, + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Collection Days from Index", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:AdjacentBiospecimenIDs", + "@type": "rdfs:Class", + "rdfs:comment": "List of HTAN Identifiers (separated by commas) of adjacent biospecimens cut from the same sample; for example HTA3_3000_3, HTA3_3000_4, ...", + "rdfs:label": "AdjacentBiospecimenIDs", + "rdfs:subClassOf": [ { - "@id": "bts:Overlappinglesionofbreast" - }, + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Adjacent Biospecimen IDs", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BiospecimenType", + "@type": "rdfs:Class", + "rdfs:comment": "Biospecimen Type", + "rdfs:label": "BiospecimenType", + "rdfs:subClassOf": [ { - "@id": "bts:Overlappinglesionofcervixuteri" - }, + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Overlappinglesionofcolon" + "@id": "bts:TissueBiospecimenType" }, { - "@id": "bts:Overlappinglesionofconnectivesubcutaneousandothersofttissues" + "@id": "bts:BloodBiospecimenType" }, { - "@id": "bts:Overlappinglesionofcorpusuteri" + "@id": "bts:AnalyteBiospecimenType" }, { - "@id": "bts:Overlappinglesionofdigestivesystem" + "@id": "bts:MouthRinseBiospecimenType" }, { - "@id": "bts:Overlappinglesionofendocrineglandsandrelatedstructures" + "@id": "bts:StoolBiospecimenType" }, { - "@id": "bts:Overlappinglesionofesophagus" + "@id": "bts:UrineBiospecimenType" }, { - "@id": "bts:Overlappinglesionofeyeandadnexa" + "@id": "bts:AscitesBiospecimenType" }, { - "@id": "bts:Overlappinglesionoffemalegenitalorgans" + "@id": "bts:SputumBiospecimenType" }, { - "@id": "bts:Overlappinglesionoffloorofmouth" + "@id": "bts:FluidsBiospecimenType" }, { - "@id": "bts:Overlappinglesionofheartmediastinumandpleura" + "@id": "bts:BoneMarrowBiospecimenType" }, { - "@id": "bts:Overlappinglesionofhypopharynx" - }, + "@id": "bts:CellsBiospecimenType" + } + ], + "sms:displayName": "Biospecimen Type", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:AcquisitionMethodType", + "@type": "rdfs:Class", + "rdfs:comment": "Records the method of acquisition or source for the specimen under consideration.", + "rdfs:label": "AcquisitionMethodType", + "rdfs:subClassOf": [ { - "@id": "bts:Overlappinglesionofill-definedsites" - }, + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Overlappinglesionoflarynx" + "@id": "bts:Autopsy" }, { - "@id": "bts:Overlappinglesionoflip" + "@id": "bts:Biopsy" }, { - "@id": "bts:Overlappinglesionofliporalcavityandpharynx" + "@id": "bts:FineNeedleAspirate" }, { - "@id": "bts:Overlappinglesionoflung" + "@id": "bts:SurgicalResection" }, { - "@id": "bts:Overlappinglesionofmajorsalivaryglands" + "@id": "bts:PunchBiopsy" }, { - "@id": "bts:Overlappinglesionofmalegenitalorgans" + "@id": "bts:ShaveBiopsy" }, { - "@id": "bts:Overlappinglesionofnasopharynx" + "@id": "bts:Excision" }, { - "@id": "bts:Overlappinglesionofotherandunspecifiedpartsofmouth" + "@id": "bts:Re-excision" }, { - "@id": "bts:Overlappinglesionofpalate" + "@id": "bts:SentinelNodeBiopsy" }, { - "@id": "bts:Overlappinglesionofpancreas" + "@id": "bts:Lymphadenectomy-RegionalNodes" }, { - "@id": "bts:Overlappinglesionofpenis" + "@id": "bts:OtherAcquisitionMethod" }, { - "@id": "bts:Overlappinglesionofperipheralnervesandautonomicnervoussystem" + "@id": "bts:Noninducedsputum" }, { - "@id": "bts:Overlappinglesionofrectumanusandanalcanal" + "@id": "bts:Inducedsputum" }, { - "@id": "bts:Overlappinglesionofrespiratorysystemandintrathoracicorgans" + "@id": "bts:BAL(bronchialalveolarlavage)" }, { - "@id": "bts:Overlappinglesionofretroperitoneumandperitoneum" + "@id": "bts:Cytobrush" }, { - "@id": "bts:Overlappinglesionofskin" + "@id": "bts:Blooddraw" }, { - "@id": "bts:Overlappinglesionofsmallintestine" + "@id": "bts:Fluidcollection" }, { - "@id": "bts:Overlappinglesionofstomach" + "@id": "bts:Forcepsbiopsy" }, { - "@id": "bts:Overlappinglesionoftongue" + "@id": "bts:Coreneedlebiopsy" }, { - "@id": "bts:Overlappinglesionoftonsil" + "@id": "bts:Endoscopicbiopsy" }, { - "@id": "bts:Overlappinglesionofurinaryorgans" - }, + "@id": "bts:Notspecified" + } + ], + "sms:displayName": "Acquisition Method Type", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:FixativeType", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to identify the type of fixative used to preserve a tissue specimen", + "rdfs:label": "FixativeType", + "rdfs:subClassOf": [ { - "@id": "bts:Overlappinglesionofvulva" - }, + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Overlappinglesionsoforopharynx" + "@id": "bts:Acetone" }, { - "@id": "bts:PalateNOS" + "@id": "bts:Alcohol" }, { - "@id": "bts:PancreasNOS" + "@id": "bts:Formalin" }, { - "@id": "bts:Pancreaticduct" + "@id": "bts:Glutaraldehyde" }, { - "@id": "bts:Parametrium" + "@id": "bts:OCTmedia" }, { - "@id": "bts:Parathyroidgland" + "@id": "bts:RNAlater" }, { - "@id": "bts:Paraurethralgland" + "@id": "bts:Saline" }, { - "@id": "bts:Parietallobe" + "@id": "bts:95%Ethanol" }, { - "@id": "bts:Parotidgland" + "@id": "bts:Dimidoester" }, { - "@id": "bts:Pelvicbonessacrumcoccyxandassociatedjoints" + "@id": "bts:Carbodiimide" }, { - "@id": "bts:Pelviclymphnodes" + "@id": "bts:Dimethylacetamide" }, { - "@id": "bts:PelvisNOS" + "@id": "bts:Para-benzoquinone" }, { - "@id": "bts:PenisNOS" + "@id": "bts:PAXgenetissue" }, { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofabdomen" + "@id": "bts:TCLlysisbuffer" }, { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofheadfaceandneck" + "@id": "bts:NP40lysisbuffer" }, { - "@id": "bts:Peripheralnervesandautonomicnervoussystemoflowerlimbandhip" + "@id": "bts:Methacarn" }, { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofpelvis" + "@id": "bts:Cryo-store" }, { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofthorax" + "@id": "bts:Carnoy'sFixative" }, { - "@id": "bts:PeripheralnervesandautonomicnervoussystemoftrunkNOS" + "@id": "bts:Polaxamer" }, { - "@id": "bts:Peripheralnervesandautonomicnervoussystemofupperlimbandshoulder" + "@id": "bts:Other" }, { - "@id": "bts:PeritoneumNOS" + "@id": "bts:None" }, { - "@id": "bts:PharynxNOS" + "@id": "bts:Unknown" }, { - "@id": "bts:Pinealgland" - }, + "@id": "bts:Unfixed" + } + ], + "sms:displayName": "Fixative Type", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:StorageMethod", + "@type": "rdfs:Class", + "rdfs:comment": "The method by which a biomaterial was stored after preservation or before another protocol was used.", + "rdfs:label": "StorageMethod", + "rdfs:subClassOf": [ { - "@id": "bts:Pituitarygland" - }, + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Placenta" + "@id": "bts:Ambienttemperature" }, { - "@id": "bts:PleuraNOS" + "@id": "bts:Cutslide" }, { - "@id": "bts:Postcricoidregion" + "@id": "bts:Fresh" }, { - "@id": "bts:Posteriormediastinum" + "@id": "bts:Frozenat-20C" }, { - "@id": "bts:Posteriorwallofbladder" + "@id": "bts:Frozenat-70C" }, { - "@id": "bts:Posteriorwallofhypopharynx" + "@id": "bts:Frozenat-80C" }, { - "@id": "bts:Posteriorwallofnasopharynx" + "@id": "bts:Frozenat-150C" }, { - "@id": "bts:Posteriorwalloforopharynx" + "@id": "bts:Frozeninliquidnitrogen" }, { - "@id": "bts:Prepuce" + "@id": "bts:Frozeninvaporphase" }, { - "@id": "bts:Prostategland" + "@id": "bts:Paraffinblock" }, { - "@id": "bts:Pylorus" + "@id": "bts:RNAlaterat4C" }, { - "@id": "bts:Pyriformsinus" + "@id": "bts:RNAlaterat25C" }, { - "@id": "bts:Rectosigmoidjunction" + "@id": "bts:RNAlaterat-20C" }, { - "@id": "bts:RectumNOS" + "@id": "bts:Refrigeratedat4degrees" }, { - "@id": "bts:Renalpelvis" + "@id": "bts:Refrigeratedvacuumchamber" }, { - "@id": "bts:ReticuloendothelialsystemNOS" + "@id": "bts:4Cinvacuumchamber" }, { - "@id": "bts:Retina" + "@id": "bts:Desiccantat4C" }, { - "@id": "bts:Retromolararea" + "@id": "bts:NotApplicable" }, { - "@id": "bts:Retroperitoneum" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Storage Method", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:ProcessingDaysfromIndex", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days from the research participant's index date that the biospecimen was processed. If not applicable please enter 'Not Applicable'", + "rdfs:label": "ProcessingDaysfromIndex", + "rdfs:subClassOf": [ { - "@id": "bts:Ribsternumclavicleandassociatedjoints" - }, + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Processing Days from Index", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:ProtocolLink", + "@type": "rdfs:Class", + "rdfs:comment": "Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.", + "rdfs:label": "ProtocolLink", + "rdfs:subClassOf": [ { - "@id": "bts:Roundligament" - }, + "@id": "bts:InformationContentEntity" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Protocol Link", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:SiteDataSource", + "@type": "rdfs:Class", + "rdfs:comment": "Text to identify the data source for the specimen/sample from within the HTAN center, if applicable. Any identifier used within the center to identify data sources. No PHI/PII is allowed.", + "rdfs:label": "SiteDataSource", + "rdfs:subClassOf": [ { - "@id": "bts:ScrotumNOS" - }, + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Site Data Source", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CollectionMedia", + "@type": "rdfs:Class", + "rdfs:comment": "Material Specimen is collected into post procedure", + "rdfs:label": "CollectionMedia", + "rdfs:subClassOf": [ { - "@id": "bts:Shortbonesoflowerlimbandassociatedjoints" - }, + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Shortbonesofupperlimbandassociatedjoints" + "@id": "bts:DMEM" }, { - "@id": "bts:Sigmoidcolon" + "@id": "bts:DMEM+Serum" }, { - "@id": "bts:SkinoflipNOS" + "@id": "bts:RPMI" }, { - "@id": "bts:Skinoflowerlimbandhip" + "@id": "bts:RPMI+Serum" }, { - "@id": "bts:Skinofotherandunspecifiedpartsofface" + "@id": "bts:PBS" }, { - "@id": "bts:Skinofscalpandneck" + "@id": "bts:PBS+Serum" }, { - "@id": "bts:Skinoftrunk" - }, + "@id": "bts:None" + } + ], + "sms:displayName": "Collection Media", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MountingMedium", + "@type": "rdfs:Class", + "rdfs:comment": "The solution in which the specimen is embedded, generally under a cover glass. It may be liquid, gum or resinous, soluble in water, alcohol or other solvents and be sealed from the external atmosphere by non-soluble ringing media", + "rdfs:label": "MountingMedium", + "rdfs:subClassOf": [ { - "@id": "bts:Skinofupperlimbandshoulder" - }, + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:SkinNOS" + "@id": "bts:Aqueouswaterbased" }, { - "@id": "bts:SmallintestineNOS" + "@id": "bts:Non-AqueousSolventbased" }, { - "@id": "bts:SoftpalateNOS" + "@id": "bts:Xylene" }, { - "@id": "bts:Specifiedpartsofperitoneum" + "@id": "bts:Toluene" }, { - "@id": "bts:Spermaticcord" + "@id": "bts:AntifadewithDAPI" }, { - "@id": "bts:Sphenoidsinus" + "@id": "bts:AntifadewithoutDAPI" }, { - "@id": "bts:Spinalcord" + "@id": "bts:PBS" }, { - "@id": "bts:Spinalmeninges" + "@id": "bts:Unknown" }, { - "@id": "bts:Spleen" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Mounting Medium", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ProcessingLocation", + "@type": "rdfs:Class", + "rdfs:comment": "Site with an HTAN center where specimen processing occurs, if applicable. Any identifier used within the center to identify processing location. No PHI/PII is allowed.", + "rdfs:label": "ProcessingLocation", + "rdfs:subClassOf": [ { - "@id": "bts:Splenicflexureofcolon" - }, + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Processing Location", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HistologyAssessmentBy", + "@type": "rdfs:Class", + "rdfs:comment": "Text term describing who (in what role) made the histological assessments of the sample", + "rdfs:label": "HistologyAssessmentBy", + "rdfs:subClassOf": [ { - "@id": "bts:StomachNOS" - }, + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Subglottis" + "@id": "bts:Pathologist" }, { - "@id": "bts:Sublingualgland" + "@id": "bts:ResearchScientist" }, { - "@id": "bts:Submandibulargland" + "@id": "bts:Other" }, { - "@id": "bts:Superiorwallofnasopharynx" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Histology Assessment By", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HistologyAssessmentMedium", + "@type": "rdfs:Class", + "rdfs:comment": "The method of assessment used to characterize histology", + "rdfs:label": "HistologyAssessmentMedium", + "rdfs:subClassOf": [ { - "@id": "bts:Supraglottis" - }, + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Tailofpancreas" + "@id": "bts:Digital" }, { - "@id": "bts:Temporallobe" + "@id": "bts:Microscopy" }, { - "@id": "bts:TestisNOS" + "@id": "bts:Other" }, { - "@id": "bts:Thoracicesophagus" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Histology Assessment Medium", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PreinvasiveMorphology", + "@type": "rdfs:Class", + "rdfs:comment": "Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the HTAN", + "rdfs:label": "PreinvasiveMorphology", + "rdfs:subClassOf": [ { - "@id": "bts:ThoraxNOS" - }, + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Thymus" + "@id": "bts:Melanocytichyperplasia" }, { - "@id": "bts:Thyroidgland" + "@id": "bts:Atypicalmelanocyticproliferation" }, { - "@id": "bts:TongueNOS" + "@id": "bts:Melanomainsitu-superficialspreading" }, { - "@id": "bts:TonsilNOS" + "@id": "bts:Melanomainsitu-lentigomalignatype" }, { - "@id": "bts:Tonsillarfossa" + "@id": "bts:Melanomainsitu-acral-lentiginous" }, { - "@id": "bts:Tonsillarpillar" + "@id": "bts:Melanomainsitu-arisinginagiantcongenitalnevus" }, { - "@id": "bts:Trachea" + "@id": "bts:Persistentmelanomainsitu" }, { - "@id": "bts:Transversecolon" + "@id": "bts:Melanomainsitu-nototherwiseclassified" }, { - "@id": "bts:Trigoneofbladder" + "@id": "bts:Scar-noresidualmelanoma" }, { - "@id": "bts:Undescendedtestis" + "@id": "bts:Invasivemelanoma-superficialspreading" }, { - "@id": "bts:Unknownprimarysite" + "@id": "bts:Invasivemelanoma-nodulartype" }, { - "@id": "bts:Uppergum" + "@id": "bts:Invasivemelanoma-lentigomaligna" }, { - "@id": "bts:UpperlimbNOS" + "@id": "bts:Invasivemelanoma-acrallentiginous" }, { - "@id": "bts:Upperlobelung" + "@id": "bts:Invasivemelanoma-desmoplastic" }, { - "@id": "bts:UpperrespiratorytractNOS" + "@id": "bts:Invasivemelanoma-nevoid" }, { - "@id": "bts:Upperthirdofesophagus" + "@id": "bts:Invasivemelanoma-other" }, { - "@id": "bts:Upper-innerquadrantofbreast" + "@id": "bts:NormalWDA" }, { - "@id": "bts:Upper-outerquadrantofbreast" + "@id": "bts:Reservecellhyperplasia" }, { - "@id": "bts:Urachus" + "@id": "bts:Squamousmetaplasia-mature" }, { - "@id": "bts:Ureter" + "@id": "bts:Squamousmetaplasia-immature" }, { - "@id": "bts:Uretericorifice" + "@id": "bts:Milddysplasia" }, { - "@id": "bts:Urethra" + "@id": "bts:Moderatedysplasia" }, { - "@id": "bts:UrinarysystemNOS" + "@id": "bts:Severedysplasia" }, { - "@id": "bts:Uterineadnexa" + "@id": "bts:SquamousCarcinomainsitu" }, { - "@id": "bts:UterusNOS" + "@id": "bts:Atypicaladenomatoushyperplasia" }, { - "@id": "bts:Uvula" + "@id": "bts:Adenocarcinomainsitu-nonmucinous" }, { - "@id": "bts:VaginaNOS" + "@id": "bts:Adenocarcinomainsitu-mucinous" }, { - "@id": "bts:Vallecula" + "@id": "bts:BenigntumorNOS" }, { - "@id": "bts:VentralsurfaceoftongueNOS" + "@id": "bts:Hamartoma" }, { - "@id": "bts:VentricleNOS" + "@id": "bts:CarcinomaNOS" }, { - "@id": "bts:Vertebralcolumn" - }, + "@id": "bts:Nodiagnosispossible" + } + ], + "sms:displayName": "Preinvasive Morphology", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TumorInfiltratingLymphocytes", + "@type": "rdfs:Class", + "rdfs:comment": "Measure of Tumor-Infiltrating Lymphocytes [Number]", + "rdfs:label": "TumorInfiltratingLymphocytes", + "rdfs:subClassOf": [ { - "@id": "bts:Vestibuleofmouth" - }, + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Tumor Infiltrating Lymphocytes", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:DegreeofDysplasia", + "@type": "rdfs:Class", + "rdfs:comment": "Information related to the presence of cells that look abnormal under a microscope but are not cancer. Records the degree of dysplasia for the cyst or lesion under consideration.", + "rdfs:label": "DegreeofDysplasia", + "rdfs:subClassOf": [ { - "@id": "bts:VulvaNOS" - }, + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Waldeyerring" + "@id": "bts:Normalorbasalcellhyperplasiaormetaplasia" }, { - "@id": "bts:BiliarytractNOS" + "@id": "bts:Milddysplasia" }, { - "@id": "bts:Cheekmucosa" + "@id": "bts:Moderatedysplasia" }, { - "@id": "bts:Clitoris" + "@id": "bts:Severedysplasia" }, { - "@id": "bts:Overlappinglesionofbiliarytract" + "@id": "bts:CarcinomainSitu" }, { "@id": "bts:Unknown" - }, + } + ], + "sms:displayName": "Degree of Dysplasia", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:DysplasiaFraction", + "@type": "rdfs:Class", + "rdfs:comment": "Resulting value to represent the number of pieces of dysplasia divided by the total number of pieces. [Text: max length 5]", + "rdfs:label": "DysplasiaFraction", + "rdfs:subClassOf": [ { - "@id": "bts:NotReported" + "@id": "bts:Biospecimen" } ], - "sms:displayName": "Treatment Anatomic Site", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Dysplasia Fraction", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DaystoTreatmentStart", + "@id": "bts:NumberProliferatingCells", "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date the treatment started. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoTreatmentStart", + "rdfs:comment": "Numeric value that represents the count of proliferating cells determined during pathologic review of the sample slide(s).", + "rdfs:label": "NumberProliferatingCells", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Number Proliferating Cells", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PercentEosinophilInfiltration", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric value to represent the percentage of infiltration by eosinophils in a tumor sample or specimen.", + "rdfs:label": "PercentEosinophilInfiltration", + "rdfs:subClassOf": [ + { + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Days to Treatment Start", + "sms:displayName": "Percent Eosinophil Infiltration", "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "sms:validationRules": [] }, { - "@id": "bts:InitialDiseaseStatus", + "@id": "bts:PercentGranulocyteInfiltration", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the status of the patient's malignancy when the treatment began.", - "rdfs:label": "InitialDiseaseStatus", + "rdfs:comment": "Numeric value to represent the percentage of infiltration by granulocytes in a tumor sample or specimen.", + "rdfs:label": "PercentGranulocyteInfiltration", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:InitialDiagnosis" - }, - { - "@id": "bts:ProgressiveDisease" - }, - { - "@id": "bts:RecurrentDisease" - }, - { - "@id": "bts:ResidualDisease" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Initial Disease Status", + "sms:displayName": "Percent Granulocyte Infiltration", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RegimenorLineofTherapy", + "@id": "bts:PercentInflamInfiltration", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the regimen or line of therapy.", - "rdfs:label": "RegimenorLineofTherapy", + "rdfs:comment": "Numeric value to represent local response to cellular injury, marked by capillary dilatation, edema and leukocyte infiltration; clinically, inflammation is manifest by redness, heat, pain, swelling and loss of function, with the need to heal damaged tissue.", + "rdfs:label": "PercentInflamInfiltration", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Regimen or Line of Therapy", + "sms:displayName": "Percent Inflam Infiltration", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TherapeuticAgents", + "@id": "bts:PercentLymphocyteInfiltration", "@type": "rdfs:Class", - "rdfs:comment": "Text identification of the individual agent(s) used as part of a treatment regimen.", - "rdfs:label": "TherapeuticAgents", + "rdfs:comment": "Numeric value to represent the percentage of infiltration by lymphocytes in a solid tissue normal sample or specimen.", + "rdfs:label": "PercentLymphocyteInfiltration", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Therapeutic Agents", + "sms:displayName": "Percent Lymphocyte Infiltration", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TreatmentIntentType", + "@id": "bts:PercentMonocyteInfiltration", "@type": "rdfs:Class", - "rdfs:comment": "Text term to identify the reason for the administration of a treatment regimen. [Manually-curated]", - "rdfs:label": "TreatmentIntentType", + "rdfs:comment": "Numeric value to represent the percentage of monocyte infiltration in a sample or specimen.", + "rdfs:label": "PercentMonocyteInfiltration", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Adjuvant" - }, - { - "@id": "bts:CancerControl" - }, - { - "@id": "bts:Cure" - }, - { - "@id": "bts:Neoadjuvant" - }, - { - "@id": "bts:Palliative" - }, - { - "@id": "bts:Prevention" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Treatment Intent Type", + "sms:displayName": "Percent Monocyte Infiltration", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ChemoConcurrenttoRadiation", + "@id": "bts:PercentNecrosis", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe whether the patient was receiving chemotherapy concurrent to radiation.", - "rdfs:label": "ChemoConcurrenttoRadiation", + "rdfs:comment": "Numeric value to represent the percentage of cell death in a malignant tumor sample or specimen.", + "rdfs:label": "PercentNecrosis", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Chemo Concurrent to Radiation", + "sms:displayName": "Percent Necrosis", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NumberofCycles", + "@id": "bts:PercentNeutrophilInfiltration", "@type": "rdfs:Class", - "rdfs:comment": "The numeric value used to describe the number of cycles of a specific treatment or regimen the patient received.", - "rdfs:label": "NumberofCycles", + "rdfs:comment": "Numeric value to represent the percentage of infiltration by neutrophils in a tumor sample or specimen.", + "rdfs:label": "PercentNeutrophilInfiltration", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Number of Cycles", + "sms:displayName": "Percent Neutrophil Infiltration", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ReasonTreatmentEnded", + "@id": "bts:PercentNormalCells", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the reason a specific treatment or regimen ended.", - "rdfs:label": "ReasonTreatmentEnded", + "rdfs:comment": "Numeric value to represent the percentage of normal cell content in a malignant tumor sample or specimen.", + "rdfs:label": "PercentNormalCells", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:AdverseTherapyEvent" - }, - { - "@id": "bts:CourseofTherapyCompleted" - }, - { - "@id": "bts:Death" - }, - { - "@id": "bts:DiseaseProgression" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:WithdrawalbySubject" - } - ], - "sms:displayName": "Reason Treatment Ended", + "sms:displayName": "Percent Normal Cells", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TreatmentArm", + "@id": "bts:PercentStromalCells", "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the treatment arm assigned to a patient at the time eligibility is determined.", - "rdfs:label": "TreatmentArm", + "rdfs:comment": "Numeric value to represent the percentage of reactive cells that are present in a malignant tumor sample or specimen but are not malignant such as fibroblasts, vascular structures, etc.", + "rdfs:label": "PercentStromalCells", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:A081105" - }, - { - "@id": "bts:E4512" - }, - { - "@id": "bts:EA5142" - } - ], - "sms:displayName": "Treatment Arm", + "sms:displayName": "Percent Stromal Cells", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TreatmentDose", + "@id": "bts:PercentTumorCells", "@type": "rdfs:Class", - "rdfs:comment": "The numeric value used to describe the dose of an agent the patient received.", - "rdfs:label": "TreatmentDose", + "rdfs:comment": "Numeric value that represents the percentage of infiltration by tumor cells in a sample.", + "rdfs:label": "PercentTumorCells", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Treatment Dose", + "sms:displayName": "Percent Tumor Cells", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TreatmentDoseUnits", + "@id": "bts:PercentTumorNuclei", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the dose units of an agent the patient received.", - "rdfs:label": "TreatmentDoseUnits", + "rdfs:comment": "Numeric value to represent the percentage of tumor nuclei in a malignant neoplasm sample or specimen.", + "rdfs:label": "PercentTumorNuclei", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:CGy" - }, - { - "@id": "bts:Gy" - } - ], - "sms:displayName": "Treatment Dose Units", + "sms:displayName": "Percent Tumor Nuclei", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TreatmentEffectIndicator", + "@id": "bts:FiducialMarker", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to indicate whether the treatment had an effect on the patient.", - "rdfs:label": "TreatmentEffectIndicator", + "rdfs:comment": "Imaging specific: fiducial markers for the alignment of images taken across multiple rounds of imaging.", + "rdfs:label": "FiducialMarker", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -26010,30 +32057,39 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:NuclearStain-DAPI" }, { - "@id": "bts:No" + "@id": "bts:FluorescentBeads" }, { - "@id": "bts:NotReported" + "@id": "bts:GridSlides-Hemocytometer" + }, + { + "@id": "bts:AdhesiveMarkers" + }, + { + "@id": "bts:Other" }, { "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Treatment Effect Indicator", + "sms:displayName": "Fiducial Marker", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TreatmentFrequency", + "@id": "bts:SlicingMethod", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the frequency the patient received an agent or regimen.", - "rdfs:label": "TreatmentFrequency", + "rdfs:comment": "Imaging specific: the method by which the tissue was sliced.", + "rdfs:label": "SlicingMethod", "rdfs:subClassOf": [ { - "@id": "bts:Therapy" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -26041,31 +32097,22 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:EveryHour" - }, - { - "@id": "bts:FiveTimesDaily" - }, - { - "@id": "bts:FourTimesDaily" - }, - { - "@id": "bts:ThreeTimesDaily" + "@id": "bts:Vibratome" }, { - "@id": "bts:TwiceDaily" + "@id": "bts:Cryosectioning" }, { - "@id": "bts:Every24Hours" + "@id": "bts:Tissuemolds" }, { - "@id": "bts:EveryOtherDay" + "@id": "bts:Slidingmicrotome" }, { - "@id": "bts:TwiceWeekly" + "@id": "bts:Sectioning" }, { - "@id": "bts:OnceWeekly" + "@id": "bts:Other" }, { "@id": "bts:Unknown" @@ -26074,165 +32121,213 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Treatment Frequency", + "sms:displayName": "Slicing Method", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:YearofDiagnosis", + "@id": "bts:LysisBuffer", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the year of an individual's initial pathologic diagnosis of cancer.", - "rdfs:label": "YearofDiagnosis", + "rdfs:comment": "scRNA-seq specific: Type of lysis buffer used", + "rdfs:label": "LysisBuffer", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Year of Diagnosis", + "sms:displayName": "Lysis Buffer", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PrecancerousConditionType", + "@id": "bts:MethodofNucleicAcidIsolation", "@type": "rdfs:Class", - "rdfs:comment": "The classification of pre-cancerous cells found in a specific collection of data being studied by the Consortium for Molecular and Cellular Characterization of Screen-Detected Lesions (MCL).", - "rdfs:label": "PrecancerousConditionType", + "rdfs:comment": "Bulk RNA & DNA-seq specific: method used for nucleic acid isolation. E.g. Qiagen Allprep, Qiagen miRNAeasy. [Text - max length 100]", + "rdfs:label": "MethodofNucleicAcidIsolation", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:DuctalCarcinomaInSitu" - }, - { - "@id": "bts:PancreaticIntraductalPapillary-MucinousNeoplasm" - }, - { - "@id": "bts:AtypicalAdenomatousLungHyperplasia" - }, - { - "@id": "bts:Other" - }, + "sms:displayName": "Method of Nucleic Acid Isolation", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Biosample", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Biosample", + "rdfs:subClassOf": [ { - "@id": "bts:PancreaticIntraepithelialNeoplasia" - }, + "@id": "bts:Thing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Biosample", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SRRSBiospecimen", + "@type": "rdfs:Class", + "rdfs:comment": "SRRS-specific HTAN biological entity; this can be tissue, blood, analyte and subsamples of those, however it can be described via fewer attributes than a standard HTAN specimen", + "rdfs:label": "SRRSBiospecimen", + "rdfs:subClassOf": [ { - "@id": "bts:ProstaticIntraepithelialNeoplasia" - }, + "@id": "bts:Biosample" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "SRRS Biospecimen", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:Melanocytichyperplasia" - }, + "@id": "bts:Patient" + } + ], + "sms:requiresDependency": [ { - "@id": "bts:Atypicalmelanocyticproliferation" + "@id": "bts:Component" }, { - "@id": "bts:Melanomainsitu" + "@id": "bts:HTANBiospecimenID" }, { - "@id": "bts:Superficialspreading" + "@id": "bts:SourceHTANBiospecimenID" }, { - "@id": "bts:Lentigomalignatype" + "@id": "bts:HTANParentID" }, { - "@id": "bts:Acral-lentiginous" + "@id": "bts:AdjacentBiospecimenIDs" }, { - "@id": "bts:Melanomainsituarisinginagiantcongenitalnevus" + "@id": "bts:BiospecimenType" }, { - "@id": "bts:Persistentmelanomainsitu" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:Melanomainsitunototherwiseclassified" + "@id": "bts:CollectionDaysfromIndex" }, { - "@id": "bts:Scar-noresidualmelanoma" + "@id": "bts:AcquisitionMethodType" }, { - "@id": "bts:Invasivemelanoma-superficialspreading" + "@id": "bts:IschemicTime" }, { - "@id": "bts:Invasivemelanoma-nodulartype" + "@id": "bts:IschemicTemperature" }, { - "@id": "bts:Invasivemelanoma-lentigomaligna" + "@id": "bts:CollectionMedia" }, { - "@id": "bts:Invasivemelanoma-acrallentiginous" + "@id": "bts:TopographyCode" }, { - "@id": "bts:Invasivemelanoma-desmoplastic" + "@id": "bts:AdditionalTopography" }, { - "@id": "bts:Invasivemelanoma-nevoid" + "@id": "bts:FixativeType" }, { - "@id": "bts:Invasivemelanoma" + "@id": "bts:StorageMethod" }, { - "@id": "bts:NormalWDA" + "@id": "bts:PreinvasiveMorphology" }, { - "@id": "bts:Reservecellhyperplasia" + "@id": "bts:HistologicMorphologyCode" }, { - "@id": "bts:Squamousmetaplasia-mature" + "@id": "bts:PreservationMethod" }, { - "@id": "bts:Squamousmetaplasia-immature" + "@id": "bts:ProcessingDaysfromIndex" }, { - "@id": "bts:Milddysplasia" - }, + "@id": "bts:ProtocolLink" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:IschemicTime", + "@type": "rdfs:Class", + "rdfs:comment": "Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value.", + "rdfs:label": "IschemicTime", + "rdfs:subClassOf": [ { - "@id": "bts:Moderatedysplasia" - }, + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Ischemic Time", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:IschemicTemperature", + "@type": "rdfs:Class", + "rdfs:comment": "Specify whether specimen experienced warm or cold ischemia.", + "rdfs:label": "IschemicTemperature", + "rdfs:subClassOf": [ { - "@id": "bts:Severedysplasia" - }, + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Atypicaladenomatoushyperplasia" + "@id": "bts:WarmIschemia" }, { - "@id": "bts:Adenocarcinomainsitu-nonmucinous" + "@id": "bts:ColdIschemia" }, { - "@id": "bts:Adenocarcinomainsitu-mucinous" + "@id": "bts:Ambientair" }, { - "@id": "bts:BenigntumorNOS" + "@id": "bts:4Cwetice" }, { - "@id": "bts:Hamartoma" + "@id": "bts:Negative-20C" }, { - "@id": "bts:CarcinomaNOS" + "@id": "bts:DryIce" }, { - "@id": "bts:Nodiagnosispossible" + "@id": "bts:LiquidNitrogen" }, { - "@id": "bts:NotApplicable" + "@id": "bts:Unknown" } ], - "sms:displayName": "Precancerous Condition Type", + "sms:displayName": "Ischemic Temperature", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MethodofDiagnosis", + "@id": "bts:TopographyCode", "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the method used to confirm the patients malignant diagnosis.", - "rdfs:label": "MethodofDiagnosis", + "rdfs:comment": "Topography Code, indicating site within the body, based on ICD-O-3.", + "rdfs:label": "TopographyCode", "rdfs:subClassOf": [ { "@id": "bts:Diagnosis" @@ -26243,1451 +32338,973 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Autopsy" + "@id": "bts:C00.0" }, { - "@id": "bts:Biopsy" + "@id": "bts:C00.1" }, { - "@id": "bts:BloodDraw" + "@id": "bts:C00.2" }, { - "@id": "bts:BoneMarrowAspirate" + "@id": "bts:C00.3" }, { - "@id": "bts:CoreBiopsy" + "@id": "bts:C00.4" }, { - "@id": "bts:Cytology" + "@id": "bts:C00.5" }, { - "@id": "bts:Cystoscopy" + "@id": "bts:C00.6" }, { - "@id": "bts:Debulking" + "@id": "bts:C00.8" }, { - "@id": "bts:DiagnosticImaging" + "@id": "bts:C01.9" }, { - "@id": "bts:DilationandCurettageProcedure" + "@id": "bts:C02.0" }, { - "@id": "bts:Enucleation" + "@id": "bts:C02.1" }, { - "@id": "bts:ExcisionalBiopsy" + "@id": "bts:C02.2" }, { - "@id": "bts:FineNeedleAspiration" + "@id": "bts:C02.3" }, { - "@id": "bts:IncisionalBiopsy" + "@id": "bts:C02.4" }, { - "@id": "bts:Laparoscopy" + "@id": "bts:C02.8" }, { - "@id": "bts:Laparotomy" + "@id": "bts:C02.9" }, { - "@id": "bts:Other" + "@id": "bts:C03.0" }, { - "@id": "bts:PapSmear" + "@id": "bts:C03.1" }, { - "@id": "bts:PhysicalExam" + "@id": "bts:C03.9" }, { - "@id": "bts:PathologicReview" + "@id": "bts:C04.0" }, { - "@id": "bts:SurgicalResection" + "@id": "bts:C04.1" }, { - "@id": "bts:Thoracentesis" + "@id": "bts:C04.8" }, { - "@id": "bts:UltrasoundGuidedBiopsy" + "@id": "bts:C04.9" }, { - "@id": "bts:Unknown" + "@id": "bts:C05.0" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Method of Diagnosis", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PriorMalignancy", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe the patient's history of prior cancer diagnosis.", - "rdfs:label": "PriorMalignancy", - "rdfs:subClassOf": [ + "@id": "bts:C05.1" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C05.2" + }, { - "@id": "bts:Yes" + "@id": "bts:C05.8" }, { - "@id": "bts:No" + "@id": "bts:C05.9" }, { - "@id": "bts:Unknown" + "@id": "bts:C06.0" }, { - "@id": "bts:NotReported" + "@id": "bts:C06.1" }, { - "@id": "bts:NotAllowedToCollect" - } - ], - "sms:displayName": "Prior Malignancy", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PriorTreatment", - "@type": "rdfs:Class", - "rdfs:comment": "A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received before the body specimen was collected.", - "rdfs:label": "PriorTreatment", - "rdfs:subClassOf": [ + "@id": "bts:C06.2" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C06.8" + }, { - "@id": "bts:Yes" + "@id": "bts:C06.9" }, { - "@id": "bts:No" + "@id": "bts:C07.9" }, { - "@id": "bts:Unknown" + "@id": "bts:C08.0" }, { - "@id": "bts:NotReported" + "@id": "bts:C08.1" }, { - "@id": "bts:NotAllowedToCollect" - } - ], - "sms:displayName": "Prior Treatment", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MetastasisatDiagnosis", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the extent of metastatic disease present at diagnosis.", - "rdfs:label": "MetastasisatDiagnosis", - "rdfs:subClassOf": [ + "@id": "bts:C08.8" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C08.9" + }, { - "@id": "bts:DistantMetastasis" + "@id": "bts:C09.0" }, { - "@id": "bts:MetastasisNOS" + "@id": "bts:C09.1" }, { - "@id": "bts:NoMetastasis" + "@id": "bts:C09.8" }, { - "@id": "bts:RegionalMetastasis" + "@id": "bts:C09.9" }, { - "@id": "bts:Unknown" + "@id": "bts:C10.0" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Metastasis at Diagnosis", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MetastasisatDiagnosisSite", - "@type": "rdfs:Class", - "rdfs:comment": "Text term to identify an anatomic site in which metastatic disease involvement is found.", - "rdfs:label": "MetastasisatDiagnosisSite", - "rdfs:subClassOf": [ + "@id": "bts:C10.1" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C10.2" + }, { - "@id": "bts:Abdomen" + "@id": "bts:C10.3" }, { - "@id": "bts:AdrenalGland" + "@id": "bts:C10.4" }, { - "@id": "bts:Ascites" + "@id": "bts:C10.8" }, { - "@id": "bts:Bone" + "@id": "bts:C10.9" }, { - "@id": "bts:BoneMarrow" + "@id": "bts:C11.0" }, { - "@id": "bts:Brain" + "@id": "bts:C11.1" }, { - "@id": "bts:CerebrospinalFluid" + "@id": "bts:C11.2" }, { - "@id": "bts:CentralNervousSystem" + "@id": "bts:C11.3" }, { - "@id": "bts:Colon" + "@id": "bts:C11.8" }, { - "@id": "bts:DistantNodes" + "@id": "bts:C11.9" }, { - "@id": "bts:DistantOrgan" + "@id": "bts:C12.9" }, { - "@id": "bts:Groin" + "@id": "bts:C13.0" }, { - "@id": "bts:Kidney" + "@id": "bts:C13.1" }, { - "@id": "bts:Liver" + "@id": "bts:C13.2" }, { - "@id": "bts:Lung" + "@id": "bts:C13.8" }, { - "@id": "bts:LymphNode" + "@id": "bts:C13.9" }, { - "@id": "bts:Axillary" + "@id": "bts:C14.0" }, { - "@id": "bts:Inguinal" + "@id": "bts:C14.2" }, { - "@id": "bts:LymphNodeNOS" + "@id": "bts:C14.8" }, { - "@id": "bts:Mediastinum" + "@id": "bts:C15.0" }, { - "@id": "bts:Omentum" + "@id": "bts:C15.1" }, { - "@id": "bts:Ovary" + "@id": "bts:C15.2" }, { - "@id": "bts:Pelvis" + "@id": "bts:C15.3" }, { - "@id": "bts:PeritonealCavity" + "@id": "bts:C15.4" }, { - "@id": "bts:Peritoneum" + "@id": "bts:C15.5" }, { - "@id": "bts:Pleura" + "@id": "bts:C15.8" }, { - "@id": "bts:Scalp" + "@id": "bts:C15.9" }, { - "@id": "bts:Skin" + "@id": "bts:C16.0" }, { - "@id": "bts:SmallIntestine" + "@id": "bts:C16.1" }, { - "@id": "bts:SoftTissue" + "@id": "bts:C16.2" }, { - "@id": "bts:SpinalCord" + "@id": "bts:C16.3" }, { - "@id": "bts:Unknown" + "@id": "bts:C16.4" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Metastasis at Diagnosis Site", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FirstSymptomPriortoDiagnosis", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the patient's first symptom experienced prior to diagnosis and thought to be related to the disease.", - "rdfs:label": "FirstSymptomPriortoDiagnosis", - "rdfs:subClassOf": [ + "@id": "bts:C16.5" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C16.6" + }, { - "@id": "bts:AlteredMentalStatus" + "@id": "bts:C16.8" }, { - "@id": "bts:Headaches" + "@id": "bts:C16.9" }, { - "@id": "bts:MotororMovementChanges" + "@id": "bts:C17.0" }, { - "@id": "bts:Seizures" + "@id": "bts:C17.1" }, { - "@id": "bts:SensoryChanges" + "@id": "bts:C17.2" }, { - "@id": "bts:VisualChanges" + "@id": "bts:C17.3" }, { - "@id": "bts:Unknown" + "@id": "bts:C17.8" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "First Symptom Prior to Diagnosis", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:DaystoDiagnosis", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date the patient was diagnosed with the malignant disease. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoDiagnosis", - "rdfs:subClassOf": [ + "@id": "bts:C17.9" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Days to Diagnosis", - "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:PercentTumorInvasion", - "@type": "rdfs:Class", - "rdfs:comment": "The percentage of tumor cells spread locally in a malignant neoplasm through infiltration or destruction of adjacent tissue.", - "rdfs:label": "PercentTumorInvasion", - "rdfs:subClassOf": [ + "@id": "bts:C18.0" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Percent Tumor Invasion", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ResidualDisease", - "@type": "rdfs:Class", - "rdfs:comment": "Text terms to describe the status of a tissue margin following surgical resection.", - "rdfs:label": "ResidualDisease", - "rdfs:subClassOf": [ + "@id": "bts:C18.1" + }, { - "@id": "bts:Diagnosis" + "@id": "bts:C18.2" }, { - "@id": "bts:InitialDiseaseStatus" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C18.3" + }, { - "@id": "bts:R0" + "@id": "bts:C18.4" }, { - "@id": "bts:R1" + "@id": "bts:C18.5" }, { - "@id": "bts:R2" + "@id": "bts:C18.6" }, { - "@id": "bts:RX" + "@id": "bts:C18.7" }, { - "@id": "bts:Unknown" + "@id": "bts:C18.8" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Residual Disease", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SynchronousMalignancy", - "@type": "rdfs:Class", - "rdfs:comment": "A yes/no/unknown indicator used to describe whether the patient had an additional malignant diagnosis at the same time the tumor used for sequencing was diagnosed. If both tumors were sequenced, both tumors would have synchronous malignancies.", - "rdfs:label": "SynchronousMalignancy", - "rdfs:subClassOf": [ + "@id": "bts:C18.9" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C19.9" + }, { - "@id": "bts:Yes" + "@id": "bts:C20.9" }, { - "@id": "bts:No" + "@id": "bts:C21.0" }, { - "@id": "bts:Unknown" + "@id": "bts:C21.1" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Synchronous Malignancy", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TumorConfinedtoOrganofOrigin", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the tumor is confined to the organ where it originated and did not spread to a proximal or distant location within the body.", - "rdfs:label": "TumorConfinedtoOrganofOrigin", - "rdfs:subClassOf": [ + "@id": "bts:C21.2" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C21.8" + }, { - "@id": "bts:Yes" + "@id": "bts:C22.0" }, { - "@id": "bts:No" + "@id": "bts:C22.1" }, { - "@id": "bts:Unknown" + "@id": "bts:C23.9" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Tumor Confined to Organ of Origin", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TumorFocality", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe whether the patient's disease originated in a single location or multiple locations.", - "rdfs:label": "TumorFocality", - "rdfs:subClassOf": [ + "@id": "bts:C24.0" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C24.1" + }, { - "@id": "bts:Multifocal" + "@id": "bts:C24.8" }, { - "@id": "bts:Unifocal" + "@id": "bts:C24.9" }, { - "@id": "bts:Unknown" + "@id": "bts:C25.0" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Tumor Focality", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:GrossTumorWeight", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the gross pathologic tumor weight, measured in grams.", - "rdfs:label": "GrossTumorWeight", - "rdfs:subClassOf": [ + "@id": "bts:C25.1" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Gross Tumor Weight", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BreslowThickness", - "@type": "rdfs:Class", - "rdfs:comment": "The number that describes the distance, in millimeters, between the upper layer of the epidermis and the deepest point of tumor penetration.", - "rdfs:label": "BreslowThickness", - "rdfs:subClassOf": [ + "@id": "bts:C25.2" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Breslow Thickness", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:VascularInvasionPresent", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no indicator to ask if large vessel or venous invasion was detected by surgery or presence in a tumor specimen.", - "rdfs:label": "VascularInvasionPresent", - "rdfs:subClassOf": [ + "@id": "bts:C25.3" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C25.4" + }, { - "@id": "bts:Yes-VascularInvasionPresent" + "@id": "bts:C25.7" }, { - "@id": "bts:No" + "@id": "bts:C25.8" }, { - "@id": "bts:Unknown" + "@id": "bts:C25.9" }, { - "@id": "bts:NotReported" + "@id": "bts:C26.0" }, { - "@id": "bts:NotAllowedToCollect" - } - ], - "sms:displayName": "Vascular Invasion Present", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:VascularInvasionType", - "@type": "rdfs:Class", - "rdfs:comment": "Text term that represents the type of vascular tumor invasion.", - "rdfs:label": "VascularInvasionType", - "rdfs:subClassOf": [ + "@id": "bts:C26.8" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C26.9" + }, { - "@id": "bts:Extramural" + "@id": "bts:C30.0" }, { - "@id": "bts:Intramural" + "@id": "bts:C30.1" }, { - "@id": "bts:Macro" + "@id": "bts:C31.0" }, { - "@id": "bts:Micro" + "@id": "bts:C31.1" }, { - "@id": "bts:NoVascularInvasion" + "@id": "bts:C31.2" }, { - "@id": "bts:Unknown" + "@id": "bts:C31.3" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Vascular Invasion Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AnaplasiaPresent", - "@type": "rdfs:Class", - "rdfs:comment": "Yes/no/unknown/Not Reported indicator used to describe whether anaplasia was present at the time of diagnosis.", - "rdfs:label": "AnaplasiaPresent", - "rdfs:subClassOf": [ + "@id": "bts:C31.8" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C31.9" + }, { - "@id": "bts:Yes-AnaplasiaPresent" + "@id": "bts:C32.0" }, { - "@id": "bts:No" + "@id": "bts:C32.1" }, { - "@id": "bts:Unknown" + "@id": "bts:C32.2" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Anaplasia Present", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AnaplasiaPresentType", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the morphologic findings indicating the presence of a malignant cellular infiltrate characterized by the presence of large pleomorphic cells, necrosis, and high mitotic activity in a tissue sample.", - "rdfs:label": "AnaplasiaPresentType", - "rdfs:subClassOf": [ + "@id": "bts:C32.3" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C32.8" + }, { - "@id": "bts:Absent" + "@id": "bts:C32.9" }, { - "@id": "bts:Diffuse" + "@id": "bts:C33.9" }, { - "@id": "bts:Equivocal" + "@id": "bts:C34.0" }, { - "@id": "bts:Focal" + "@id": "bts:C34.1" }, { - "@id": "bts:Present" + "@id": "bts:C34.2" }, { - "@id": "bts:Sclerosis" + "@id": "bts:C34.3" }, { - "@id": "bts:Unknown" + "@id": "bts:C34.8" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Anaplasia Present Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Laterality", - "@type": "rdfs:Class", - "rdfs:comment": "For tumors in paired organs, designates the side on which the cancer originates.", - "rdfs:label": "Laterality", - "rdfs:subClassOf": [ + "@id": "bts:C34.9" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C37.9" + }, { - "@id": "bts:Bilateral" + "@id": "bts:C38.0" }, { - "@id": "bts:Left" + "@id": "bts:C38.1" }, { - "@id": "bts:Midline" + "@id": "bts:C38.2" }, { - "@id": "bts:Right" + "@id": "bts:C38.3" }, { - "@id": "bts:Unilateral" + "@id": "bts:C38.4" }, { - "@id": "bts:Unknown" + "@id": "bts:C38.8" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Laterality", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PerineuralInvasionPresent", - "@type": "rdfs:Class", - "rdfs:comment": "A yes/no indicator to ask if perineural invasion or infiltration of tumor or cancer is present.", - "rdfs:label": "PerineuralInvasionPresent", - "rdfs:subClassOf": [ + "@id": "bts:C39.0" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C39.8" + }, { - "@id": "bts:Yes" + "@id": "bts:C39.9" }, { - "@id": "bts:No" + "@id": "bts:C40.0" }, { - "@id": "bts:Unknown" + "@id": "bts:C40.1" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Perineural Invasion Present", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LymphaticInvasionPresent", - "@type": "rdfs:Class", - "rdfs:comment": "A yes/no indicator to ask if small or thin-walled vessel invasion is present, indicating lymphatic involvement", - "rdfs:label": "LymphaticInvasionPresent", - "rdfs:subClassOf": [ + "@id": "bts:C40.3" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C40.8" + }, { - "@id": "bts:Yes" + "@id": "bts:C40.9" }, { - "@id": "bts:No" + "@id": "bts:C41.0" }, { - "@id": "bts:Unknown" + "@id": "bts:C41.1" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Lymphatic Invasion Present", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LymphNodesPositive", - "@type": "rdfs:Class", - "rdfs:comment": "The number of lymph nodes involved with disease as determined by pathologic examination.", - "rdfs:label": "LymphNodesPositive", - "rdfs:subClassOf": [ + "@id": "bts:C41.2" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Lymph Nodes Positive", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LymphNodesTested", - "@type": "rdfs:Class", - "rdfs:comment": "The number of lymph nodes tested to determine whether lymph nodes were involved with disease as determined by a pathologic examination.", - "rdfs:label": "LymphNodesTested", - "rdfs:subClassOf": [ + "@id": "bts:C41.3" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Lymph Nodes Tested", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PeritonealFluidCytologicalStatus", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the malignant status of the peritoneal fluid determined by cytologic testing.", - "rdfs:label": "PeritonealFluidCytologicalStatus", - "rdfs:subClassOf": [ + "@id": "bts:C41.4" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C41.8" + }, { - "@id": "bts:Atypical" + "@id": "bts:C41.9" }, { - "@id": "bts:Malignant" + "@id": "bts:C42.0" }, { - "@id": "bts:Non-Malignant" + "@id": "bts:C42.1" }, { - "@id": "bts:Unsatisfactory" + "@id": "bts:C42.2" }, { - "@id": "bts:Unknown" + "@id": "bts:C42.3" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Peritoneal Fluid Cytological Status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ClassificationofTumor", - "@type": "rdfs:Class", - "rdfs:comment": "Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint.", - "rdfs:label": "ClassificationofTumor", - "rdfs:subClassOf": [ + "@id": "bts:C42.4" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C44.0" + }, { - "@id": "bts:Primary" + "@id": "bts:C44.1" }, { - "@id": "bts:Metastasis" + "@id": "bts:C44.2" }, { - "@id": "bts:Recurrence" + "@id": "bts:C44.3" }, { - "@id": "bts:Other" + "@id": "bts:C44.4" }, { - "@id": "bts:Unknown" + "@id": "bts:C44.5" }, { - "@id": "bts:NotReported" + "@id": "bts:C44.6" }, { - "@id": "bts:NotAllowedToCollect" - } - ], - "sms:displayName": "Classification of Tumor", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BestOverallResponse", - "@type": "rdfs:Class", - "rdfs:comment": "The best improvement achieved throughout the entire course of protocol treatment.", - "rdfs:label": "BestOverallResponse", - "rdfs:subClassOf": [ + "@id": "bts:C44.7" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C47.0" + }, { - "@id": "bts:AJ-AdjuvantTherapy" + "@id": "bts:C47.1" }, { - "@id": "bts:CPD-ClinicalProgression" + "@id": "bts:C47.2" }, { - "@id": "bts:CR-CompleteResponse" + "@id": "bts:C47.3" }, { - "@id": "bts:CRU-CompleteResponseUnconfirmed" + "@id": "bts:C47.4" }, { - "@id": "bts:DU-DiseaseUnchanged" + "@id": "bts:C47.5" }, { - "@id": "bts:IMR-Immunoresponse" + "@id": "bts:C47.6" }, { - "@id": "bts:IPD-Immunoprogression" + "@id": "bts:C47.8" }, { - "@id": "bts:MR-Minimal/MarginalResponse" + "@id": "bts:C47.9" }, { - "@id": "bts:MX-MixedResponse" + "@id": "bts:C48.0" }, { - "@id": "bts:Non-CR/Non-PD-Non-CR/Non-PD" + "@id": "bts:C48.1" }, { - "@id": "bts:NPB-NoPalliativeBenefit" + "@id": "bts:C48.2" }, { - "@id": "bts:NR-NoResponse" + "@id": "bts:C48.8" }, { - "@id": "bts:PA-PalliativeTherapy" + "@id": "bts:C49.0" }, { - "@id": "bts:PB-PalliativeBenefit" + "@id": "bts:C49.1" }, { - "@id": "bts:PD-ProgressiveDisease" + "@id": "bts:C49.2" }, { - "@id": "bts:PPD-Pseudoprogression" + "@id": "bts:C49.3" }, { - "@id": "bts:PR-PartialResponse" + "@id": "bts:C49.4" }, { - "@id": "bts:PSR-Pseudoresponse" + "@id": "bts:C49.5" }, { - "@id": "bts:RD-ResponsiveDisease" + "@id": "bts:C49.6" }, { - "@id": "bts:RP-Response" + "@id": "bts:C49.8" }, { - "@id": "bts:RPD-RadiographicProgressiveDisease" + "@id": "bts:C49.9" }, { - "@id": "bts:SCR-StringentCompleteResponse" + "@id": "bts:C50.0" }, { - "@id": "bts:SD-StableDisease" + "@id": "bts:C50.1" }, { - "@id": "bts:SPD-SurgicalProgression" + "@id": "bts:C50.2" }, { - "@id": "bts:TE-TooEarly" + "@id": "bts:C50.3" }, { - "@id": "bts:VGPR-VeryGoodPartialResponse" - } - ], - "sms:displayName": "Best Overall Response", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MitoticCount", - "@type": "rdfs:Class", - "rdfs:comment": "The number of mitoses identified under the microscope in tumors. The method of counting varies, according to the specific tumor examined. Usually, the mitotic count is determined based on the number of mitoses per high power field (40X) or 10 high power fields.", - "rdfs:label": "MitoticCount", - "rdfs:subClassOf": [ + "@id": "bts:C50.4" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Mitotic Count", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AJCCClinicalM", - "@type": "rdfs:Class", - "rdfs:comment": "Extent of the distant metastasis for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.", - "rdfs:label": "AJCCClinicalM", - "rdfs:subClassOf": [ + "@id": "bts:C50.5" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C50.6" + }, { - "@id": "bts:M0" + "@id": "bts:C50.8" }, { - "@id": "bts:M1" + "@id": "bts:C50.9" }, { - "@id": "bts:M1a" + "@id": "bts:C51.0" }, { - "@id": "bts:M1b" + "@id": "bts:C51.1" }, { - "@id": "bts:M1c" + "@id": "bts:C51.2" }, { - "@id": "bts:MX" + "@id": "bts:C51.8" }, { - "@id": "bts:CM0(i+)" + "@id": "bts:C51.9" }, { - "@id": "bts:Unknown" + "@id": "bts:C52.9" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "AJCC Clinical M", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AJCCClinicalN", - "@type": "rdfs:Class", - "rdfs:comment": "Extent of the regional lymph node involvement for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.", - "rdfs:label": "AJCCClinicalN", - "rdfs:subClassOf": [ + "@id": "bts:C53.0" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C53.1" + }, { - "@id": "bts:N0" + "@id": "bts:C53.8" }, { - "@id": "bts:N0(i+)" + "@id": "bts:C53.9" }, { - "@id": "bts:N0(i-)" + "@id": "bts:C54.0" }, { - "@id": "bts:N0(mol+)" + "@id": "bts:C54.1" }, { - "@id": "bts:N0(mol-)" + "@id": "bts:C54.2" }, { - "@id": "bts:N1" + "@id": "bts:C54.3" }, { - "@id": "bts:N1a" + "@id": "bts:C54.8" }, { - "@id": "bts:N1b" + "@id": "bts:C54.9" }, { - "@id": "bts:N1bI" + "@id": "bts:C55.9" }, { - "@id": "bts:N1bII" + "@id": "bts:C56.9" }, { - "@id": "bts:N1bIII" + "@id": "bts:C57.0" }, { - "@id": "bts:N1bIV" + "@id": "bts:C57.1" }, { - "@id": "bts:N1c" + "@id": "bts:C57.2" }, { - "@id": "bts:N1mi" + "@id": "bts:C57.3" }, { - "@id": "bts:N2" + "@id": "bts:C57.4" }, { - "@id": "bts:N2a" + "@id": "bts:C57.7" }, { - "@id": "bts:N2b" + "@id": "bts:C57.8" }, { - "@id": "bts:N2c" + "@id": "bts:C57.9" }, { - "@id": "bts:N3" + "@id": "bts:C60.0" }, { - "@id": "bts:N3a" + "@id": "bts:C60.1" }, { - "@id": "bts:N3b" + "@id": "bts:C60.2" }, { - "@id": "bts:N3c" + "@id": "bts:C60.8" }, { - "@id": "bts:N4" + "@id": "bts:C60.9" }, { - "@id": "bts:NX" + "@id": "bts:C61.9" }, { - "@id": "bts:Unknown" + "@id": "bts:C62.0" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "AJCC Clinical N", - 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"@id": "bts:StageIC" + "@id": "bts:C67.1" }, { - "@id": "bts:StageII" + "@id": "bts:C67.2" }, { - "@id": "bts:StageIIA" + "@id": "bts:C67.4" }, { - "@id": "bts:StageIIA1" + "@id": "bts:C67.6" }, { - "@id": "bts:StageIIA2" + "@id": "bts:C67.7" }, { - "@id": "bts:StageIIB" + "@id": "bts:C67.8" }, { - "@id": "bts:StageIIC" + "@id": "bts:C67.9" }, { - "@id": "bts:StageIIC1" + "@id": "bts:C68.0" }, { - "@id": "bts:StageIII" + "@id": "bts:C68.1" }, { - "@id": "bts:StageIIIA" + "@id": "bts:C68.8" }, { - "@id": "bts:StageIIIB" + "@id": "bts:C68.9" }, { - "@id": "bts:StageIIIC" + "@id": "bts:C69.0" }, { - "@id": "bts:StageIIIC1" + "@id": "bts:C69.1" }, { - "@id": "bts:StageIIIC2" + "@id": "bts:C69.2" }, { - "@id": "bts:StageIS" + "@id": "bts:C69.3" }, { - "@id": "bts:StageIV" + "@id": "bts:C69.4" }, { - "@id": "bts:StageIVA" + "@id": "bts:C69.5" }, { - "@id": "bts:StageIVB" + "@id": "bts:C69.6" }, { - "@id": "bts:StageIVC" + "@id": "bts:C69.8" }, { - "@id": "bts:StageTis" + "@id": "bts:C69.9" }, { - "@id": "bts:StageX" + "@id": "bts:C70.0" }, { - "@id": "bts:Unknown" + "@id": "bts:C70.1" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "AJCC Clinical Stage", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AJCCClinicalT", - "@type": "rdfs:Class", - "rdfs:comment": "Extent of the primary cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.", - "rdfs:label": "AJCCClinicalT", - "rdfs:subClassOf": [ + "@id": "bts:C70.9" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C71.0" + }, { - "@id": "bts:T0" + "@id": "bts:C71.1" }, { - "@id": "bts:T1" + "@id": "bts:C71.2" }, { - "@id": "bts:T1a" + "@id": "bts:C71.3" }, { - "@id": "bts:T1a1" + "@id": "bts:C71.4" }, { - "@id": "bts:T1a2" + "@id": "bts:C71.5" }, { - "@id": "bts:T1b" + "@id": "bts:C71.6" }, { - "@id": "bts:T1b1" + "@id": "bts:C71.7" }, { - "@id": "bts:T1b2" + "@id": "bts:C71.8" }, { - "@id": "bts:T1c" + "@id": "bts:C71.9" }, { - "@id": "bts:T1mi" + "@id": "bts:C72.0" }, { - "@id": "bts:T2" + "@id": "bts:C72.1" }, { - "@id": "bts:T2a" + "@id": "bts:C72.2" }, { - "@id": "bts:T2a1" + "@id": "bts:C72.3" }, { - "@id": "bts:T2a2" + "@id": "bts:C72.4" }, { - "@id": "bts:T2b" + "@id": "bts:C72.5" }, { - "@id": "bts:T2c" + "@id": "bts:C72.8" }, { - "@id": "bts:T2d" + "@id": "bts:C72.9" }, { - "@id": "bts:T3" + "@id": "bts:C73.9" }, { - "@id": "bts:T3a" + "@id": "bts:C74.0" }, { - "@id": "bts:T3b" + "@id": "bts:C74.1" }, { - "@id": "bts:T3c" + "@id": "bts:C74.9" }, { - "@id": "bts:T3d" + "@id": "bts:C75.0" }, { - "@id": "bts:T4" + "@id": "bts:C75.1" }, { - "@id": "bts:T4a" + "@id": "bts:C75.2" }, { - "@id": "bts:T4b" + "@id": "bts:C75.3" }, { - "@id": "bts:T4c" + "@id": "bts:C75.4" }, { - "@id": "bts:T4d" + "@id": "bts:C75.5" }, { - "@id": "bts:T4e" + "@id": "bts:C75.8" }, { - "@id": "bts:TX" + "@id": "bts:C75.9" }, { - "@id": "bts:Ta" + "@id": "bts:C76.0" }, { - "@id": "bts:Tis" + "@id": "bts:C76.1" }, { - "@id": "bts:Tis(DCIS)" + "@id": "bts:C76.2" }, { - "@id": "bts:Tis(LCIS)" + "@id": "bts:C76.3" }, { - "@id": "bts:Tis(Paget's)" + "@id": "bts:C76.4" }, { - "@id": "bts:Unknown" + "@id": "bts:C76.5" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "AJCC Clinical T", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AJCCPathologicM", - "@type": "rdfs:Class", - "rdfs:comment": "Code to represent the defined absence or presence of distant spread or metastases (M) to locations via vascular channels or lymphatics beyond the regional lymph nodes, using criteria established by the American Joint Committee on Cancer (AJCC).", - "rdfs:label": "AJCCPathologicM", - "rdfs:subClassOf": [ + "@id": "bts:C76.7" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C76.8" + }, { - "@id": "bts:M0" + "@id": "bts:C77.0" }, { - "@id": "bts:M1" + "@id": "bts:C77.1" }, { - "@id": "bts:M1a" + "@id": "bts:C77.2" }, { - "@id": "bts:M1b" + "@id": "bts:C77.3" }, { - "@id": "bts:M1c" + "@id": "bts:C77.4" }, { - "@id": "bts:MX" + "@id": "bts:C77.5" }, { - "@id": "bts:CM0(i+)" + "@id": "bts:C77.8" + }, + { + "@id": "bts:C77.9" + }, + { + "@id": "bts:C80.9" }, { "@id": "bts:Unknown" @@ -27696,15 +33313,15 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "AJCC Pathologic M", + "sms:displayName": "Topography Code", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AJCCPathologicN", + "@id": "bts:AdditionalTopography", "@type": "rdfs:Class", - "rdfs:comment": "The codes that represent the stage of cancer based on the nodes present (N stage) according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.", - "rdfs:label": "AJCCPathologicN", + "rdfs:comment": "Topography not included in the ICD-O-3 Topography codes.", + "rdfs:label": "AdditionalTopography", "rdfs:subClassOf": [ { "@id": "bts:Diagnosis" @@ -27715,96 +33332,104 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:N0" - }, - { - "@id": "bts:N0(i+)" - }, - { - "@id": "bts:N0(i-)" - }, - { - "@id": "bts:N0(mol+)" + "@id": "bts:Skinofscalp" }, { - "@id": "bts:N0(mol-)" + "@id": "bts:Skinofeyelid" }, { - "@id": "bts:N1" + "@id": "bts:Skinofnose" }, { - "@id": "bts:N1a" + "@id": "bts:Skinoflip" }, { - "@id": "bts:N1b" + "@id": "bts:Skinofear" }, { - "@id": "bts:N1bI" + "@id": "bts:Skinofneck" }, { - "@id": "bts:N1bII" + "@id": "bts:Skinofotherpartsofface" }, { - "@id": "bts:N1bIII" + "@id": "bts:Skinofchest" }, { - "@id": "bts:N1bIV" + "@id": "bts:Skinofback" }, { - "@id": "bts:N1c" + "@id": "bts:Skinofabdomen" }, { - "@id": "bts:N1mi" + "@id": "bts:Skinoftrunk" }, { - "@id": "bts:N2" + "@id": "bts:Skinofbreast" }, { - "@id": "bts:N2a" + "@id": "bts:Skinofupperlimbandshoulder" }, { - "@id": "bts:N2b" + "@id": "bts:Skinofpalm" }, { - "@id": "bts:N2c" + "@id": "bts:Skinoflowerlimbandhip" }, { - "@id": "bts:N3" + "@id": "bts:Skinofsole" }, { - "@id": "bts:N3a" + "@id": "bts:Skinofpenis" }, { - "@id": "bts:N3b" + "@id": "bts:Skinofscrotum" }, { - "@id": "bts:N3c" + "@id": "bts:Skinofvulva" }, { - "@id": "bts:N4" + "@id": "bts:SkinNOS" }, { - "@id": "bts:NX" + "@id": "bts:HilarAirway" }, { - "@id": "bts:Unknown" + "@id": "bts:Peri-tumoralAirway" }, { "@id": "bts:NotReported" } ], - "sms:displayName": "AJCC Pathologic N", + "sms:displayName": "Additional Topography", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AJCCPathologicStage", + "@id": "bts:HistologicMorphologyCode", "@type": "rdfs:Class", - "rdfs:comment": "The extent of a cancer, especially whether the disease has spread from the original site to other parts of the body based on AJCC staging criteria.", - "rdfs:label": "AJCCPathologicStage", + "rdfs:comment": "Histologic Morphology Code, based on ICD-O-3. Any valid ICD-O-3 morphology code. See https://seer.cancer.gov/icd-o-3/ and https://seer.cancer.gov/icd-o-3/sitetype.icdo3.20200629.xlsx. Examples: 80510", + "rdfs:label": "HistologicMorphologyCode", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Histologic Morphology Code", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:PreservationMethod", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that represents the method used to preserve the sample.", + "rdfs:label": "PreservationMethod", + "rdfs:subClassOf": [ + { + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -27812,244 +33437,340 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Stage0" + "@id": "bts:Cryopreserved" }, { - "@id": "bts:Stage0a" + "@id": "bts:Cryopreservationinliquidnitrogen-deadtissue" }, { - "@id": "bts:Stage0is" + "@id": "bts:Cryopreservationindryice-deadtissue" }, { - "@id": "bts:StageI" + "@id": "bts:Cryopreservationinliquidnitrogen-livecells" }, { - "@id": "bts:StageIA" + "@id": "bts:Formalinfixedparaffinembedded-FFPE" }, { - "@id": "bts:StageIA1" + "@id": "bts:Formalinfixed-unbuffered" }, { - "@id": "bts:StageIA2" + "@id": "bts:Formalinfixed-buffered" }, { - "@id": "bts:StageIB" + "@id": "bts:Fresh" }, { - "@id": "bts:StageIB1" + "@id": "bts:FreshdissociatedandsinglecellsortedintoplatesinNP40buffer" }, { - "@id": "bts:StageIB2" + "@id": "bts:OCT" }, { - "@id": "bts:StageIC" + "@id": "bts:SnapFrozen" }, { - "@id": "bts:StageII" + "@id": "bts:Frozen" }, { - "@id": "bts:StageIIA" + "@id": "bts:Negative80DegC" }, { - "@id": "bts:StageIIA1" + "@id": "bts:LiquidNitrogen" }, { - "@id": "bts:StageIIA2" + "@id": "bts:Freshdissociated" }, { - "@id": "bts:StageIIB" + "@id": "bts:Freshdissociatedandsinglecellsorted" }, { - "@id": "bts:StageIIC" + "@id": "bts:Freshdissociatedandsinglecellsortedintoplates" }, { - "@id": "bts:StageIIC1" + "@id": "bts:Methacarnfixedparaffinembedded-MFPE" }, { - "@id": "bts:StageIII" + "@id": "bts:Unknown" }, { - "@id": "bts:StageIIIA" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Preservation Method", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:OtherAssay", + "@type": "rdfs:Class", + "rdfs:comment": "Metadata applying to any assay without standard descriptors. Can be used as a placeholder for minimal amount of metadata until the assay descriptors are standardized", + "rdfs:label": "OtherAssay", + "rdfs:subClassOf": [ { - "@id": "bts:StageIIIB" + "@id": "bts:Assay" }, { - "@id": "bts:StageIIIC" - }, + "@id": "bts:DataType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Other Assay", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:StageIIIC1" + "@id": "bts:Biospecimen" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:StageIIIC2" + "@id": "bts:Filename" }, { - "@id": "bts:StageIS" + "@id": "bts:FileFormat" }, { - "@id": "bts:StageIV" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:StageIVA" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:StageIVB" + "@id": "bts:AssayType" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:AssayType", + "@type": "rdfs:Class", + "rdfs:comment": "The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)", + "rdfs:label": "AssayType", + "rdfs:subClassOf": [ + { + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Assay Type", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:ExSeqMinimal", + "@type": "rdfs:Class", + "rdfs:comment": "Minimal metadata for the ExSeq assay", + "rdfs:label": "ExSeqMinimal", + "rdfs:subClassOf": [ + { + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "ExSeq Minimal", + "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:Biospecimen" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:StageIVC" + "@id": "bts:Filename" }, { - "@id": "bts:StageTis" + "@id": "bts:FileFormat" }, { - "@id": "bts:StageX" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:Unknown" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:NotReported" + "@id": "bts:AssayType" } ], - "sms:displayName": "AJCC Pathologic Stage", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AJCCPathologicT", + "@id": "bts:ScRNA-seqLevel1", "@type": "rdfs:Class", - "rdfs:comment": "Code of pathological T (primary tumor) to define the size or contiguous extension of the primary tumor (T), using staging criteria from the American Joint Committee on Cancer (AJCC).", - "rdfs:label": "AJCCPathologicT", + "rdfs:comment": "Single-cell RNA-seq [EFO_0008913]", + "rdfs:label": "ScRNA-seqLevel1", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:T0" - }, + "sms:displayName": "scRNA-seq Level 1", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:T1" - }, + "@id": "bts:Biospecimen" + } + ], + "sms:requiresDependency": [ { - "@id": "bts:T1a" + "@id": "bts:Component" }, { - "@id": "bts:T1a1" + "@id": "bts:Filename" }, { - "@id": "bts:T1a2" + "@id": "bts:FileFormat" }, { - "@id": "bts:T1b" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:T1b1" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:T1b2" + "@id": "bts:NucleicAcidSource" }, { - "@id": "bts:T1c" + "@id": "bts:CryopreservedCellsinSample" }, { - "@id": "bts:T1mi" + "@id": "bts:SingleCellIsolationMethod" }, { - "@id": "bts:T2" + "@id": "bts:DissociationMethod" }, { - "@id": "bts:T2a" + "@id": "bts:LibraryConstructionMethod" }, { - "@id": "bts:T2a1" + "@id": "bts:ReadIndicator" }, { - "@id": "bts:T2a2" + "@id": "bts:Read1" }, { - "@id": "bts:T2b" + "@id": "bts:Read2" }, { - "@id": "bts:T2c" + "@id": "bts:EndBias" }, { - "@id": "bts:T2d" + "@id": "bts:ReverseTranscriptionPrimer" }, { - "@id": "bts:T3" + "@id": "bts:SpikeIn" }, { - "@id": "bts:T3a" + "@id": "bts:SequencingPlatform" }, { - "@id": "bts:T3b" + "@id": "bts:TotalNumberofInputCells" }, { - "@id": "bts:T3c" + "@id": "bts:InputCellsandNuclei" }, { - "@id": "bts:T3d" + "@id": "bts:LibraryPreparationDaysfromIndex" }, { - "@id": "bts:T4" + "@id": "bts:SingleCellDissociationDaysfromIndex" }, { - "@id": "bts:T4a" + "@id": "bts:SequencingLibraryConstructionDaysfromIndex" }, { - "@id": "bts:T4b" + "@id": "bts:NucleicAcidCaptureDaysfromIndex" }, { - "@id": "bts:T4c" + "@id": "bts:ProtocolLink" }, { - "@id": "bts:T4d" - }, + "@id": "bts:TechnicalReplicateGroup" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:NucleicAcidSource", + "@type": "rdfs:Class", + "rdfs:comment": "The source of the input nucleic molecule", + "rdfs:label": "NucleicAcidSource", + "rdfs:subClassOf": [ { - "@id": "bts:T4e" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:TX" + "@id": "bts:SingleCell" }, { - "@id": "bts:Ta" + "@id": "bts:BulkWholeCell" }, { - "@id": "bts:Tis" + "@id": "bts:SingleNucleus" }, { - "@id": "bts:Tis(DCIS)" + "@id": "bts:BulkNuclei" }, { - "@id": "bts:Tis(LCIS)" - }, + "@id": "bts:Micro-region" + } + ], + "sms:displayName": "Nucleic Acid Source", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:CryopreservedCellsinSample", + "@type": "rdfs:Class", + "rdfs:comment": "Indicate if library preparation was based on revived frozen cells.", + "rdfs:label": "CryopreservedCellsinSample", + "rdfs:subClassOf": [ { - "@id": "bts:Tis(Paget's)" - }, + "@id": "bts:ScRNA-seqLevel1" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Unknown" + "@id": "bts:Yes" }, { - "@id": "bts:NotReported" + "@id": "bts:No" } ], - "sms:displayName": "AJCC Pathologic T", - "sms:required": "sms:false", + "sms:displayName": "Cryopreserved Cells in Sample", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AJCCStagingSystemEdition", + "@id": "bts:SingleCellIsolationMethod", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the version or edition of the American Joint Committee on Cancer Staging Handbooks, a publication by the group formed for the purpose of developing a system of staging for cancer that is acceptable to the American medical profession and is compatible with other accepted classifications.", - "rdfs:label": "AJCCStagingSystemEdition", + "rdfs:comment": "The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)", + "rdfs:label": "SingleCellIsolationMethod", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { @@ -28057,48 +33778,36 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:1st" - }, - { - "@id": "bts:2nd" - }, - { - "@id": "bts:3rd" - }, - { - "@id": "bts:4th" - }, - { - "@id": "bts:5th" + "@id": "bts:MicrofluidicsChip" }, { - "@id": "bts:6th" + "@id": "bts:Droplets" }, { - "@id": "bts:7th" + "@id": "bts:FACS" }, { - "@id": "bts:8th" + "@id": "bts:Plates" }, { - "@id": "bts:Unknown" + "@id": "bts:10x" }, { - "@id": "bts:NotReported" + "@id": "bts:NucleiIsolation" } ], - "sms:displayName": "AJCC Staging System Edition", - "sms:required": "sms:false", + "sms:displayName": "Single Cell Isolation Method", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:CogNeuroblastomaRiskGroup", + "@id": "bts:DissociationMethod", "@type": "rdfs:Class", - "rdfs:comment": "Text term that represents the categorization of patients on the basis of prognostic factors per a system developed by Children's Oncology Group (COG). Risk level is used to assign treatment intensity.", - "rdfs:label": "CogNeuroblastomaRiskGroup", + "rdfs:comment": "The tissue dissociation method used for scRNASeq or scATAC-seq assays", + "rdfs:label": "DissociationMethod", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { @@ -28106,33 +33815,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:HighRisk" - }, - { - "@id": "bts:IntermediateRisk" + "@id": "bts:GentleMACS" }, { - "@id": "bts:LowRisk" + "@id": "bts:Dounce" }, { - "@id": "bts:Unknown" + "@id": "bts:EnzymaticDigestion" }, { - "@id": "bts:NotReported" + "@id": "bts:NotApplicable" } ], - "sms:displayName": "Cog Neuroblastoma Risk Group", - "sms:required": "sms:false", + "sms:displayName": "Dissociation Method", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:CogRhabdomyosarcomaRiskGroup", + "@id": "bts:LibraryConstructionMethod", "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the classification of rhabdomyosarcoma, as defined by the Children's Oncology Group (COG).", - "rdfs:label": "CogRhabdomyosarcomaRiskGroup", + "rdfs:comment": "Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711]", + "rdfs:label": "LibraryConstructionMethod", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -28140,33 +33846,72 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:HighRisk" + "@id": "bts:Smart-seq2" }, { - "@id": "bts:IntermediateRisk" + "@id": "bts:Smart-SeqV4" }, { - "@id": "bts:LowRisk" + "@id": "bts:10xV1.0" }, { - "@id": "bts:Unknown" + "@id": "bts:10xV1.1" }, { - "@id": "bts:NotReported" + "@id": "bts:10xV2" + }, + { + "@id": "bts:10xV3" + }, + { + "@id": "bts:10xV3.1" + }, + { + "@id": "bts:CEL-seq2" + }, + { + "@id": "bts:Drop-seq" + }, + { + "@id": "bts:InDropsV2" + }, + { + "@id": "bts:InDropsV3" + }, + { + "@id": "bts:TruDrop" + }, + { + "@id": "bts:Sci-ATAC-seq" + }, + { + "@id": "bts:NexteraXT" + }, + { + "@id": "bts:10xMultiome" + }, + { + "@id": "bts:10xFLEX" + }, + { + "@id": "bts:10xGEM3'" + }, + { + "@id": "bts:10xGEM5'" } ], - "sms:displayName": "Cog Rhabdomyosarcoma Risk Group", - "sms:required": "sms:false", + "sms:displayName": "Library Construction Method", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:GleasonGradeGroup", + "@id": "bts:ReadIndicator", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the overall grouping of grades defined by the Gleason grading classification, which is used to determine the aggressiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.", - "rdfs:label": "GleasonGradeGroup", + "rdfs:comment": "Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other", + "rdfs:label": "ReadIndicator", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -28174,33 +33919,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Group1" + "@id": "bts:R1" }, { - "@id": "bts:Group2" + "@id": "bts:R2" }, { - "@id": "bts:Group3" + "@id": "bts:R1&R2" }, { - "@id": "bts:Group4" + "@id": "bts:I1" }, { - "@id": "bts:Group5" + "@id": "bts:Other" } ], - "sms:displayName": "Gleason Grade Group", - "sms:required": "sms:false", + "sms:displayName": "Read Indicator", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:GleasonGradeTertiary", + "@id": "bts:Read1", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the tertiary pattern as described by the Gleason Grading System.", - "rdfs:label": "GleasonGradeTertiary", + "rdfs:comment": "Read 1 content description", + "rdfs:label": "Read1", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { @@ -28208,58 +33953,49 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Pattern4" + "@id": "bts:CellBarcodeandUMI" }, { - "@id": "bts:Pattern5" + "@id": "bts:CDNA" } ], - "sms:displayName": "Gleason Grade Tertiary", - "sms:required": "sms:false", + "sms:displayName": "Read1", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:GleasonPatternsPercent", + "@id": "bts:Read2", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the percentage of Patterns 4 and 5, which is used when the Gleason score is greater than 7 to predict prognosis.", - "rdfs:label": "GleasonPatternsPercent", + "rdfs:comment": "Read 2 content description", + "rdfs:label": "Read2", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Gleason Patterns Percent", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:GreatestTumorDimension", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the measurement of the widest portion of the tumor in centimeters.", - "rdfs:label": "GreatestTumorDimension", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:Diagnosis" + "@id": "bts:CellBarcodeandUMI" + }, + { + "@id": "bts:CDNA" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Greatest Tumor Dimension", - "sms:required": "sms:false", + "sms:displayName": "Read2", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:IGCCCGStage", + "@id": "bts:EndBias", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the International Germ Cell Cancer Collaborative Group (IGCCCG), a grouping used to further classify metastatic testicular tumors.", - "rdfs:label": "IGCCCGStage", + "rdfs:comment": "The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript", + "rdfs:label": "EndBias", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { @@ -28267,33 +34003,27 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:GoodPrognosis" - }, - { - "@id": "bts:IntermediatePrognosis" - }, - { - "@id": "bts:PoorPrognosis" + "@id": "bts:3Prime" }, { - "@id": "bts:Unknown" + "@id": "bts:5Prime" }, { - "@id": "bts:NotReported" + "@id": "bts:FullLengthTranscript" } ], - "sms:displayName": "IGCCCG Stage", - "sms:required": "sms:false", + "sms:displayName": "End Bias", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:INPCGrade", + "@id": "bts:ReverseTranscriptionPrimer", "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the classification of neuroblastic differentiation within neuroblastoma tumors, as defined by the International Neuroblastoma Pathology Classification (INPC).", - "rdfs:label": "INPCGrade", + "rdfs:comment": "An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA", + "rdfs:label": "ReverseTranscriptionPrimer", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { @@ -28301,33 +34031,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Differentiating" - }, - { - "@id": "bts:PoorlyDifferentiated" + "@id": "bts:Oligo-dT" }, { - "@id": "bts:Undifferentiated" + "@id": "bts:Poly-dT" }, { - "@id": "bts:Unknown" + "@id": "bts:Featurebarcoding" }, { - "@id": "bts:NotReported" + "@id": "bts:Random" } ], - "sms:displayName": "INPC Grade", - "sms:required": "sms:false", + "sms:displayName": "Reverse Transcription Primer", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:INPCHistologicGroup", + "@id": "bts:SpikeIn", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the classification of neuroblastomas distinguishing between favorable and unfavorable histologic groups. The histologic score, defined by the International Neuroblastoma Pathology Classification (INPC), is based on age, mitosis-karyorrhexis index (MKI), stromal content and degree of tumor cell differentiation.", - "rdfs:label": "INPCHistologicGroup", + "rdfs:comment": "A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix", + "rdfs:label": "SpikeIn", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { @@ -28335,30 +34062,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Favorable" + "@id": "bts:ERCC" }, { - "@id": "bts:Unfavorable" + "@id": "bts:OtherSpikeIn" }, { - "@id": "bts:Unknown" + "@id": "bts:NoSpikeIn" }, { - "@id": "bts:NotReported" + "@id": "bts:PhiX" } ], - "sms:displayName": "INPC Histologic Group", - "sms:required": "sms:false", + "sms:displayName": "Spike In", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:INRGStage", + "@id": "bts:SequencingPlatform", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the staging classification of neuroblastic tumors, as defined by the International Neuroblastoma Risk Group (INRG).", - "rdfs:label": "INRGStage", + "rdfs:comment": "A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.", + "rdfs:label": "SequencingPlatform", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Device" } ], "schema:isPartOf": { @@ -28366,145 +34093,103 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:L1" + "@id": "bts:IlluminaNextSeq500" }, { - "@id": "bts:L2" + "@id": "bts:IlluminaNextSeq550" }, { - "@id": "bts:M" + "@id": "bts:IlluminaNextSeq2500" }, { - "@id": "bts:Ms" + "@id": "bts:IlluminaNovaSeq6000" }, { - "@id": "bts:Unknown" + "@id": "bts:IlluminaMiSeq" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "INRG Stage", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:INSSStage", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the staging classification of neuroblastic tumors, as defined by the International Neuroblastoma Staging System (INSS).", - "rdfs:label": "INSSStage", - "rdfs:subClassOf": [ + "@id": "bts:454GSFLXTitanium" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:ABSOLiD4" + }, { - "@id": "bts:Stage1" + "@id": "bts:ABSOLiD2" }, { - "@id": "bts:Stage2A" + "@id": "bts:ABSOLiD3" }, { - "@id": "bts:Stage2B" + "@id": "bts:CompleteGenomics" }, { - "@id": "bts:Stage3" + "@id": "bts:IlluminaHiSeqXTen" }, { - "@id": "bts:Stage4" + "@id": "bts:IlluminaHiSeqXFive" }, { - "@id": "bts:Stage4S" + "@id": "bts:IlluminaGenomeAnalyzerII" }, { - "@id": "bts:Unknown" + "@id": "bts:IlluminaGenomeAnalyzerIIx" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "INSS Stage", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:InternationalPrognosticIndex", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the International Prognostic Index, which classifies the prognosis of patients with aggressive non-Hodgkin's lymphoma.", - "rdfs:label": "InternationalPrognosticIndex", - "rdfs:subClassOf": [ + "@id": "bts:IlluminaHiSeq2000" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:IlluminaHiSeq2500" + }, { - "@id": "bts:LowRisk" + "@id": "bts:IlluminaHiSeq4000" }, { - "@id": "bts:Low-IntermediateRisk" + "@id": "bts:IlluminaNextSeq" }, { - "@id": "bts:High-IntermediateRisk" + "@id": "bts:IonTorrentPGM" }, { - "@id": "bts:HighRisk" - } - ], - "sms:displayName": "International Prognostic Index", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:IRSGroup", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the classification of rhabdomyosarcoma tumors, as defined by the Intergroup Rhabdomyosarcoma Study (IRS).", - "rdfs:label": "IRSGroup", - "rdfs:subClassOf": [ + "@id": "bts:IonTorrentProton" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:IonTorrentS5" + }, { - "@id": "bts:GroupI" + "@id": "bts:PacBioRS" }, { - "@id": "bts:GroupIa" + "@id": "bts:NovaSeq6000" }, { - "@id": "bts:GroupIb" + "@id": "bts:NovaSeqS4" }, { - "@id": "bts:GroupII" + "@id": "bts:UltimaGenomicsUG100" }, { - "@id": "bts:GroupIIa" + "@id": "bts:OxfordNanoporeminION" }, { - "@id": "bts:GroupIIc" + "@id": "bts:GridION" }, { - "@id": "bts:GroupIII" + "@id": "bts:PromethION" }, { - "@id": "bts:GroupIIIa" + "@id": "bts:PacBioSequel2" }, { - "@id": "bts:GroupIIIb" + "@id": "bts:Revio" }, { - "@id": "bts:GroupIV" + "@id": "bts:IlluminaNextSeq1000" + }, + { + "@id": "bts:IlluminaNextSeq2000" + }, + { + "@id": "bts:Other" }, { "@id": "bts:Unknown" @@ -28513,274 +34198,425 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "IRS Group", - "sms:required": "sms:false", + "sms:displayName": "Sequencing Platform", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:IRSStage", + "@id": "bts:TotalNumberofInputCells", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the classification of rhabdomyosarcoma tumors, as defined by the Intergroup Rhabdomyosarcoma Study (IRS).", - "rdfs:label": "IRSStage", + "rdfs:comment": "Number of cells loaded/placed on plates", + "rdfs:label": "TotalNumberofInputCells", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:1" - }, - { - "@id": "bts:2" - }, - { - "@id": "bts:3" - }, - { - "@id": "bts:4" - }, - { - "@id": "bts:Unknown" - }, + "sms:displayName": "Total Number of Input Cells", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:InputCellsandNuclei", + "@type": "rdfs:Class", + "rdfs:comment": "Number of cells and number of nuclei input; entry format: number, number", + "rdfs:label": "InputCellsandNuclei", + "rdfs:subClassOf": [ { - "@id": "bts:NotReported" + "@id": "bts:ScRNA-seqLevel1" } ], - "sms:displayName": "IRS Stage", - "sms:required": "sms:false", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Input Cells and Nuclei", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ISSStage", + "@id": "bts:LibraryPreparationDaysfromIndex", "@type": "rdfs:Class", - "rdfs:comment": "The multiple myeloma disease stage at diagnosis.", - "rdfs:label": "ISSStage", + "rdfs:comment": "Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable'", + "rdfs:label": "LibraryPreparationDaysfromIndex", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:I" - }, + "sms:displayName": "Library Preparation Days from Index", + "sms:required": "sms:false", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:SingleCellDissociationDaysfromIndex", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days between sample for single cell assay was received in lab and when the sample was dissociated and cells were isolated [number]. If not applicable please enter 'Not Applicable'", + "rdfs:label": "SingleCellDissociationDaysfromIndex", + "rdfs:subClassOf": [ { - "@id": "bts:II" - }, + "@id": "bts:ScRNA-seqLevel1" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Single Cell Dissociation Days from Index", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:SequencingLibraryConstructionDaysfromIndex", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days between sample for assay was received in lab and day of sequencing library construction [number]. If not applicable please enter 'Not Applicable'", + "rdfs:label": "SequencingLibraryConstructionDaysfromIndex", + "rdfs:subClassOf": [ { - "@id": "bts:III" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Sequencing Library Construction Days from Index", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:NucleicAcidCaptureDaysfromIndex", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days between sample for single cell assay was received in lab and day of nucleic acid capture part of library construction (in number of days since sample received in lab) [number]. If not applicable please enter 'Not Applicable'", + "rdfs:label": "NucleicAcidCaptureDaysfromIndex", + "rdfs:subClassOf": [ { - "@id": "bts:NotReported" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Nucleic Acid Capture Days from Index", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:TechnicalReplicateGroup", + "@type": "rdfs:Class", + "rdfs:comment": "A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch)", + "rdfs:label": "TechnicalReplicateGroup", + "rdfs:subClassOf": [ { - "@id": "bts:Unknown" + "@id": "bts:Sequencing" } ], - "sms:displayName": "ISS Stage", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Technical Replicate Group", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LymphNodeInvolvedSite", + "@id": "bts:ScRNA-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the anatomic site of lymph node involvement.", - "rdfs:label": "LymphNodeInvolvedSite", + "rdfs:comment": "Alignment workflows downstream of scRNA-seq Level 1", + "rdfs:label": "ScRNA-seqLevel2", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "scRNA-seq Level 2", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:Axillary" + "@id": "bts:ScRNA-seqLevel1" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:Cervical" + "@id": "bts:Filename" }, { - "@id": "bts:Epitrochlear" + "@id": "bts:FileFormat" }, { - "@id": "bts:Femoral" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:Hilar" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:Iliac-common" + "@id": "bts:ScRNAseqWorkflowType" }, { - "@id": "bts:Iliac-external" + "@id": "bts:WorkflowVersion" }, { - "@id": "bts:Iliac" + "@id": "bts:ScRNAseqWorkflowParametersDescription" }, { - "@id": "bts:NOS" + "@id": "bts:WorkflowLink" }, { - "@id": "bts:Inguinal" + "@id": "bts:GenomicReference" }, { - "@id": "bts:Mediastinal" + "@id": "bts:GenomicReferenceURL" }, { - "@id": "bts:Mesenteric" + "@id": "bts:GenomeAnnotationURL" }, { - "@id": "bts:None" + "@id": "bts:Checksum" }, { - "@id": "bts:Occipital" + "@id": "bts:WhitelistCellBarcodeFileLink" }, { - "@id": "bts:Paraaortic" + "@id": "bts:CellBarcodeTag" }, { - "@id": "bts:Parotid" + "@id": "bts:UMITag" }, { - "@id": "bts:Popliteal" + "@id": "bts:AppliedHardTrimming" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:ScRNAseqWorkflowType", + "@type": "rdfs:Class", + "rdfs:comment": "Generic name for the workflow used to analyze a data set.", + "rdfs:label": "ScRNAseqWorkflowType", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:CellRanger" }, { - "@id": "bts:Retroperitoneal" + "@id": "bts:STARsolo" }, { - "@id": "bts:Splenic" + "@id": "bts:HCAOptimus" }, { - "@id": "bts:Submandibular" + "@id": "bts:DropEST" }, { - "@id": "bts:Supraclavicular" + "@id": "bts:SEQC" }, { - "@id": "bts:Unknown" + "@id": "bts:Cufflinks" }, { - "@id": "bts:NotReported" + "@id": "bts:DEXSeq" + }, + { + "@id": "bts:HTSeq-FPKM" + }, + { + "@id": "bts:Cellannotation" + }, + { + "@id": "bts:Differentiationtrajectoryanalysis" + }, + { + "@id": "bts:Other" } ], - "sms:displayName": "Lymph Node Involved Site", - "sms:required": "sms:false", + "sms:displayName": "scRNAseq Workflow Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MarginDistance", + "@id": "bts:WorkflowVersion", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value (in centimeters) that represents the distance between the tumor and the surgical margin.", - "rdfs:label": "MarginDistance", + "rdfs:comment": "Major version of the workflow (e.g. Cell Ranger v3.1)", + "rdfs:label": "WorkflowVersion", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Margin Distance", - "sms:required": "sms:false", + "sms:displayName": "Workflow Version", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MarginsInvolvedSite", + "@id": "bts:ScRNAseqWorkflowParametersDescription", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the anatomic sites that were involved in the survival margins.", - "rdfs:label": "MarginsInvolvedSite", + "rdfs:comment": "Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion", + "rdfs:label": "ScRNAseqWorkflowParametersDescription", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:GerotaFascia" - }, - { - "@id": "bts:Parenchyma" - }, - { - "@id": "bts:PerinephricFat" - }, - { - "@id": "bts:Renal" - }, - { - "@id": "bts:RenalCapsule" - }, - { - "@id": "bts:RenalSinus" - }, - { - "@id": "bts:RenalVein" - }, + "sms:displayName": "scRNAseq Workflow Parameters Description", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:WorkflowLink", + "@type": "rdfs:Class", + "rdfs:comment": "Link to workflow or command. DockStore.org recommended. URL", + "rdfs:label": "WorkflowLink", + "rdfs:subClassOf": [ { - "@id": "bts:Ureter" + "@id": "bts:Sequencing" } ], - "sms:displayName": "Margins Involved Site", - "sms:required": "sms:false", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Workflow Link", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MedulloblastomaMolecularClassification", + "@id": "bts:GenomicReference", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the classification of medulloblastoma tumors based on molecular features.", - "rdfs:label": "MedulloblastomaMolecularClassification", + "rdfs:comment": "Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39)", + "rdfs:label": "GenomicReference", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:NotDetermined" - }, + "sms:displayName": "Genomic Reference", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:GenomicReferenceURL", + "@type": "rdfs:Class", + "rdfs:comment": "Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz)", + "rdfs:label": "GenomicReferenceURL", + "rdfs:subClassOf": [ { - "@id": "bts:Non-WNT/non-SHHActivated" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Genomic Reference URL", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:GenomeAnnotationURL", + "@type": "rdfs:Class", + "rdfs:comment": "Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz)", + "rdfs:label": "GenomeAnnotationURL", + "rdfs:subClassOf": [ { - "@id": "bts:SHH-Activated" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Genome Annotation URL", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:WhitelistCellBarcodeFileLink", + "@type": "rdfs:Class", + "rdfs:comment": "Link to file listing all possible cell barcodes. URL", + "rdfs:label": "WhitelistCellBarcodeFileLink", + "rdfs:subClassOf": [ { - "@id": "bts:WNT-Activated" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Whitelist Cell Barcode File Link", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:CellBarcodeTag", + "@type": "rdfs:Class", + "rdfs:comment": "SAM tag for cell barcode field; please provide a valid cell barcode tag (e.g. CB:Z)", + "rdfs:label": "CellBarcodeTag", + "rdfs:subClassOf": [ { - "@id": "bts:Unknown" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Cell Barcode Tag", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:UMITag", + "@type": "rdfs:Class", + "rdfs:comment": "SAM tag for the UMI field; please provide a valid UB, UMI (e.g. UB:Z or UR:Z)", + "rdfs:label": "UMITag", + "rdfs:subClassOf": [ { - "@id": "bts:NotReported" + "@id": "bts:Sequencing" } ], - "sms:displayName": "Medulloblastoma Molecular Classification", - "sms:required": "sms:false", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "UMI Tag", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MicropapillaryFeatures", + "@id": "bts:AppliedHardTrimming", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether micropapillary features were determined to be present.", - "rdfs:label": "MicropapillaryFeatures", + "rdfs:comment": "Was Hard Trimming applied", + "rdfs:label": "AppliedHardTrimming", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -28788,64 +34624,93 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Absent" - }, - { - "@id": "bts:Present" - }, - { - "@id": "bts:Unknown" + "@id": "bts:Yes-AppliedHardTrimming" }, { - "@id": "bts:NotReported" + "@id": "bts:No" } ], - "sms:displayName": "Micropapillary Features", - "sms:required": "sms:false", + "sms:displayName": "Applied Hard Trimming", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MitosisKaryorrhexisIndex", + "@id": "bts:ScRNA-seqLevel3", "@type": "rdfs:Class", - "rdfs:comment": "Text term that represents the component of the International Neuroblastoma Pathology Classification (INPC) for mitosis-karyorrhexis index (MKI).", - "rdfs:label": "MitosisKaryorrhexisIndex", + "rdfs:comment": "Gene and Isoform expression files", + "rdfs:label": "ScRNA-seqLevel3", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "scRNA-seq Level 3", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:High" + "@id": "bts:ScRNA-seqLevel2" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:Intermediate" + "@id": "bts:Filename" }, { - "@id": "bts:Low" + "@id": "bts:FileFormat" }, { - "@id": "bts:Unknown" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:NotReported" + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:DataCategory" + }, + { + "@id": "bts:MatrixType" + }, + { + "@id": "bts:LinkedMatrices" + }, + { + "@id": "bts:CellMedianNumberReads" + }, + { + "@id": "bts:CellMedianNumberGenes" + }, + { + "@id": "bts:CellTotal" + }, + { + "@id": "bts:ScRNAseqWorkflowType" + }, + { + "@id": "bts:ScRNAseqWorkflowParametersDescription" + }, + { + "@id": "bts:WorkflowLink" + }, + { + "@id": "bts:WorkflowVersion" } ], - "sms:displayName": "Mitosis Karyorrhexis Index", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NonNodalRegionalDisease", + "@id": "bts:DataCategory", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe whether the patient had non-nodal regional disease.", - "rdfs:label": "NonNodalRegionalDisease", + "rdfs:comment": "Specific content type of the data file.", + "rdfs:label": "DataCategory", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -28853,33 +34718,39 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Absent" + "@id": "bts:GeneExpression" }, { - "@id": "bts:Indeterminate" + "@id": "bts:TranscriptExpression" }, { - "@id": "bts:Present" + "@id": "bts:ExonExpressionQuantification" }, { - "@id": "bts:Unknown" + "@id": "bts:GeneExpressionQuantification" }, { - "@id": "bts:NotReported" + "@id": "bts:IsoformExpressionQuantification" + }, + { + "@id": "bts:SpliceJunctionQuantification" + }, + { + "@id": "bts:Other" } ], - "sms:displayName": "Non Nodal Regional Disease", - "sms:required": "sms:false", + "sms:displayName": "Data Category", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:NonNodalTumorDeposits", + "@id": "bts:MatrixType", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe the presence of tumor deposits in the pericolic or perirectal fat or in adjacent mesentery away from the leading edge of the tumor.", - "rdfs:label": "NonNodalTumorDeposits", + "rdfs:comment": "Type of data stored in matrix.", + "rdfs:label": "MatrixType", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -28887,251 +34758,236 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:RawCounts" }, { - "@id": "bts:No" + "@id": "bts:NormalizedCounts" }, { - "@id": "bts:Unknown" + "@id": "bts:ScaledCounts" }, { - "@id": "bts:NotReported" + "@id": "bts:BatchCorrectedCounts" } ], - "sms:displayName": "Non Nodal Tumor Deposits", - "sms:required": "sms:false", + "sms:displayName": "Matrix Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:OvarianSpecimenStatus", + "@id": "bts:LinkedMatrices", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the physical condition of the involved ovary.", - "rdfs:label": "OvarianSpecimenStatus", + "rdfs:comment": "All matrices associated with every part of a SingleCellExperiment object. Comma-delimited list of filenames", + "rdfs:label": "LinkedMatrices", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:OvarianCapsuleIntact" - }, - { - "@id": "bts:OvarianCapsuleRuptured" - }, - { - "@id": "bts:OvarianCapsuleFragmented" - }, - { - "@id": "bts:Unknown" - }, + "sms:displayName": "Linked Matrices", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CellMedianNumberReads", + "@type": "rdfs:Class", + "rdfs:comment": "Median number of reads per cell. Number", + "rdfs:label": "CellMedianNumberReads", + "rdfs:subClassOf": [ { - "@id": "bts:NotReported" + "@id": "bts:ScRNA-seqLevel3" } ], - "sms:displayName": "Ovarian Specimen Status", - "sms:required": "sms:false", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Cell Median Number Reads", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:OvarianSurfaceInvolvement", + "@id": "bts:CellMedianNumberGenes", "@type": "rdfs:Class", - "rdfs:comment": "The text term that describes whether the surface tissue (outer boundary) of the ovary shows evidence of involvement or presence of cancer.", - "rdfs:label": "OvarianSurfaceInvolvement", + "rdfs:comment": "Median number of genes detected per cell. Number", + "rdfs:label": "CellMedianNumberGenes", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:ScRNA-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Absent" - }, - { - "@id": "bts:Present" - }, - { - "@id": "bts:Indeterminate" - }, - { - "@id": "bts:Unknown" - }, + "sms:displayName": "Cell Median Number Genes", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:CellTotal", + "@type": "rdfs:Class", + "rdfs:comment": "Number of sequenced cells. Applies to raw counts matrix only.", + "rdfs:label": "CellTotal", + "rdfs:subClassOf": [ { - "@id": "bts:NotReported" + "@id": "bts:ScRNA-seqLevel3" } ], - "sms:displayName": "Ovarian Surface Involvement", - "sms:required": "sms:false", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Cell Total", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PregnantatDiagnosis", + "@id": "bts:ScRNA-seqLevel4", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to indicate whether the patient was pregnant at the time they were diagnosed.", - "rdfs:label": "PregnantatDiagnosis", + "rdfs:comment": "Data represents the relationships between cells derived from Level 3 expression data and shown as tSNE or UMAP coordinates per cell, plus all other cell-specific meta information (e.g., cell type)", + "rdfs:label": "ScRNA-seqLevel4", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "scRNA-seq Level 4", + "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:ScRNA-seqLevel3" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentDataFileID" + }, { - "@id": "bts:Yes" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:No" + "@id": "bts:ScRNAseqWorkflowType" }, { - "@id": "bts:Unknown" + "@id": "bts:ScRNAseqWorkflowParametersDescription" }, { - "@id": "bts:NotReported" + "@id": "bts:WorkflowVersion" + }, + { + "@id": "bts:WorkflowLink" } ], - "sms:displayName": "Pregnant at Diagnosis", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PrimaryGleasonGrade", + "@id": "bts:Slide-seqLevel1", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the primary Gleason score, which describes the pattern of cells making up the largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.", - "rdfs:label": "PrimaryGleasonGrade", + "rdfs:comment": "Raw sequencing files for the Slide-seq assay.", + "rdfs:label": "Slide-seqLevel1", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Slide-seq Level 1", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:Pattern1" + "@id": "bts:Biospecimen" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:Pattern2" + "@id": "bts:Filename" }, { - "@id": "bts:Pattern3" + "@id": "bts:FileFormat" }, { - "@id": "bts:Pattern4" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:Pattern5" - } - ], - "sms:displayName": "Primary Gleason Grade", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SecondaryGleasonGrade", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the secondary Gleason score, which describes the pattern of cells making up the second largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.", - "rdfs:label": "SecondaryGleasonGrade", - "rdfs:subClassOf": [ + "@id": "bts:HTANDataFileID" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:NucleicAcidSource" + }, { - "@id": "bts:Pattern1" + "@id": "bts:ReadIndicator" }, { - "@id": "bts:Pattern2" + "@id": "bts:SpatialRead1" }, { - "@id": "bts:Pattern3" + "@id": "bts:SpatialRead2" }, { - "@id": "bts:Pattern4" + "@id": "bts:EndBias" }, { - "@id": "bts:Pattern5" - } - ], - "sms:displayName": "Secondary Gleason Grade", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SupratentorialLocalization", - "@type": "rdfs:Class", - "rdfs:comment": "Text term to specify the location of the supratentorial tumor.", - "rdfs:label": "SupratentorialLocalization", - "rdfs:subClassOf": [ + "@id": "bts:ReverseTranscriptionPrimer" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:SpatialBarcodeOffset" + }, { - "@id": "bts:CerebralCortex" + "@id": "bts:SpatialBarcodeandUMI" }, { - "@id": "bts:DeepGray" + "@id": "bts:SpikeIn" }, { - "@id": "bts:SpinalCord" + "@id": "bts:SequencingPlatform" }, { - "@id": "bts:WhiteMatter" + "@id": "bts:TechnicalReplicateGroup" }, { - "@id": "bts:Unknown" + "@id": "bts:ProtocolLink" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Supratentorial Localization", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TumorDepth", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the depth of tumor invasion, measured in millimeters (mm).", - "rdfs:label": "TumorDepth", - "rdfs:subClassOf": [ + "@id": "bts:SpatialLibraryConstructionMethod" + }, { - "@id": "bts:Diagnosis" + "@id": "bts:LibraryPreparationDaysfromIndex" + }, + { + "@id": "bts:SequencingLibraryConstructionDaysfromIndex" + }, + { + "@id": "bts:NucleicAcidCaptureDaysfromIndex" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Tumor Depth", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:WHOCNSGrade", + "@id": "bts:SpatialRead1", "@type": "rdfs:Class", - "rdfs:comment": "WHO CNS Grade", - "rdfs:label": "WHOCNSGrade", + "rdfs:comment": "Read 1 content description", + "rdfs:label": "SpatialRead1", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { @@ -29139,39 +34995,24 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:GradeI" - }, - { - "@id": "bts:GradeII" - }, - { - "@id": "bts:GradeIII" - }, - { - "@id": "bts:GradeIV" - }, - { - "@id": "bts:GradeNotAssigned" - }, - { - "@id": "bts:Unknown" + "@id": "bts:CDNA" }, { - "@id": "bts:NotReported" + "@id": "bts:SpatialBarcodeandUMI" } ], - "sms:displayName": "WHO CNS Grade", - "sms:required": "sms:false", + "sms:displayName": "Spatial Read1", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:WHONTEGrade", + "@id": "bts:SpatialRead2", "@type": "rdfs:Class", - "rdfs:comment": "WHO NTE Grade", - "rdfs:label": "WHONTEGrade", + "rdfs:comment": "Read 2 content description", + "rdfs:label": "SpatialRead2", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { @@ -29179,483 +35020,462 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:G1" - }, - { - "@id": "bts:G2" - }, - { - "@id": "bts:G3" - }, - { - "@id": "bts:GX" - }, - { - "@id": "bts:Unknown" + "@id": "bts:CDNA" }, { - "@id": "bts:NotReported" + "@id": "bts:SpatialBarcodeandUMI" } ], - "sms:displayName": "WHO NTE Grade", - "sms:required": "sms:false", + "sms:displayName": "Spatial Read2", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AAChange", + "@id": "bts:SpatialBarcodeOffset", "@type": "rdfs:Class", - "rdfs:comment": "Alphanumeric value used to describe the amino acid change for a specific genetic variant. Example: R116Q. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "AAChange", + "rdfs:comment": "Offset in sequence for spot barcode read (in bp): number", + "rdfs:label": "SpatialBarcodeOffset", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "AA Change", - "sms:required": "sms:false", + "sms:displayName": "Spatial Barcode Offset", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Antigen", + "@id": "bts:SpatialBarcodeandUMI", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe an antigen included in molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "Antigen", + "rdfs:comment": "Spot and transcript identifiers", + "rdfs:label": "SpatialBarcodeandUMI", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:SpatialTranscriptomics" + }, + { + "@id": "bts:SpatialRead1" + }, + { + "@id": "bts:SpatialRead2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:BCL6" - }, - { - "@id": "bts:CA-125" - }, - { - "@id": "bts:CA19-9" - }, - { - "@id": "bts:CCND1" - }, - { - "@id": "bts:CD10" - }, - { - "@id": "bts:CD117" - }, - { - "@id": "bts:CD138" - }, - { - "@id": "bts:CD14" - }, - { - "@id": "bts:CD15" - }, - { - "@id": "bts:CD19" - }, - { - "@id": "bts:CD20" - }, - { - "@id": "bts:CD22" - }, + "sms:displayName": "Spatial Barcode and UMI", + "sms:required": "sms:true", + "sms:requiresDependency": [ { - "@id": "bts:CD23" + "@id": "bts:SpatialBarcodeOffset" }, { - "@id": "bts:CD25" + "@id": "bts:SpatialBarcodeLength" }, { - "@id": "bts:CD3" + "@id": "bts:UMIBarcodeOffset" }, { - "@id": "bts:CD30" - }, + "@id": "bts:UMIBarcodeLength" + } + ], + "sms:validationRules": [ + "num" + ] + }, + { + "@id": "bts:SpatialLibraryConstructionMethod", + "@type": "rdfs:Class", + "rdfs:comment": "Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711]", + "rdfs:label": "SpatialLibraryConstructionMethod", + "rdfs:subClassOf": [ { - "@id": "bts:CD33" - }, + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:CD34" + "@id": "bts:Smart-seq2" }, { - "@id": "bts:CD45" + "@id": "bts:Smart-SeqV4" }, { - "@id": "bts:CD5" + "@id": "bts:10xV1.0" }, { - "@id": "bts:CD56" + "@id": "bts:10xV1.1" }, { - "@id": "bts:CD7" + "@id": "bts:10xV2" }, { - "@id": "bts:CD79A" + "@id": "bts:10xV3" }, { - "@id": "bts:CEA" + "@id": "bts:10xV3.1" }, { - "@id": "bts:HLA-DR" + "@id": "bts:Drop-seq" }, { - "@id": "bts:Mesothelin" + "@id": "bts:InDropsV2" }, { - "@id": "bts:NSE" + "@id": "bts:InDropsV3" }, { - "@id": "bts:SquamousCellCarcinomaAntigen" + "@id": "bts:TruDrop" }, { - "@id": "bts:Unknown" - }, + "@id": "bts:NexteraXT" + } + ], + "sms:displayName": "Spatial Library Construction Method", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:SpatialTranscriptomics", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "SpatialTranscriptomics", + "rdfs:subClassOf": [ { - "@id": "bts:NotReported" + "@id": "bts:Thing" } ], - "sms:displayName": "Antigen", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Spatial Transcriptomics", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ClinicalBiospecimenType", + "@id": "bts:Slide-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the biological material used for testing, diagnostic, treatment or research purposes. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "ClinicalBiospecimenType", + "rdfs:comment": "Aligned sequencing files and QC for the Slide-seq assay.", + "rdfs:label": "Slide-seqLevel2", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Blood" - }, - { - "@id": "bts:BoneMarrow" - }, - { - "@id": "bts:BuccalMucosa" - }, - { - "@id": "bts:BuffyCoat" - }, - { - "@id": "bts:CerebrospinalFluid" - }, - { - "@id": "bts:ConnectiveTissue" - }, + "sms:displayName": "Slide-seq Level 2", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:EmbryonicFluid" - }, + "@id": "bts:Slide-seqLevel1" + } + ], + "sms:requiresDependency": [ { - "@id": "bts:EmbryonicTissue" + "@id": "bts:Component" }, { - "@id": "bts:Feces" + "@id": "bts:Filename" }, { - "@id": "bts:Granulocyte" + "@id": "bts:FileFormat" }, { - "@id": "bts:MuscleTissue" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:NerveTissue" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:PeritonealFluid" + "@id": "bts:Slide-seqWorkflowType" }, { - "@id": "bts:Plasma" + "@id": "bts:WorkflowVersion" }, { - "@id": "bts:PleuralFluid" + "@id": "bts:Slide-seqWorkflowParameterDescription" }, { - "@id": "bts:Saliva" + "@id": "bts:WorkflowLink" }, { - "@id": "bts:Serum" + "@id": "bts:GenomicReference" }, { - "@id": "bts:Skin" + "@id": "bts:GenomicReferenceURL" }, { - "@id": "bts:SoftTissue" + "@id": "bts:GenomeAnnotationURL" }, { - "@id": "bts:TissueNOS" + "@id": "bts:Checksum" }, { - "@id": "bts:UninvolvedTissueNOS" + "@id": "bts:SpatialBarcodeTag" }, { - "@id": "bts:Urine" + "@id": "bts:MatchedSpatialBarcodeTag" }, { - "@id": "bts:Unknown" + "@id": "bts:UMITag" }, { - "@id": "bts:NotReported" + "@id": "bts:AppliedHardTrimming" } ], - "sms:displayName": "Clinical Biospecimen Type", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BloodTestNormalRangeUpper", + "@id": "bts:Slide-seqWorkflowType", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the upper limit of the normal range used to describe a healthy individual at the institution where the test was completed.", - "rdfs:label": "BloodTestNormalRangeUpper", + "rdfs:comment": "Generic name for the workflow used to analyze the Slide-seq data set. String", + "rdfs:label": "Slide-seqWorkflowType", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Blood Test Normal Range Upper", - "sms:required": "sms:false", + "sms:displayName": "Slide-seq Workflow Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BloodTestNormalRangeLower", + "@id": "bts:Slide-seqWorkflowParameterDescription", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the lower limit of the normal range used to describe a healthy individual at the institution where the test was completed.", - "rdfs:label": "BloodTestNormalRangeLower", + "rdfs:comment": "Parameters used to run the Slide-seq workflow. String", + "rdfs:label": "Slide-seqWorkflowParameterDescription", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Blood Test Normal Range Lower", - "sms:required": "sms:false", + "sms:displayName": "Slide-seq Workflow Parameter Description", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:CellCount", + "@id": "bts:SpatialBarcodeTag", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the number of cells used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "CellCount", + "rdfs:comment": "SAM tag for spot barcode field; please provide a valid spot barcode tag (e.g. CB:Z)", + "rdfs:label": "SpatialBarcodeTag", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cell Count", - "sms:required": "sms:false", + "sms:displayName": "Spatial Barcode Tag", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Chromosome", + "@id": "bts:MatchedSpatialBarcodeTag", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a chromosome targeted or included in molecular testing. If a specific genetic variant is being reported, this property can be used to capture the chromosome where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "Chromosome", + "rdfs:comment": "SAM tag for matched spot barcode field; please provide a valid spot barcode tag (e.g. CB:Z) (Slide-seq specific)", + "rdfs:label": "MatchedSpatialBarcodeTag", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Chr1" - }, - { - "@id": "bts:Chr2" - }, - { - "@id": "bts:Chr3" - }, - { - "@id": "bts:Chr4" - }, - { - "@id": "bts:Chr5" - }, - { - "@id": "bts:Chr6" - }, - { - "@id": "bts:Chr7" - }, - { - "@id": "bts:Chr8" - }, + "sms:displayName": "Matched Spatial Barcode Tag", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Slide-seqLevel3", + "@type": "rdfs:Class", + "rdfs:comment": "Gene matrices with features and barcodes for Slide-seq as well as spatial information (bead location files).", + "rdfs:label": "Slide-seqLevel3", + "rdfs:subClassOf": [ { - "@id": "bts:Chr9" - }, + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Slide-seq Level 3", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:Chr10" - }, + "@id": "bts:Slide-seqLevel2" + } + ], + "sms:requiresDependency": [ { - "@id": "bts:Chr11" + "@id": "bts:Component" }, { - "@id": "bts:Chr12" + "@id": "bts:Filename" }, { - "@id": "bts:Chr13" + "@id": "bts:FileFormat" }, { - "@id": "bts:Chr14" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:Chr15" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:Chr16" + "@id": "bts:RunID" }, { - "@id": "bts:Chr17" + "@id": "bts:SequencingBatchID" }, { - "@id": "bts:Chr18" + "@id": "bts:DataCategory" }, { - "@id": "bts:Chr19" + "@id": "bts:MatrixType" }, { - "@id": "bts:Chr20" + "@id": "bts:Slide-seqWorkflowType" }, { - "@id": "bts:Chr21" + "@id": "bts:WorkflowVersion" }, { - "@id": "bts:Chr22" + "@id": "bts:Slide-seqWorkflowParameterDescription" }, { - "@id": "bts:Chr23" + "@id": "bts:WorkflowLink" }, { - "@id": "bts:ChrM" + "@id": "bts:BeadsTotal" }, { - "@id": "bts:ChrX" + "@id": "bts:MedianUMICountsperSpot" }, { - "@id": "bts:ChrY" + "@id": "bts:MedianNumberGenesperSpatialSpot" }, { - "@id": "bts:Unknown" + "@id": "bts:Slide-seqBeadFileType" }, { - "@id": "bts:NotReported" + "@id": "bts:Slide-seqFragmentSize" } ], - "sms:displayName": "Chromosome", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Clonality", + "@id": "bts:RunID", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "Clonality", + "rdfs:comment": "A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.", + "rdfs:label": "RunID", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Clonal" - }, + "sms:displayName": "Run ID", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:SequencingBatchID", + "@type": "rdfs:Class", + "rdfs:comment": "Links samples to a specific local sequencer run. Can be string or 'null'", + "rdfs:label": "SequencingBatchID", + "rdfs:subClassOf": [ { - "@id": "bts:Non-clonal" + "@id": "bts:Sequencing" } ], - "sms:displayName": "Clonality", - "sms:required": "sms:false", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Sequencing Batch ID", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:CopyNumber", + "@id": "bts:BeadsTotal", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the number of times a section of the genome is repeated or copied within an insertion, duplication or deletion variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "CopyNumber", + "rdfs:comment": "Number of sequenced beads. Applies to raw counts matrix only. Integer", + "rdfs:label": "BeadsTotal", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Copy Number", + "sms:displayName": "Beads Total", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Cytoband", + "@id": "bts:MedianUMICountsperSpot", "@type": "rdfs:Class", - "rdfs:comment": "Alphanumeric value used to describe the cytoband or chromosomal location targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the cytoband where the variant is located. Format: [chromosome][chromosome arm].[band+sub-bands]. Example: 17p13.1. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "Cytoband", + "rdfs:comment": "The median number of UMI counts per tissue covered spot.", + "rdfs:label": "MedianUMICountsperSpot", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cytoband", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "Median UMI Counts per Spot", + "sms:required": "sms:true", + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:Exon", + "@id": "bts:MedianNumberGenesperSpatialSpot", "@type": "rdfs:Class", - "rdfs:comment": "Exon number targeted or included in a molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the exon where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "Exon", + "rdfs:comment": "The median number of genes detected per spot under tissue-associated barcode. Detection is defined as the presence of at least 1 UMI count.", + "rdfs:label": "MedianNumberGenesperSpatialSpot", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Exon", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "Median Number Genes per Spatial Spot", + "sms:required": "sms:true", + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:HistoneFamily", + "@id": "bts:Slide-seqBeadFileType", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the family, or classification of a group of basic proteins found in chromatin, called histones.", - "rdfs:label": "HistoneFamily", + "rdfs:comment": "The type of Level 3 file submitted as part of the Slide-seq workflow.", + "rdfs:label": "Slide-seqBeadFileType", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { @@ -29663,498 +35483,505 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:H1" + "@id": "bts:MatrixFeatures" }, { - "@id": "bts:H2A" + "@id": "bts:MatrixBarcodes" }, { - "@id": "bts:H2B" + "@id": "bts:AllBeadLocations" }, { - "@id": "bts:H3" + "@id": "bts:AllBeadBarcodes" }, { - "@id": "bts:H4" + "@id": "bts:MatchedBeadBarcodes" }, { - "@id": "bts:Unknown" + "@id": "bts:MatchedBeadLocations" }, { - "@id": "bts:NotReported" + "@id": "bts:NotApplicable" } ], - "sms:displayName": "Histone Family", - "sms:required": "sms:false", + "sms:displayName": "Slide-seq Bead File Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:HistoneVariant", + "@id": "bts:Slide-seqFragmentSize", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.", - "rdfs:label": "HistoneVariant", + "rdfs:comment": "Average cDNA length associated with the experiemtn. Integer", + "rdfs:label": "Slide-seqFragmentSize", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:CENP-A" - }, - { - "@id": "bts:H2A-Bbd" - }, - { - "@id": "bts:H2A.X" - }, - { - "@id": "bts:H2A.Z" - }, - { - "@id": "bts:H2A.Z.1" - }, - { - "@id": "bts:H2A.Z.2" - }, - { - "@id": "bts:H2A.Z.2.2" - }, - { - "@id": "bts:H3.1" - }, - { - "@id": "bts:H3.2" - }, - { - "@id": "bts:H3.3" - }, - { - "@id": "bts:H3.5" - }, - { - "@id": "bts:H3.X" - }, - { - "@id": "bts:H3.Y" - }, - { - "@id": "bts:H3t(H3.4)" - }, - { - "@id": "bts:MH2A" - }, + "sms:displayName": "Slide-seq Fragment Size", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MatrixFeatures", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "MatrixFeatures", + "rdfs:subClassOf": [ { - "@id": "bts:MH2A.1" - }, + "@id": "bts:Slide-seqBeadFileType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Matrix Features", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MatrixBarcodes", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "MatrixBarcodes", + "rdfs:subClassOf": [ { - "@id": "bts:MH2A.2" - }, + "@id": "bts:Slide-seqBeadFileType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Matrix Barcodes", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AllBeadLocations", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "AllBeadLocations", + "rdfs:subClassOf": [ { - "@id": "bts:Unknown" - }, + "@id": "bts:Slide-seqBeadFileType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "All Bead Locations", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AllBeadBarcodes", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "AllBeadBarcodes", + "rdfs:subClassOf": [ { - "@id": "bts:NotReported" + "@id": "bts:Slide-seqBeadFileType" } ], - "sms:displayName": "Histone Variant", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "All Bead Barcodes", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Intron", + "@id": "bts:MatchedBeadBarcodes", "@type": "rdfs:Class", - "rdfs:comment": "Intron number targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the intron where that variant is located.", - "rdfs:label": "Intron", + "rdfs:comment": "TBD", + "rdfs:label": "MatchedBeadBarcodes", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Slide-seqBeadFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Intron", + "sms:displayName": "Matched Bead Barcodes", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LaboratoryTest", + "@id": "bts:MatchedBeadLocations", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the medical testing used to diagnose, treat or further understand a patient's disease.", - "rdfs:label": "LaboratoryTest", + "rdfs:comment": "TBD", + "rdfs:label": "MatchedBeadLocations", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Slide-seqBeadFileType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Matched Bead Locations", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:NotApplicable", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "NotApplicable", + "rdfs:subClassOf": [ { - "@id": "bts:AbsoluteNeutrophil" + "@id": "bts:TargetCaptureKit" }, { - "@id": "bts:Albumin" + "@id": "bts:SomaticVariantsSampleType" }, { - "@id": "bts:AlphaFetoprotein" + "@id": "bts:HistoryofPriorColonPolyps" }, { - "@id": "bts:B-cellgenotyping" + "@id": "bts:FamilyColonCancerHistoryIndicator" }, { - "@id": "bts:Basophil" + "@id": "bts:FamilyMedicalHistoryColorectalPolypDiagnosis" }, { - "@id": "bts:Beta2Microglobulin" + "@id": "bts:PatientColonoscopyPerformedIndicator" }, { - "@id": "bts:BloodUreaNitrogen" + "@id": "bts:ReplicateType" }, { - "@id": "bts:C-ReactiveProtein" + "@id": "bts:DissociationMethod" }, { - "@id": "bts:Calcium" + "@id": "bts:LibraryStrand" }, { - "@id": "bts:Cellularity" + "@id": "bts:Immunosuppression" }, { - "@id": "bts:CirculatingTumorCells" + "@id": "bts:COVID19OccurrenceIndicator" }, { - "@id": "bts:Creatinine" + "@id": "bts:COVID19PositiveLabTestIndicator" }, { - "@id": "bts:Eosinophil" + "@id": "bts:COVID19CancerTreatmentFollowup" }, { - "@id": "bts:Epstein-BarrVirus" + "@id": "bts:ImmediateFamilyHistoryEndometrialCancer" }, { - "@id": "bts:Glucose" + "@id": "bts:ImmediateFamilyHistoryOvarianCancer" }, { - "@id": "bts:Hematocrit" + "@id": "bts:ColorectalCancerKRASIndicator" }, { - "@id": "bts:Hemoglobin" + "@id": "bts:ColonPolypOccurenceIndicator" }, { - "@id": "bts:HPV-E6/E7" + "@id": "bts:FamilyHistoryColorectalPolyp" }, { - "@id": "bts:HumanChorionicGonadotropin" + "@id": "bts:ColorectalPolypNewIndicator" }, { - "@id": "bts:HumanPapillomavirus" + "@id": "bts:HormoneTherapyBreastCancerPreventionIndicator" }, { - "@id": "bts:ImmunoglobulinA" + "@id": "bts:GliomaSpecificRadiationField" }, { - "@id": "bts:ImmunoglobulinG" + "@id": "bts:SupraTentorialEpendymomaMolecularSubgroup" }, { - "@id": "bts:ImmunoglobulinM" + "@id": "bts:RefluxTreatmentType" }, { - "@id": "bts:LactateDehydrogenase" + "@id": "bts:COVID19ComplicationsSeverity" }, { - "@id": "bts:Leukocytes" + "@id": "bts:PatientInflammatoryBowelDiseasePersonalMedicaHistory" }, { - "@id": "bts:LuteinizingHormone" + "@id": "bts:ColorectalCancerTumorBorderConfiguration" }, { - "@id": "bts:Lymphoblasts" + "@id": "bts:ColorectalPolypShape" }, { - "@id": "bts:Lymphocytes" + "@id": "bts:InfraTentorialEpendymomaMolecularSubgroup" }, { - "@id": "bts:MProtein" + "@id": "bts:SpecimenLaterality" }, { - "@id": "bts:Metamyelocytes" + "@id": "bts:LabTestsforMMRStatus" }, { - "@id": "bts:Myeloblasts" + "@id": "bts:Slide-seqBeadFileType" }, { - "@id": "bts:Myelocytes" + "@id": "bts:GliomaSpecificMetastasisSites" }, { - "@id": "bts:NeutrophilBands" + "@id": "bts:COVID19AntibodyTesting" }, { - "@id": "bts:Platelets" + "@id": "bts:ColorectalPolypAdenomaType" }, { - "@id": "bts:Prolymphocytes" + "@id": "bts:LastKnownDiseaseStatus" }, { - "@id": "bts:Promonocytes" + "@id": "bts:CutaneousMelanomaAdditionalFindings" }, { - "@id": "bts:Promyelocytes" + "@id": "bts:CauseofDeath" }, { - "@id": "bts:SegmentedNeutrophil" + "@id": "bts:TumorGrade" }, { - "@id": "bts:SerumFreeImmunoglobulinLightChain" + "@id": "bts:ImagingAssayType" }, { - "@id": "bts:Kappa" + "@id": "bts:ExtentofTumorResection" }, { - "@id": "bts:Lambda" + "@id": "bts:TestResult" }, { - "@id": "bts:NOS" + "@id": "bts:StorageMethod" }, { - "@id": "bts:Testosterone" + "@id": "bts:MolecularAnalysisMethod" }, { - "@id": "bts:TotalBilirubin" + "@id": "bts:ConcomitantMedicationReceivedType" }, { - "@id": "bts:TotalProtein" + "@id": "bts:HereditaryCancerPredispositionSyndrome" }, { - "@id": "bts:Unknown" + "@id": "bts:CancerAssociatedGeneMutations" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Laboratory Test", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LociAbnormalCount", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the number of loci determined to be abnormal.", - "rdfs:label": "LociAbnormalCount", - "rdfs:subClassOf": [ + "@id": "bts:MutationalSignatures" + }, { - "@id": "bts:MolecularTest" + "@id": "bts:PrecancerousConditionType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Loci Abnormal Count", + "sms:displayName": "Not Applicable", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LociCount", + "@id": "bts:BulkRNA-seqLevel1", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the number of loci tested.", - "rdfs:label": "LociCount", + "rdfs:comment": "Bulk RNA-seq [EFO_0003738]", + "rdfs:label": "BulkRNA-seqLevel1", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Loci Count", + "sms:displayName": "Bulk RNA-seq Level 1", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Locus", - "@type": "rdfs:Class", - "rdfs:comment": "Alphanumeric value used to describe the locus of a specific genetic variant. Example: NM_001126114.", - "rdfs:label": "Locus", - "rdfs:subClassOf": [ + "sms:requiresComponent": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Biospecimen" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Locus", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MismatchRepairMutation", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the mutation included in molecular testing was known to have an affect on the mismatch repair process. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "MismatchRepairMutation", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Component" + }, { - "@id": "bts:Yes" + "@id": "bts:Filename" }, { - "@id": "bts:No" + "@id": "bts:FileFormat" }, { - "@id": "bts:Unknown" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Mismatch Repair Mutation", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MolecularConsequence", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the molecular consequence of genetic variation. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "MolecularConsequence", - "rdfs:subClassOf": [ + "@id": "bts:HTANDataFileID" + }, { - "@id": "bts:MolecularTest" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:LibraryLayout" + }, { - "@id": "bts:3PrimeUTRVariant" + "@id": "bts:ReadIndicator" }, { - "@id": "bts:5PrimeUTRVariant" + "@id": "bts:NucleicAcidSource" }, { - "@id": "bts:CodingSequenceVariant" + "@id": "bts:Micro-regionSeqPlatform" }, { - "@id": "bts:DownstreamGeneVariant" + "@id": "bts:ROITag" + }, + { + "@id": "bts:SequencingPlatform" + }, + { + "@id": "bts:SequencingBatchID" + }, + { + "@id": "bts:ReadLength" + }, + { + "@id": "bts:LibrarySelectionMethod" + }, + { + "@id": "bts:LibraryPreparationKitName" + }, + { + "@id": "bts:LibraryPreparationKitVendor" + }, + { + "@id": "bts:LibraryPreparationKitVersion" + }, + { + "@id": "bts:LibraryPreparationDaysfromIndex" + }, + { + "@id": "bts:SpikeIn" + }, + { + "@id": "bts:AdapterName" + }, + { + "@id": "bts:AdapterSequence" + }, + { + "@id": "bts:BaseCallerName" + }, + { + "@id": "bts:BaseCallerVersion" + }, + { + "@id": "bts:FlowCellBarcode" }, { - "@id": "bts:FeatureElongation" + "@id": "bts:FragmentMaximumLength" }, { - "@id": "bts:FeatureTruncation" + "@id": "bts:FragmentMeanLength" }, { - "@id": "bts:FrameshiftVariant" + "@id": "bts:FragmentMinimumLength" }, { - "@id": "bts:IncompleteTerminalCodonVariant" + "@id": "bts:FragmentStandardDeviationLength" }, { - "@id": "bts:InframeDeletion" + "@id": "bts:LaneNumber" }, { - "@id": "bts:InframeInsertion" + "@id": "bts:LibraryStrand" }, { - "@id": "bts:IntergenicVariant" + "@id": "bts:MultiplexBarcode" }, { - "@id": "bts:IntronVariant" + "@id": "bts:SizeSelectionRange" }, { - "@id": "bts:MaturemiRNAVariant" + "@id": "bts:TargetDepth" }, { - "@id": "bts:MissenseVariant" + "@id": "bts:ToTrimAdapterSequence" }, { - "@id": "bts:NMDTranscriptVariant" + "@id": "bts:TranscriptIntegrityNumber" }, { - "@id": "bts:Non-codingTranscriptExonVariant" + "@id": "bts:RIN" }, { - "@id": "bts:Non-codingTranscriptVariant" + "@id": "bts:DV200" }, { - "@id": "bts:ProteinAlteringVariant" + "@id": "bts:AdapterContent" }, { - "@id": "bts:RegulatoryRegionAblation" + "@id": "bts:BasicStatistics" }, { - "@id": "bts:RegulatoryRegionAmplification" + "@id": "bts:Encoding" }, { - "@id": "bts:RegulatoryRegionVariant" + "@id": "bts:KmerContent" }, { - "@id": "bts:SpliceAcceptorVariant" + "@id": "bts:OverrepresentedSequences" }, { - "@id": "bts:SpliceDonorVariant" + "@id": "bts:PerBaseNContent" }, { - "@id": "bts:SpliceRegionVariant" + "@id": "bts:PerBaseSequenceContent" }, { - "@id": "bts:StartLost" + "@id": "bts:PerBaseSequenceQuality" }, { - "@id": "bts:StopGain" + "@id": "bts:PerSequenceGCContent" }, { - "@id": "bts:StopLost" + "@id": "bts:PerSequenceQualityScore" }, { - "@id": "bts:StopRetainedVariant" + "@id": "bts:PerTileSequenceQuality" }, { - "@id": "bts:SynonymousVariant" + "@id": "bts:PercentGCContent" }, { - "@id": "bts:TFBindingSiteVariant" + "@id": "bts:SequenceDuplicationLevels" }, { - "@id": "bts:TFBSAblation" + "@id": "bts:SequenceLengthDistribution" }, { - "@id": "bts:TFBSAmplification" + "@id": "bts:TotalReads" }, { - "@id": "bts:TranscriptAblation" + "@id": "bts:QCWorkflowType" }, { - "@id": "bts:TranscriptAmplification" + "@id": "bts:QCWorkflowVersion" }, { - "@id": "bts:UpstreamGeneVariant" + "@id": "bts:QCWorkflowLink" } ], - "sms:displayName": "Molecular Consequence", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Pathogenicity", + "@id": "bts:LibraryLayout", "@type": "rdfs:Class", - "rdfs:comment": "The text used to describe a variant's level of involvement in the cause of the patient's disease according to the standards outlined by the American College of Medical Genetics and Genomics (ACMG).", - "rdfs:label": "Pathogenicity", + "rdfs:comment": "Sequencing read type", + "rdfs:label": "LibraryLayout", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -30162,33 +35989,89 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Benign" + "@id": "bts:PairedEnd" }, { - "@id": "bts:LikelyBenign" + "@id": "bts:SingleRead" }, { - "@id": "bts:LikelyPathogenic" + "@id": "bts:Mid-length" }, { - "@id": "bts:Pathogenic" + "@id": "bts:LongRead" + } + ], + "sms:displayName": "Library Layout", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Micro-regionSeqPlatform", + "@type": "rdfs:Class", + "rdfs:comment": "The platform used for micro-regional RNA sequencing (if applicable)", + "rdfs:label": "Micro-regionSeqPlatform", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:RarecytePick-Seq" }, { - "@id": "bts:UncertainSignificance" + "@id": "bts:LaserCaptureMicrodissection" } ], - "sms:displayName": "Pathogenicity", + "sms:displayName": "Micro-region Seq Platform", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Ploidy", + "@id": "bts:ROITag", "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the number of sets of homologous chromosomes.", - "rdfs:label": "Ploidy", + "rdfs:comment": "The tag or grouping used to identify the ROI in micro-regional RNA sequencing (if applicable). Must match the ROI tag within the count matrix in level 3.", + "rdfs:label": "ROITag", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "ROI Tag", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ReadLength", + "@type": "rdfs:Class", + "rdfs:comment": "The length of the sequencing reads. Can be integer, null", + "rdfs:label": "ReadLength", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Read Length", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:LibrarySelectionMethod", + "@type": "rdfs:Class", + "rdfs:comment": "How RNA molecules are isolated.", + "rdfs:label": "LibrarySelectionMethod", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -30196,212 +36079,263 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Aneuploid" + "@id": "bts:HybridSelection" }, { - "@id": "bts:Diploid" + "@id": "bts:PCR" }, { - "@id": "bts:Hyperdiploid" + "@id": "bts:AffinityEnrichment" }, { - "@id": "bts:Hypodiploid" + "@id": "bts:Poly-TEnrichment" }, { - "@id": "bts:NearDiploid" + "@id": "bts:Random" }, { - "@id": "bts:Tetraploid" + "@id": "bts:RRNADepletion" }, { - "@id": "bts:Unknown" + "@id": "bts:MiRNASizeFractionation" }, { - "@id": "bts:NotReported" + "@id": "bts:Other" } ], - "sms:displayName": "Ploidy", - "sms:required": "sms:false", + "sms:displayName": "Library Selection Method", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SecondExon", + "@id": "bts:LibraryPreparationKitName", "@type": "rdfs:Class", - "rdfs:comment": "The second exon number involved in molecular variation. If a specific genetic variant is being reported, this property can be used to capture the second exon where that variant is located. This property is typically used for a translocation where two different locations are involved in the variation.", - "rdfs:label": "SecondExon", + "rdfs:comment": "Name of Library Preparation Kit. String", + "rdfs:label": "LibraryPreparationKitName", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Second Exon", - "sms:required": "sms:false", + "sms:displayName": "Library Preparation Kit Name", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SecondGeneSymbol", + "@id": "bts:LibraryPreparationKitVendor", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe a secondary gene targeted or included in molecular analysis. For rearrangements, this is should represent the location of the variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "SecondGeneSymbol", + "rdfs:comment": "Vendor of Library Preparation Kit. String", + "rdfs:label": "LibraryPreparationKitVendor", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Second Gene Symbol", - "sms:required": "sms:false", + "sms:displayName": "Library Preparation Kit Vendor", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SpecializedMolecularTest", + "@id": "bts:LibraryPreparationKitVersion", "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe a specific test that is not covered in the list of molecular analysis methods. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "SpecializedMolecularTest", + "rdfs:comment": "Version of Library Preparation Kit. String", + "rdfs:label": "LibraryPreparationKitVersion", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Specialized Molecular Test", - "sms:required": "sms:false", + "sms:displayName": "Library Preparation Kit Version", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TestAnalyteType", + "@id": "bts:AdapterName", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the type of analyte used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "TestAnalyteType", + "rdfs:comment": "Name of the sequencing adapter. String", + "rdfs:label": "AdapterName", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:DNA" - }, - { - "@id": "bts:MRNA" - }, - { - "@id": "bts:MiRNA" - }, - { - "@id": "bts:ProteinAnalyte" - }, - { - "@id": "bts:TotalRNA" - }, + "sms:displayName": "Adapter Name", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AdapterSequence", + "@type": "rdfs:Class", + "rdfs:comment": "Base sequence of the sequencing adapter. String", + "rdfs:label": "AdapterSequence", + "rdfs:subClassOf": [ { - "@id": "bts:Unknown" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Adapter Sequence", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BaseCallerName", + "@type": "rdfs:Class", + "rdfs:comment": "Name of the base caller. String", + "rdfs:label": "BaseCallerName", + "rdfs:subClassOf": [ { - "@id": "bts:NotReported" + "@id": "bts:Sequencing" } ], - "sms:displayName": "Test Analyte Type", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Base Caller Name", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TestUnits", + "@id": "bts:BaseCallerVersion", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the units of the test value for a molecular test. This property is used in conjunction with test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "TestUnits", + "rdfs:comment": "Version of the base caller. String", + "rdfs:label": "BaseCallerVersion", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Test Units", + "sms:displayName": "Base Caller Version", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TestValue", + "@id": "bts:FlowCellBarcode", "@type": "rdfs:Class", - "rdfs:comment": "The text term or numeric value used to describe a specific result of a molecular test. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here", - "rdfs:label": "TestValue", + "rdfs:comment": "Flow cell barcode. Wrong or missing information may affect analysis results. String", + "rdfs:label": "FlowCellBarcode", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Test Value", + "sms:displayName": "Flow Cell Barcode", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Transcript", + "@id": "bts:FragmentMaximumLength", "@type": "rdfs:Class", - "rdfs:comment": "Alphanumeric value used to describe the transcript of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "Transcript", + "rdfs:comment": "Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer", + "rdfs:label": "FragmentMaximumLength", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Transcript", + "sms:displayName": "Fragment Maximum Length", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:VariantOrigin", + "@id": "bts:FragmentMeanLength", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the biological origin of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label": "VariantOrigin", + "rdfs:comment": "Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number", + "rdfs:label": "FragmentMeanLength", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Fragment Mean Length", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:FragmentMinimumLength", + "@type": "rdfs:Class", + "rdfs:comment": "Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer", + "rdfs:label": "FragmentMinimumLength", + "rdfs:subClassOf": [ { - "@id": "bts:Germline" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Fragment Minimum Length", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:FragmentStandardDeviationLength", + "@type": "rdfs:Class", + "rdfs:comment": "Standard deviation of the sequenced fragments length (e.g., as predicted by Agilent Bioanalyzer). Number", + "rdfs:label": "FragmentStandardDeviationLength", + "rdfs:subClassOf": [ { - "@id": "bts:Somatic" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Fragment Standard Deviation Length", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:LaneNumber", + "@type": "rdfs:Class", + "rdfs:comment": "The basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer", + "rdfs:label": "LaneNumber", + "rdfs:subClassOf": [ { - "@id": "bts:Unknown" + "@id": "bts:Sequencing" } ], - "sms:displayName": "Variant Origin", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Lane Number", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:VariantType", + "@id": "bts:LibraryStrand", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the type of genetic variation.", - "rdfs:label": "VariantType", + "rdfs:comment": "Library stranded-ness.", + "rdfs:label": "LibraryStrand", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -30409,90 +36343,81 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Alleles" - }, - { - "@id": "bts:Amplification" - }, - { - "@id": "bts:Chrimerism" - }, - { - "@id": "bts:Conversion" - }, - { - "@id": "bts:Deletion" - }, - { - "@id": "bts:Deletion-Insertion" - }, - { - "@id": "bts:Duplication" - }, - { - "@id": "bts:Extension" - }, - { - "@id": "bts:Gain" - }, - { - "@id": "bts:Hypermethylation" - }, - { - "@id": "bts:Insertion" - }, - { - "@id": "bts:Inversion" - }, - { - "@id": "bts:Loss" - }, - { - "@id": "bts:Methylation" - }, - { - "@id": "bts:Mosaicism" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:PartialMethylation" - }, - { - "@id": "bts:Rearrangement" + "@id": "bts:Unstranded" }, { - "@id": "bts:RepeatedSequences" + "@id": "bts:FirstStranded" }, { - "@id": "bts:Splice" + "@id": "bts:SecondStranded" }, { - "@id": "bts:Substitution" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Library Strand", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MultiplexBarcode", + "@type": "rdfs:Class", + "rdfs:comment": "The barcode/index sequence used. Wrong or missing information may affect analysis results. String", + "rdfs:label": "MultiplexBarcode", + "rdfs:subClassOf": [ { - "@id": "bts:Translocation" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Multiplex Barcode", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SizeSelectionRange", + "@type": "rdfs:Class", + "rdfs:comment": "Range of size selection. String", + "rdfs:label": "SizeSelectionRange", + "rdfs:subClassOf": [ { - "@id": "bts:Unknown" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Size Selection Range", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TargetDepth", + "@type": "rdfs:Class", + "rdfs:comment": "The targeted read depth prior to sequencing. Integer", + "rdfs:label": "TargetDepth", + "rdfs:subClassOf": [ { - "@id": "bts:NotReported" + "@id": "bts:Sequencing" } ], - "sms:displayName": "Variant Type", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Target Depth", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Zygosity", + "@id": "bts:ToTrimAdapterSequence", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the zygosity of a specific genetic variant.", - "rdfs:label": "Zygosity", + "rdfs:comment": "Does the user suggest adapter trimming?", + "rdfs:label": "ToTrimAdapterSequence", "rdfs:subClassOf": [ { - "@id": "bts:MolecularTest" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -30500,89 +36425,75 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Heterozygous" - }, - { - "@id": "bts:Hemizygous" - }, - { - "@id": "bts:Homozygous" - }, - { - "@id": "bts:Nullizygous" - }, - { - "@id": "bts:Unknown" + "@id": "bts:Yes-TrimAdapterSequence" }, { - "@id": "bts:NotReported" + "@id": "bts:No" } ], - "sms:displayName": "Zygosity", + "sms:displayName": "To Trim Adapter Sequence", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SourceHTANBiospecimenID", + "@id": "bts:TranscriptIntegrityNumber", "@type": "rdfs:Class", - "rdfs:comment": "This is the HTAN ID that may have been assigned to the biospecimen at the site of biospecimen origin (e.g. BU).", - "rdfs:label": "SourceHTANBiospecimenID", + "rdfs:comment": "Used to describe the quality of the starting material, esp. in regards to FFPE samples. Number", + "rdfs:label": "TranscriptIntegrityNumber", "rdfs:subClassOf": [ { - "@id": "bts:Biosample" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Source HTAN Biospecimen ID", + "sms:displayName": "Transcript Integrity Number", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CollectionDaysfromIndex", + "@id": "bts:RIN", "@type": "rdfs:Class", - "rdfs:comment": "Number of days from the research participant's index date that the biospecimen was obtained. If not applicable please enter 'Not Applicable'", - "rdfs:label": "CollectionDaysfromIndex", + "rdfs:comment": "A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products. Number", + "rdfs:label": "RIN", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Collection Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "sms:displayName": "RIN", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:AdjacentBiospecimenIDs", + "@id": "bts:DV200", "@type": "rdfs:Class", - "rdfs:comment": "List of HTAN Identifiers (separated by commas) of adjacent biospecimens cut from the same sample; for example HTA3_3000_3, HTA3_3000_4, ...", - "rdfs:label": "AdjacentBiospecimenIDs", + "rdfs:comment": "Represents the percentage of RNA fragments that are >200 nucleotides in size. Number", + "rdfs:label": "DV200", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Adjacent Biospecimen IDs", + "sms:displayName": "DV200", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BiospecimenType", + "@id": "bts:AdapterContent", "@type": "rdfs:Class", - "rdfs:comment": "Biospecimen Type", - "rdfs:label": "BiospecimenType", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "AdapterContent", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -30590,51 +36501,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:TissueBiospecimenType" - }, - { - "@id": "bts:BloodBiospecimenType" - }, - { - "@id": "bts:AnalyteBiospecimenType" - }, - { - "@id": "bts:MouthRinseBiospecimenType" - }, - { - "@id": "bts:StoolBiospecimenType" - }, - { - "@id": "bts:UrineBiospecimenType" - }, - { - "@id": "bts:AscitesBiospecimenType" + "@id": "bts:FAIL" }, { - "@id": "bts:SputumBiospecimenType" + "@id": "bts:PASS" }, { - "@id": "bts:FluidsBiospecimenType" + "@id": "bts:WARN" }, { - "@id": "bts:BoneMarrowBiospecimenType" + "@id": "bts:Unknown" }, { - "@id": "bts:CellsBiospecimenType" + "@id": "bts:NotReported" } ], - "sms:displayName": "Biospecimen Type", - "sms:required": "sms:true", + "sms:displayName": "Adapter Content", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AcquisitionMethodType", + "@id": "bts:BasicStatistics", "@type": "rdfs:Class", - "rdfs:comment": "Records the method of acquisition or source for the specimen under consideration.", - "rdfs:label": "AcquisitionMethodType", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "BasicStatistics", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -30642,81 +36535,50 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Autopsy" - }, - { - "@id": "bts:Biopsy" - }, - { - "@id": "bts:FineNeedleAspirate" - }, - { - "@id": "bts:SurgicalResection" - }, - { - "@id": "bts:PunchBiopsy" - }, - { - "@id": "bts:ShaveBiopsy" - }, - { - "@id": "bts:Excision" - }, - { - "@id": "bts:Re-excision" - }, - { - "@id": "bts:SentinelNodeBiopsy" - }, - { - "@id": "bts:Lymphadenectomy-RegionalNodes" - }, - { - "@id": "bts:OtherAcquisitionMethod" - }, - { - "@id": "bts:Noninducedsputum" - }, - { - "@id": "bts:Inducedsputum" - }, - { - "@id": "bts:BAL(bronchialalveolarlavage)" - }, - { - "@id": "bts:Cytobrush" - }, - { - "@id": "bts:Blooddraw" + "@id": "bts:FAIL" }, { - "@id": "bts:Fluidcollection" + "@id": "bts:PASS" }, { - "@id": "bts:Forcepsbiopsy" + "@id": "bts:WARN" }, { - "@id": "bts:Coreneedlebiopsy" + "@id": "bts:Unknown" }, { - "@id": "bts:Endoscopicbiopsy" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Basic Statistics", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Encoding", + "@type": "rdfs:Class", + "rdfs:comment": "Version of ASCII encoding of quality values found in the file. String", + "rdfs:label": "Encoding", + "rdfs:subClassOf": [ { - "@id": "bts:Notspecified" + "@id": "bts:Sequencing" } ], - "sms:displayName": "Acquisition Method Type", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Encoding", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FixativeType", + "@id": "bts:KmerContent", "@type": "rdfs:Class", - "rdfs:comment": "Text term to identify the type of fixative used to preserve a tissue specimen", - "rdfs:label": "FixativeType", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "KmerContent", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -30724,87 +36586,135 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Acetone" + "@id": "bts:FAIL" }, { - "@id": "bts:Alcohol" + "@id": "bts:PASS" }, { - "@id": "bts:Formalin" + "@id": "bts:WARN" }, { - "@id": "bts:Glutaraldehyde" + "@id": "bts:Unknown" }, { - "@id": "bts:OCTmedia" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Kmer Content", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:OverrepresentedSequences", + "@type": "rdfs:Class", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "OverrepresentedSequences", + "rdfs:subClassOf": [ { - "@id": "bts:RNAlater" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Saline" + "@id": "bts:FAIL" }, { - "@id": "bts:95%Ethanol" + "@id": "bts:PASS" }, { - "@id": "bts:Dimidoester" + "@id": "bts:WARN" }, { - "@id": "bts:Carbodiimide" + "@id": "bts:Unknown" }, { - "@id": "bts:Dimethylacetamide" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Overrepresented Sequences", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PerBaseNContent", + "@type": "rdfs:Class", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerBaseNContent", + "rdfs:subClassOf": [ { - "@id": "bts:Para-benzoquinone" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:PAXgenetissue" + "@id": "bts:FAIL" }, { - "@id": "bts:TCLlysisbuffer" + "@id": "bts:PASS" }, { - "@id": "bts:NP40lysisbuffer" + "@id": "bts:WARN" }, { - "@id": "bts:Methacarn" + "@id": "bts:Unknown" }, { - "@id": "bts:Cryo-store" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Per Base N Content", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PerBaseSequenceContent", + "@type": "rdfs:Class", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerBaseSequenceContent", + "rdfs:subClassOf": [ { - "@id": "bts:Carnoy'sFixative" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Polaxamer" + "@id": "bts:FAIL" }, { - "@id": "bts:Other" + "@id": "bts:PASS" }, { - "@id": "bts:None" + "@id": "bts:WARN" }, { "@id": "bts:Unknown" }, { - "@id": "bts:Unfixed" + "@id": "bts:NotReported" } ], - "sms:displayName": "Fixative Type", - "sms:required": "sms:true", + "sms:displayName": "Per Base Sequence Content", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:StorageMethod", + "@id": "bts:PerBaseSequenceQuality", "@type": "rdfs:Class", - "rdfs:comment": "The method by which a biomaterial was stored after preservation or before another protocol was used.", - "rdfs:label": "StorageMethod", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerBaseSequenceQuality", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -30812,128 +36722,152 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Ambienttemperature" - }, - { - "@id": "bts:Cutslide" - }, - { - "@id": "bts:Fresh" + "@id": "bts:FAIL" }, { - "@id": "bts:Frozenat-20C" + "@id": "bts:PASS" }, { - "@id": "bts:Frozenat-70C" + "@id": "bts:WARN" }, { - "@id": "bts:Frozenat-80C" + "@id": "bts:Unknown" }, { - "@id": "bts:Frozenat-150C" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Per Base Sequence Quality", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PerSequenceGCContent", + "@type": "rdfs:Class", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerSequenceGCContent", + "rdfs:subClassOf": [ { - "@id": "bts:Frozeninliquidnitrogen" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Frozeninvaporphase" + "@id": "bts:FAIL" }, { - "@id": "bts:Paraffinblock" + "@id": "bts:PASS" }, { - "@id": "bts:RNAlaterat4C" + "@id": "bts:WARN" }, { - "@id": "bts:RNAlaterat25C" + "@id": "bts:Unknown" }, { - "@id": "bts:RNAlaterat-20C" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Per Sequence GC Content", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PerSequenceQualityScore", + "@type": "rdfs:Class", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerSequenceQualityScore", + "rdfs:subClassOf": [ { - "@id": "bts:Refrigeratedat4degrees" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Refrigeratedvacuumchamber" + "@id": "bts:FAIL" }, { - "@id": "bts:4Cinvacuumchamber" + "@id": "bts:PASS" }, { - "@id": "bts:Desiccantat4C" + "@id": "bts:WARN" }, { - "@id": "bts:NotApplicable" + "@id": "bts:Unknown" }, { - "@id": "bts:Unknown" + "@id": "bts:NotReported" } ], - "sms:displayName": "Storage Method", - "sms:required": "sms:true", + "sms:displayName": "Per Sequence Quality Score", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ProcessingDaysfromIndex", + "@id": "bts:PerTileSequenceQuality", "@type": "rdfs:Class", - "rdfs:comment": "Number of days from the research participant's index date that the biospecimen was processed. If not applicable please enter 'Not Applicable'", - "rdfs:label": "ProcessingDaysfromIndex", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerTileSequenceQuality", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Processing Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:ProtocolLink", - "@type": "rdfs:Class", - "rdfs:comment": "Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.", - "rdfs:label": "ProtocolLink", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:InformationContentEntity" + "@id": "bts:FAIL" + }, + { + "@id": "bts:PASS" + }, + { + "@id": "bts:WARN" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Protocol Link", - "sms:required": "sms:true", + "sms:displayName": "Per Tile Sequence Quality", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SiteDataSource", + "@id": "bts:PercentGCContent", "@type": "rdfs:Class", - "rdfs:comment": "Text to identify the data source for the specimen/sample from within the HTAN center, if applicable. Any identifier used within the center to identify data sources. No PHI/PII is allowed.", - "rdfs:label": "SiteDataSource", + "rdfs:comment": "The overall %GC of all bases in all sequences. Integer", + "rdfs:label": "PercentGCContent", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Site Data Source", + "sms:displayName": "Percent GC Content", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CollectionMedia", + "@id": "bts:SequenceDuplicationLevels", "@type": "rdfs:Class", - "rdfs:comment": "Material Specimen is collected into post procedure", - "rdfs:label": "CollectionMedia", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "SequenceDuplicationLevels", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -30941,39 +36875,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:DMEM" - }, - { - "@id": "bts:DMEM+Serum" - }, - { - "@id": "bts:RPMI" + "@id": "bts:FAIL" }, { - "@id": "bts:RPMI+Serum" + "@id": "bts:PASS" }, { - "@id": "bts:PBS" + "@id": "bts:WARN" }, { - "@id": "bts:PBS+Serum" + "@id": "bts:Unknown" }, { - "@id": "bts:None" + "@id": "bts:NotReported" } ], - "sms:displayName": "Collection Media", + "sms:displayName": "Sequence Duplication Levels", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MountingMedium", + "@id": "bts:SequenceLengthDistribution", "@type": "rdfs:Class", - "rdfs:comment": "The solution in which the specimen is embedded, generally under a cover glass. It may be liquid, gum or resinous, soluble in water, alcohol or other solvents and be sealed from the external atmosphere by non-soluble ringing media", - "rdfs:label": "MountingMedium", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "SequenceLengthDistribution", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -30981,25 +36909,13 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Aqueouswaterbased" - }, - { - "@id": "bts:Non-AqueousSolventbased" - }, - { - "@id": "bts:Xylene" - }, - { - "@id": "bts:Toluene" - }, - { - "@id": "bts:AntifadewithDAPI" + "@id": "bts:FAIL" }, { - "@id": "bts:AntifadewithoutDAPI" + "@id": "bts:PASS" }, { - "@id": "bts:PBS" + "@id": "bts:WARN" }, { "@id": "bts:Unknown" @@ -31008,226 +36924,214 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Mounting Medium", + "sms:displayName": "Sequence Length Distribution", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ProcessingLocation", + "@id": "bts:TotalReads", "@type": "rdfs:Class", - "rdfs:comment": "Site with an HTAN center where specimen processing occurs, if applicable. Any identifier used within the center to identify processing location. No PHI/PII is allowed.", - "rdfs:label": "ProcessingLocation", + "rdfs:comment": "Total number of reads per sample. Integer", + "rdfs:label": "TotalReads", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Processing Location", + "sms:displayName": "Total Reads", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HistologyAssessmentBy", + "@id": "bts:QCWorkflowType", "@type": "rdfs:Class", - "rdfs:comment": "Text term describing who (in what role) made the histological assessments of the sample", - "rdfs:label": "HistologyAssessmentBy", + "rdfs:comment": "Generic name for the workflow used to analyze a data set. String", + "rdfs:label": "QCWorkflowType", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Pathologist" - }, - { - "@id": "bts:ResearchScientist" - }, - { - "@id": "bts:Other" - }, + "sms:displayName": "QC Workflow Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:QCWorkflowVersion", + "@type": "rdfs:Class", + "rdfs:comment": "Major version for a workflow. String", + "rdfs:label": "QCWorkflowVersion", + "rdfs:subClassOf": [ { - "@id": "bts:Unknown" + "@id": "bts:Sequencing" } ], - "sms:displayName": "Histology Assessment By", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "QC Workflow Version", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HistologyAssessmentMedium", + "@id": "bts:QCWorkflowLink", "@type": "rdfs:Class", - "rdfs:comment": "The method of assessment used to characterize histology", - "rdfs:label": "HistologyAssessmentMedium", + "rdfs:comment": "Link to workflow used. String", + "rdfs:label": "QCWorkflowLink", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Digital" - }, - { - "@id": "bts:Microscopy" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Histology Assessment Medium", + "sms:displayName": "QC Workflow Link", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PreinvasiveMorphology", + "@id": "bts:BulkRNA-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the HTAN", - "rdfs:label": "PreinvasiveMorphology", + "rdfs:comment": "Bulk RNA-seq alignment protocol description", + "rdfs:label": "BulkRNA-seqLevel2", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Melanocytichyperplasia" - }, + "sms:displayName": "Bulk RNA-seq Level 2", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:Atypicalmelanocyticproliferation" - }, + "@id": "bts:BulkRNA-seqLevel1" + } + ], + "sms:requiresDependency": [ { - "@id": "bts:Melanomainsitu-superficialspreading" + "@id": "bts:Component" }, { - "@id": "bts:Melanomainsitu-lentigomalignatype" + "@id": "bts:Filename" }, { - "@id": "bts:Melanomainsitu-acral-lentiginous" + "@id": "bts:FileFormat" }, { - "@id": "bts:Melanomainsitu-arisinginagiantcongenitalnevus" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:Persistentmelanomainsitu" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:Melanomainsitu-nototherwiseclassified" + "@id": "bts:AlignmentWorkflowUrl" }, { - "@id": "bts:Scar-noresidualmelanoma" + "@id": "bts:AlignmentWorkflowType" }, { - "@id": "bts:Invasivemelanoma-superficialspreading" + "@id": "bts:GenomicReference" }, { - "@id": "bts:Invasivemelanoma-nodulartype" + "@id": "bts:GenomicReferenceURL" }, { - "@id": "bts:Invasivemelanoma-lentigomaligna" + "@id": "bts:IndexFileName" }, { - "@id": "bts:Invasivemelanoma-acrallentiginous" + "@id": "bts:AverageBaseQuality" }, { - "@id": "bts:Invasivemelanoma-desmoplastic" + "@id": "bts:AverageInsertSize" }, { - "@id": "bts:Invasivemelanoma-nevoid" + "@id": "bts:AverageReadLength" }, { - "@id": "bts:Invasivemelanoma-other" + "@id": "bts:Contamination" }, { - "@id": "bts:NormalWDA" + "@id": "bts:ContaminationError" }, { - "@id": "bts:Reservecellhyperplasia" + "@id": "bts:MeanCoverage" }, { - "@id": "bts:Squamousmetaplasia-mature" + "@id": "bts:MSIWorkflowLink" }, { - "@id": "bts:Squamousmetaplasia-immature" + "@id": "bts:MSIScore" }, { - "@id": "bts:Milddysplasia" + "@id": "bts:MSIStatus" }, { - "@id": "bts:Moderatedysplasia" + "@id": "bts:PairsOnDiffCHR" }, { - "@id": "bts:Severedysplasia" + "@id": "bts:TotalReads" }, { - "@id": "bts:SquamousCarcinomainsitu" + "@id": "bts:TotalUniquelyMapped" }, { - "@id": "bts:Atypicaladenomatoushyperplasia" + "@id": "bts:TotalUnmappedreads" }, { - "@id": "bts:Adenocarcinomainsitu-nonmucinous" + "@id": "bts:ProportionReadsDuplicated" }, { - "@id": "bts:Adenocarcinomainsitu-mucinous" + "@id": "bts:ProportionReadsMapped" }, { - "@id": "bts:BenigntumorNOS" + "@id": "bts:ProportionTargetsNoCoverage" }, { - "@id": "bts:Hamartoma" + "@id": "bts:ProportionBaseMismatch" }, { - "@id": "bts:CarcinomaNOS" + "@id": "bts:ShortReads" }, { - "@id": "bts:Nodiagnosispossible" + "@id": "bts:Islowestlevel" } ], - "sms:displayName": "Preinvasive Morphology", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TumorInfiltratingLymphocytes", + "@id": "bts:AlignmentWorkflowUrl", "@type": "rdfs:Class", - "rdfs:comment": "Measure of Tumor-Infiltrating Lymphocytes [Number]", - "rdfs:label": "TumorInfiltratingLymphocytes", + "rdfs:comment": "Link to workflow used for read alignment. DockStore.org recommended. String", + "rdfs:label": "AlignmentWorkflowUrl", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Tumor Infiltrating Lymphocytes", - "sms:required": "sms:false", + "sms:displayName": "Alignment Workflow Url", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:DegreeofDysplasia", + "@id": "bts:AlignmentWorkflowType", "@type": "rdfs:Class", - "rdfs:comment": "Information related to the presence of cells that look abnormal under a microscope but are not cancer. Records the degree of dysplasia for the cyst or lesion under consideration.", - "rdfs:label": "DegreeofDysplasia", + "rdfs:comment": "Generic name for the workflow used to analyze a data set.", + "rdfs:label": "AlignmentWorkflowType", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -31235,495 +37139,428 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Normalorbasalcellhyperplasiaormetaplasia" + "@id": "bts:BWA" }, { - "@id": "bts:Milddysplasia" + "@id": "bts:BWAwithBQSR" }, { - "@id": "bts:Moderatedysplasia" + "@id": "bts:BWA-aln" }, { - "@id": "bts:Severedysplasia" + "@id": "bts:BWA-mem" }, { - "@id": "bts:CarcinomainSitu" + "@id": "bts:BWAwithMarkDuplicatesandBQSR" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Degree of Dysplasia", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:DysplasiaFraction", - "@type": "rdfs:Class", - "rdfs:comment": "Resulting value to represent the number of pieces of dysplasia divided by the total number of pieces. [Text: max length 5]", - "rdfs:label": "DysplasiaFraction", - "rdfs:subClassOf": [ + "@id": "bts:STAR2-Pass" + }, { - "@id": "bts:Biospecimen" + "@id": "bts:STAR2-PassChimeric" + }, + { + "@id": "bts:STAR2-PassGenome" + }, + { + "@id": "bts:STAR2-PassTranscriptome" + }, + { + "@id": "bts:Bowtie" + }, + { + "@id": "bts:Bismark" + }, + { + "@id": "bts:GSNAP" + }, + { + "@id": "bts:BSMAP" + }, + { + "@id": "bts:BSmooth" + }, + { + "@id": "bts:BS-Seeker2" + }, + { + "@id": "bts:BS-Seeker" + }, + { + "@id": "bts:RMAP" + }, + { + "@id": "bts:MethylCoder" + }, + { + "@id": "bts:BRAT-BW" + }, + { + "@id": "bts:Pash" + }, + { + "@id": "bts:Segemehl" + }, + { + "@id": "bts:Bisulfighter" + }, + { + "@id": "bts:BatMeth" + }, + { + "@id": "bts:LAST" + }, + { + "@id": "bts:ERNE-BS5" + }, + { + "@id": "bts:B-SOLANA" + }, + { + "@id": "bts:SOCS-B" + }, + { + "@id": "bts:BWA-meth" + }, + { + "@id": "bts:OtherAlignmentWorkflow" + }, + { + "@id": "bts:None" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Dysplasia Fraction", - "sms:required": "sms:false", + "sms:displayName": "Alignment Workflow Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:NumberProliferatingCells", + "@id": "bts:IndexFileName", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the count of proliferating cells determined during pathologic review of the sample slide(s).", - "rdfs:label": "NumberProliferatingCells", + "rdfs:comment": "The name (or part of a name) of a file (of any type). String", + "rdfs:label": "IndexFileName", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Number Proliferating Cells", - "sms:required": "sms:false", + "sms:displayName": "Index File Name", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PercentEosinophilInfiltration", + "@id": "bts:AverageBaseQuality", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of infiltration by eosinophils in a tumor sample or specimen.", - "rdfs:label": "PercentEosinophilInfiltration", + "rdfs:comment": "Average base quality collected from samtools. Number", + "rdfs:label": "AverageBaseQuality", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Eosinophil Infiltration", + "sms:displayName": "Average Base Quality", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentGranulocyteInfiltration", + "@id": "bts:AverageInsertSize", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of infiltration by granulocytes in a tumor sample or specimen.", - "rdfs:label": "PercentGranulocyteInfiltration", + "rdfs:comment": "Average insert size collected from samtools. Integer", + "rdfs:label": "AverageInsertSize", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Granulocyte Infiltration", + "sms:displayName": "Average Insert Size", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentInflamInfiltration", + "@id": "bts:AverageReadLength", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent local response to cellular injury, marked by capillary dilatation, edema and leukocyte infiltration; clinically, inflammation is manifest by redness, heat, pain, swelling and loss of function, with the need to heal damaged tissue.", - "rdfs:label": "PercentInflamInfiltration", + "rdfs:comment": "Average read length collected from samtools. Integer", + "rdfs:label": "AverageReadLength", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Inflam Infiltration", + "sms:displayName": "Average Read Length", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentLymphocyteInfiltration", + "@id": "bts:Contamination", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of infiltration by lymphocytes in a solid tissue normal sample or specimen.", - "rdfs:label": "PercentLymphocyteInfiltration", + "rdfs:comment": "Fraction of reads coming from cross-sample contamination collected from GATK4. Number", + "rdfs:label": "Contamination", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Lymphocyte Infiltration", + "sms:displayName": "Contamination", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentMonocyteInfiltration", + "@id": "bts:ContaminationError", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of monocyte infiltration in a sample or specimen.", - "rdfs:label": "PercentMonocyteInfiltration", + "rdfs:comment": "Estimation error of cross-sample contamination collected from GATK4. Number", + "rdfs:label": "ContaminationError", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Monocyte Infiltration", + "sms:displayName": "Contamination Error", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentNecrosis", + "@id": "bts:MeanCoverage", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of cell death in a malignant tumor sample or specimen.", - "rdfs:label": "PercentNecrosis", + "rdfs:comment": "Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number", + "rdfs:label": "MeanCoverage", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Necrosis", + "sms:displayName": "Mean Coverage", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentNeutrophilInfiltration", + "@id": "bts:MSIWorkflowLink", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of infiltration by neutrophils in a tumor sample or specimen.", - "rdfs:label": "PercentNeutrophilInfiltration", + "rdfs:comment": "Link to method workflow (or command) used in estimating the MSI. URL", + "rdfs:label": "MSIWorkflowLink", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Neutrophil Infiltration", + "sms:displayName": "MSI Workflow Link", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentNormalCells", + "@id": "bts:MSIScore", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of normal cell content in a malignant tumor sample or specimen.", - "rdfs:label": "PercentNormalCells", + "rdfs:comment": "Numeric score denoting the aligned reads file's MSI score from MSIsensor. Number", + "rdfs:label": "MSIScore", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Normal Cells", + "sms:displayName": "MSI Score", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentStromalCells", + "@id": "bts:MSIStatus", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of reactive cells that are present in a malignant tumor sample or specimen but are not malignant such as fibroblasts, vascular structures, etc.", - "rdfs:label": "PercentStromalCells", + "rdfs:comment": "MSIsensor determination of either microsatellite stability or instability.", + "rdfs:label": "MSIStatus", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Stromal Cells", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PercentTumorCells", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the percentage of infiltration by tumor cells in a sample.", - "rdfs:label": "PercentTumorCells", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:Biospecimen" + "@id": "bts:MSI" + }, + { + "@id": "bts:MSI-low" + }, + { + "@id": "bts:MSI-high" + }, + { + "@id": "bts:MSS" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Percent Tumor Cells", + "sms:displayName": "MSI Status", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentTumorNuclei", + "@id": "bts:PairsOnDiffCHR", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of tumor nuclei in a malignant neoplasm sample or specimen.", - "rdfs:label": "PercentTumorNuclei", + "rdfs:comment": "Pairs on different chromosomes collected from samtools. Integer", + "rdfs:label": "PairsOnDiffCHR", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Tumor Nuclei", + "sms:displayName": "Pairs On Diff CHR", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FiducialMarker", + "@id": "bts:TotalUniquelyMapped", "@type": "rdfs:Class", - "rdfs:comment": "Imaging specific: fiducial markers for the alignment of images taken across multiple rounds of imaging.", - "rdfs:label": "FiducialMarker", + "rdfs:comment": "Number of reads that map to genome. Integer", + "rdfs:label": "TotalUniquelyMapped", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:NuclearStain-DAPI" - }, - { - "@id": "bts:FluorescentBeads" - }, - { - "@id": "bts:GridSlides-Hemocytometer" - }, - { - "@id": "bts:AdhesiveMarkers" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Fiducial Marker", + "sms:displayName": "Total Uniquely Mapped", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SlicingMethod", + "@id": "bts:TotalUnmappedreads", "@type": "rdfs:Class", - "rdfs:comment": "Imaging specific: the method by which the tissue was sliced.", - "rdfs:label": "SlicingMethod", + "rdfs:comment": "Number of reads that did not map to genome. Integer", + "rdfs:label": "TotalUnmappedreads", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Vibratome" - }, - { - "@id": "bts:Cryosectioning" - }, - { - "@id": "bts:Tissuemolds" - }, - { - "@id": "bts:Slidingmicrotome" - }, - { - "@id": "bts:Sectioning" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Slicing Method", + "sms:displayName": "Total Unmapped reads", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LysisBuffer", + "@id": "bts:ProportionReadsDuplicated", "@type": "rdfs:Class", - "rdfs:comment": "scRNA-seq specific: Type of lysis buffer used", - "rdfs:label": "LysisBuffer", + "rdfs:comment": "Proportion of duplicated reads collected from samtools. Number", + "rdfs:label": "ProportionReadsDuplicated", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Lysis Buffer", + "sms:displayName": "Proportion Reads Duplicated", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MethodofNucleicAcidIsolation", + "@id": "bts:ProportionReadsMapped", "@type": "rdfs:Class", - "rdfs:comment": "Bulk RNA & DNA-seq specific: method used for nucleic acid isolation. E.g. Qiagen Allprep, Qiagen miRNAeasy. [Text - max length 100]", - "rdfs:label": "MethodofNucleicAcidIsolation", + "rdfs:comment": "Proportion of mapped reads collected from samtools. Number", + "rdfs:label": "ProportionReadsMapped", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Method of Nucleic Acid Isolation", + "sms:displayName": "Proportion Reads Mapped", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Biosample", + "@id": "bts:ProportionTargetsNoCoverage", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Biosample", + "rdfs:comment": "Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number", + "rdfs:label": "ProportionTargetsNoCoverage", "rdfs:subClassOf": [ { - "@id": "bts:Thing" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Biosample", + "sms:displayName": "Proportion Targets No Coverage", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SRRSBiospecimen", + "@id": "bts:ProportionBaseMismatch", "@type": "rdfs:Class", - "rdfs:comment": "SRRS-specific HTAN biological entity; this can be tissue, blood, analyte and subsamples of those, however it can be described via fewer attributes than a standard HTAN specimen", - "rdfs:label": "SRRSBiospecimen", + "rdfs:comment": "Proportion of mismatched bases collected from samtools. Number", + "rdfs:label": "ProportionBaseMismatch", "rdfs:subClassOf": [ { - "@id": "bts:Biosample" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SRRS Biospecimen", + "sms:displayName": "Proportion Base Mismatch", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Patient" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:HTANBiospecimenID" - }, - { - "@id": "bts:SourceHTANBiospecimenID" - }, - { - "@id": "bts:HTANParentID" - }, - { - "@id": "bts:AdjacentBiospecimenIDs" - }, - { - "@id": "bts:BiospecimenType" - }, - { - "@id": "bts:TimepointLabel" - }, - { - "@id": "bts:CollectionDaysfromIndex" - }, - { - "@id": "bts:AcquisitionMethodType" - }, - { - "@id": "bts:IschemicTime" - }, - { - "@id": "bts:IschemicTemperature" - }, - { - "@id": "bts:CollectionMedia" - }, - { - "@id": "bts:TopographyCode" - }, - { - "@id": "bts:AdditionalTopography" - }, - { - "@id": "bts:FixativeType" - }, - { - "@id": "bts:StorageMethod" - }, - { - "@id": "bts:PreinvasiveMorphology" - }, - { - "@id": "bts:HistologicMorphologyCode" - }, - { - "@id": "bts:PreservationMethod" - }, - { - "@id": "bts:ProcessingDaysfromIndex" - }, - { - "@id": "bts:ProtocolLink" - } - ], "sms:validationRules": [] }, { - "@id": "bts:IschemicTime", + "@id": "bts:ShortReads", "@type": "rdfs:Class", - "rdfs:comment": "Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value.", - "rdfs:label": "IschemicTime", + "rdfs:comment": "Number of reads that were too short. Integer", + "rdfs:label": "ShortReads", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ischemic Time", + "sms:displayName": "Short Reads", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:IschemicTemperature", + "@id": "bts:Islowestlevel", "@type": "rdfs:Class", - "rdfs:comment": "Specify whether specimen experienced warm or cold ischemia.", - "rdfs:label": "IschemicTemperature", + "rdfs:comment": "Denotes that the manifest represents the lowest data level submitted. Use when L1 data is missing", + "rdfs:label": "Islowestlevel", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ScRNA-seqLevel2" } ], "schema:isPartOf": { @@ -31731,1036 +37568,772 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:WarmIschemia" - }, - { - "@id": "bts:ColdIschemia" - }, - { - "@id": "bts:Ambientair" - }, - { - "@id": "bts:4Cwetice" - }, - { - "@id": "bts:Negative-20C" - }, - { - "@id": "bts:DryIce" - }, - { - "@id": "bts:LiquidNitrogen" + "@id": "bts:Yes-Islowestlevel" }, { - "@id": "bts:Unknown" + "@id": "bts:No" } ], - "sms:displayName": "Ischemic Temperature", + "sms:displayName": "Is lowest level", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TopographyCode", - "@type": "rdfs:Class", - "rdfs:comment": "Topography Code, indicating site within the body, based on ICD-O-3.", - "rdfs:label": "TopographyCode", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:C00.0" - }, - { - "@id": "bts:C00.1" - }, - { - "@id": "bts:C00.2" - }, - { - "@id": "bts:C00.3" - }, - { - "@id": "bts:C00.4" - }, - { - "@id": "bts:C00.5" - }, - { - "@id": "bts:C00.6" - }, - { - "@id": "bts:C00.8" - }, - { - "@id": "bts:C01.9" - }, - { - "@id": "bts:C02.0" - }, - { - "@id": "bts:C02.1" - }, - { - "@id": "bts:C02.2" - }, - { - "@id": "bts:C02.3" - }, - { - "@id": "bts:C02.4" - }, - { - "@id": "bts:C02.8" - }, - { - "@id": "bts:C02.9" - }, - { - "@id": "bts:C03.0" - }, - { - "@id": "bts:C03.1" - }, - { - "@id": "bts:C03.9" - }, - { - "@id": "bts:C04.0" - }, - { - "@id": "bts:C04.1" - }, - { - "@id": "bts:C04.8" - }, - { - "@id": "bts:C04.9" - }, - { - "@id": "bts:C05.0" - }, - { - "@id": "bts:C05.1" - }, - { - "@id": "bts:C05.2" - }, - { - "@id": "bts:C05.8" - }, - { - "@id": "bts:C05.9" - }, - { - "@id": "bts:C06.0" - }, - { - "@id": "bts:C06.1" - }, - { - "@id": "bts:C06.2" - }, - { - "@id": "bts:C06.8" - }, - { - "@id": "bts:C06.9" - }, - { - "@id": "bts:C07.9" - }, - { - "@id": "bts:C08.0" - }, - { - "@id": "bts:C08.1" - }, - { - "@id": "bts:C08.8" - }, - { - "@id": "bts:C08.9" - }, - { - "@id": "bts:C09.0" - }, - { - "@id": "bts:C09.1" - }, - { - "@id": "bts:C09.8" - }, - { - "@id": "bts:C09.9" - }, - { - "@id": "bts:C10.0" - }, - { - "@id": "bts:C10.1" - }, - { - "@id": "bts:C10.2" - }, - { - "@id": "bts:C10.3" - }, - { - "@id": "bts:C10.4" - }, - { - "@id": "bts:C10.8" - }, - { - "@id": "bts:C10.9" - }, - { - "@id": "bts:C11.0" - }, - { - "@id": "bts:C11.1" - }, - { - "@id": "bts:C11.2" - }, - { - "@id": "bts:C11.3" - }, - { - "@id": "bts:C11.8" - }, - { - "@id": "bts:C11.9" - }, - { - "@id": "bts:C12.9" - }, - { - "@id": "bts:C13.0" - }, - { - "@id": "bts:C13.1" - }, - { - "@id": "bts:C13.2" - }, - { - "@id": "bts:C13.8" - }, - { - "@id": "bts:C13.9" - }, - { - "@id": "bts:C14.0" - }, - { - "@id": "bts:C14.2" - }, - { - "@id": "bts:C14.8" - }, - { - "@id": "bts:C15.0" - }, - { - "@id": "bts:C15.1" - }, - { - "@id": "bts:C15.2" - }, - { - "@id": "bts:C15.3" - }, - { - "@id": "bts:C15.4" - }, - { - "@id": "bts:C15.5" - }, - { - "@id": "bts:C15.8" - }, - { - "@id": "bts:C15.9" - }, - { - "@id": "bts:C16.0" - }, - { - "@id": "bts:C16.1" - }, - { - "@id": "bts:C16.2" - }, - { - "@id": "bts:C16.3" - }, - { - "@id": "bts:C16.4" - }, - { - "@id": "bts:C16.5" - }, - { - "@id": "bts:C16.6" - }, - { - "@id": "bts:C16.8" - }, - { - "@id": "bts:C16.9" - }, - { - "@id": "bts:C17.0" - }, - { - "@id": "bts:C17.1" - }, - { - "@id": "bts:C17.2" - }, - { - "@id": "bts:C17.3" - }, - { - "@id": "bts:C17.8" - }, - { - "@id": "bts:C17.9" - }, - { - "@id": "bts:C18.0" - }, - { - "@id": "bts:C18.1" - }, - { - "@id": "bts:C18.2" - }, - { - "@id": "bts:C18.3" - }, - { - "@id": "bts:C18.4" - }, - { - "@id": "bts:C18.5" - }, - { - "@id": "bts:C18.6" - }, - { - "@id": "bts:C18.7" - }, - { - "@id": "bts:C18.8" - }, - { - "@id": "bts:C18.9" - }, - { - "@id": "bts:C19.9" - }, - { - "@id": "bts:C20.9" - }, - { - "@id": "bts:C21.0" - }, - { - "@id": "bts:C21.1" - }, - { - "@id": "bts:C21.2" - }, - { - "@id": "bts:C21.8" - }, - { - "@id": "bts:C22.0" - }, - { - "@id": "bts:C22.1" - }, - { - "@id": "bts:C23.9" - }, - { - "@id": "bts:C24.0" - }, - { - "@id": "bts:C24.1" - }, - { - "@id": "bts:C24.8" - }, - { - "@id": "bts:C24.9" - }, - { - "@id": "bts:C25.0" - }, - { - "@id": "bts:C25.1" - }, - { - "@id": "bts:C25.2" - }, - { - "@id": "bts:C25.3" - }, - { - "@id": "bts:C25.4" - }, - { - "@id": "bts:C25.7" - }, - { - "@id": "bts:C25.8" - }, - { - "@id": "bts:C25.9" - }, - { - "@id": "bts:C26.0" - }, - { - "@id": "bts:C26.8" - }, - { - "@id": "bts:C26.9" - }, - { - "@id": "bts:C30.0" - }, - { - "@id": "bts:C30.1" - }, - { - "@id": "bts:C31.0" - }, - { - "@id": "bts:C31.1" - }, - { - "@id": "bts:C31.2" - }, - { - "@id": "bts:C31.3" - }, - { - "@id": "bts:C31.8" - }, - { - "@id": "bts:C31.9" - }, - { - "@id": "bts:C32.0" - }, - { - "@id": "bts:C32.1" - }, - { - "@id": "bts:C32.2" - }, - { - "@id": "bts:C32.3" - }, - { - "@id": "bts:C32.8" - }, - { - "@id": "bts:C32.9" - 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"@id": "bts:Diagnosis" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -32768,104 +38341,135 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Skinofscalp" - }, - { - "@id": "bts:Skinofeyelid" - }, - { - "@id": "bts:Skinofnose" - }, - { - "@id": "bts:Skinoflip" - }, - { - "@id": "bts:Skinofear" - }, - { - "@id": "bts:Skinofneck" + "@id": "bts:GATK4" }, { - "@id": "bts:Skinofotherpartsofface" + "@id": "bts:OtherGermlineVariantsWorkflowType" }, { - "@id": "bts:Skinofchest" - }, + "@id": "bts:None" + } + ], + "sms:displayName": "Germline Variants Workflow Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SomaticVariantsWorkflowURL", + "@type": "rdfs:Class", + "rdfs:comment": "Generic name for the workflow used to analyze a data set.", + "rdfs:label": "SomaticVariantsWorkflowURL", + "rdfs:subClassOf": [ { - "@id": "bts:Skinofback" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Somatic Variants Workflow URL", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:SomaticVariantsWorkflowType", + "@type": "rdfs:Class", + "rdfs:comment": "Generic name for the workflow used to analyze a data set.", + "rdfs:label": "SomaticVariantsWorkflowType", + "rdfs:subClassOf": [ { - "@id": "bts:Skinofabdomen" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Skinoftrunk" + "@id": "bts:CaVEMan" }, { - "@id": "bts:Skinofbreast" + "@id": "bts:GATK4" }, { - "@id": "bts:Skinofupperlimbandshoulder" + "@id": "bts:MuTect2" }, { - "@id": "bts:Skinofpalm" + "@id": "bts:MuSE" }, { - "@id": "bts:Skinoflowerlimbandhip" + "@id": "bts:Pindel" }, { - "@id": "bts:Skinofsole" + "@id": "bts:SomaticSniper" }, { - "@id": "bts:Skinofpenis" + "@id": "bts:VarScan2" }, { - "@id": "bts:Skinofscrotum" + "@id": "bts:OtherSomaticVariantsWorkflowType" }, { - "@id": "bts:Skinofvulva" - }, + "@id": "bts:None" + } + ], + "sms:displayName": "Somatic Variants Workflow Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SomaticVariantsSampleType", + "@type": "rdfs:Class", + "rdfs:comment": "Is the sample case or control in somatic variant analysis", + "rdfs:label": "SomaticVariantsSampleType", + "rdfs:subClassOf": [ { - "@id": "bts:SkinNOS" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:HilarAirway" + "@id": "bts:CaseSample" }, { - "@id": "bts:Peri-tumoralAirway" + "@id": "bts:ControlSample" }, { - "@id": "bts:NotReported" + "@id": "bts:NotApplicable" } ], - "sms:displayName": "Additional Topography", - "sms:required": "sms:false", + "sms:displayName": "Somatic Variants Sample Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:HistologicMorphologyCode", + "@id": "bts:StructuralVariantWorkflowURL", "@type": "rdfs:Class", - "rdfs:comment": "Histologic Morphology Code, based on ICD-O-3. Any valid ICD-O-3 morphology code. See https://seer.cancer.gov/icd-o-3/ and https://seer.cancer.gov/icd-o-3/sitetype.icdo3.20200629.xlsx. Examples: 80510", - "rdfs:label": "HistologicMorphologyCode", + "rdfs:comment": "Link to workflow document. DockStore.org recommended. URL", + "rdfs:label": "StructuralVariantWorkflowURL", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Histologic Morphology Code", + "sms:displayName": "Structural Variant Workflow URL", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PreservationMethod", + "@id": "bts:StructuralVariantWorkflowType", "@type": "rdfs:Class", - "rdfs:comment": "Text term that represents the method used to preserve the sample.", - "rdfs:label": "PreservationMethod", + "rdfs:comment": "Generic name for the workflow used to analyze a data set.", + "rdfs:label": "StructuralVariantWorkflowType", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -32873,92 +38477,190 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Cryopreserved" + "@id": "bts:BRASS" }, { - "@id": "bts:Cryopreservationinliquidnitrogen-deadtissue" + "@id": "bts:GATK4" }, { - "@id": "bts:Cryopreservationindryice-deadtissue" + "@id": "bts:CNV" }, { - "@id": "bts:Cryopreservationinliquidnitrogen-livecells" + "@id": "bts:CNVkit" }, { - "@id": "bts:Formalinfixedparaffinembedded-FFPE" + "@id": "bts:OtherStructuralVariantWorkflowType" }, { - "@id": "bts:Formalinfixed-unbuffered" - }, + "@id": "bts:None" + } + ], + "sms:displayName": "Structural Variant Workflow Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MicroarrayLevel1", + "@type": "rdfs:Class", + "rdfs:comment": "Microarray Level 1 refers to the raw text table of probe level intensities", + "rdfs:label": "MicroarrayLevel1", + "rdfs:subClassOf": [ { - "@id": "bts:Formalinfixed-buffered" - }, + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Microarray Level 1", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:Fresh" + "@id": "bts:Biospecimen" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:FreshdissociatedandsinglecellsortedintoplatesinNP40buffer" + "@id": "bts:Filename" }, { - "@id": "bts:OCT" + "@id": "bts:FileFormat" }, { - "@id": "bts:SnapFrozen" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:Frozen" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:Negative80DegC" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:LiquidNitrogen" + "@id": "bts:NucleicAcidSource" }, { - "@id": "bts:Freshdissociated" + "@id": "bts:MicroarrayPlatformID" }, { - "@id": "bts:Freshdissociatedandsinglecellsorted" + "@id": "bts:MicroarrayMolecule" }, { - "@id": "bts:Freshdissociatedandsinglecellsortedintoplates" + "@id": "bts:MicroarrayLabel" }, { - "@id": "bts:Methacarnfixedparaffinembedded-MFPE" + "@id": "bts:MicroarrayValueDefinition" }, { - "@id": "bts:Unknown" + "@id": "bts:MicroarrayProtocolAuxiliaryFile" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:MicroarrayPlatformID", + "@type": "rdfs:Class", + "rdfs:comment": "The NCBI GEO Microarray Platform ID that links to the table containing the array definition", + "rdfs:label": "MicroarrayPlatformID", + "rdfs:subClassOf": [ + { + "@id": "bts:MicroarrayLevel1" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Microarray Platform ID", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match GPL\\d+" + ] + }, + { + "@id": "bts:MicroarrayMolecule", + "@type": "rdfs:Class", + "rdfs:comment": "Microarray is measuring this kind of molecule", + "rdfs:label": "MicroarrayMolecule", + "rdfs:subClassOf": [ + { + "@id": "bts:MicroarrayLevel1" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:DNA" }, { - "@id": "bts:NotReported" + "@id": "bts:RNA" } ], - "sms:displayName": "Preservation Method", + "sms:displayName": "Microarray Molecule", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AssayType", + "@id": "bts:MicroarrayLabel", "@type": "rdfs:Class", - "rdfs:comment": "The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)", - "rdfs:label": "AssayType", + "rdfs:comment": "Microarray used this kind of label", + "rdfs:label": "MicroarrayLabel", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:MicroarrayLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Assay Type", + "sms:displayName": "Microarray Label", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ExSeqMinimal", + "@id": "bts:MicroarrayValueDefinition", "@type": "rdfs:Class", - "rdfs:comment": "Minimal metadata for the ExSeq assay", - "rdfs:label": "ExSeqMinimal", + "rdfs:comment": "What the provided value signifies", + "rdfs:label": "MicroarrayValueDefinition", + "rdfs:subClassOf": [ + { + "@id": "bts:MicroarrayLevel1" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Microarray Value Definition", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:MicroarrayProtocolAuxiliaryFile", + "@type": "rdfs:Class", + "rdfs:comment": "Auxiliary file describing the experimental protocols used, as described in the NCBI GEO microarray template, recorded as synapse ID (syn12345).", + "rdfs:label": "MicroarrayProtocolAuxiliaryFile", + "rdfs:subClassOf": [ + { + "@id": "bts:MicroarrayLevel1" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Microarray Protocol Auxiliary File", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match syn\\d+" + ] + }, + { + "@id": "bts:MicroarrayLevel2", + "@type": "rdfs:Class", + "rdfs:comment": "Microarray Level 2 provides a normalized matrix of values.", + "rdfs:label": "MicroarrayLevel2", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -32967,11 +38669,11 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "ExSeq Minimal", + "sms:displayName": "Microarray Level 2", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:Biospecimen" + "@id": "bts:MicroarrayLevel1" } ], "sms:requiresDependency": [ @@ -32984,23 +38686,49 @@ { "@id": "bts:FileFormat" }, + { + "@id": "bts:HTANParticipantID" + }, { "@id": "bts:HTANParentBiospecimenID" }, + { + "@id": "bts:HTANParentDataFileID" + }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:AssayType" + "@id": "bts:MicroarrayPlatformID" + }, + { + "@id": "bts:NormalizationMethod" } ], "sms:validationRules": [] }, { - "@id": "bts:ScRNA-seqLevel1", + "@id": "bts:NormalizationMethod", "@type": "rdfs:Class", - "rdfs:comment": "Single-cell RNA-seq [EFO_0008913]", - "rdfs:label": "ScRNA-seqLevel1", + "rdfs:comment": "Description of Normalization Process", + "rdfs:label": "NormalizationMethod", + "rdfs:subClassOf": [ + { + "@id": "bts:RPPALevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Normalization Method", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ScATAC-seqLevel1", + "@type": "rdfs:Class", + "rdfs:comment": "scATAC-seq files containing sequence read information, with or without alignment, as FASTQ or BAM files", + "rdfs:label": "ScATAC-seqLevel1", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -33009,7 +38737,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scRNA-seq Level 1", + "sms:displayName": "scATAC-seq Level 1", "sms:required": "sms:false", "sms:requiresComponent": [ { @@ -33036,73 +38764,113 @@ "@id": "bts:NucleicAcidSource" }, { - "@id": "bts:CryopreservedCellsinSample" + "@id": "bts:DissociationMethod" + }, + { + "@id": "bts:SingleNucleusBuffer" }, { "@id": "bts:SingleCellIsolationMethod" }, { - "@id": "bts:DissociationMethod" + "@id": "bts:TranspositionReaction" }, { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:ScATACseqLibraryLayout" }, { - "@id": "bts:ReadIndicator" + "@id": "bts:NucleusIdentifier" }, { - "@id": "bts:Read1" + "@id": "bts:NucleiBarcodeLength" }, { - "@id": "bts:Read2" + "@id": "bts:NucleiBarcodeRead" }, { - "@id": "bts:EndBias" + "@id": "bts:ScATACseqRead1" }, { - "@id": "bts:ReverseTranscriptionPrimer" + "@id": "bts:ScATACseqRead2" }, { - "@id": "bts:SpikeIn" + "@id": "bts:ScATACseqRead3" + }, + { + "@id": "bts:LibraryConstructionMethod" }, { "@id": "bts:SequencingPlatform" }, { - "@id": "bts:TotalNumberofInputCells" + "@id": "bts:ThresholdforMinimumPassingReads" }, { - "@id": "bts:InputCellsandNuclei" + "@id": "bts:TotalNumberofPassingNuclei" }, { - "@id": "bts:LibraryPreparationDaysfromIndex" + "@id": "bts:MedianFractionofReadsinPeaks" }, { - "@id": "bts:SingleCellDissociationDaysfromIndex" + "@id": "bts:MedianFractionofReadsinAnnotatedcisDNAElements" }, { - "@id": "bts:SequencingLibraryConstructionDaysfromIndex" + "@id": "bts:MedianPassingReadPercentage" }, { - "@id": "bts:NucleicAcidCaptureDaysfromIndex" + "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus" + }, + { + "@id": "bts:TechnicalReplicateGroup" + }, + { + "@id": "bts:TotalReads" }, { "@id": "bts:ProtocolLink" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:SingleNucleusBuffer", + "@type": "rdfs:Class", + "rdfs:comment": "Nuclei isolation buffer", + "rdfs:label": "SingleNucleusBuffer", + "rdfs:subClassOf": [ + { + "@id": "bts:ScATAC-seqLevel1" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:NIB" }, { - "@id": "bts:TechnicalReplicateGroup" + "@id": "bts:10x" + }, + { + "@id": "bts:Omni" + }, + { + "@id": "bts:TST" } ], + "sms:displayName": "Single Nucleus Buffer", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:NucleicAcidSource", + "@id": "bts:TranspositionReaction", "@type": "rdfs:Class", - "rdfs:comment": "The source of the input nucleic molecule", - "rdfs:label": "NucleicAcidSource", + "rdfs:comment": "Name of the transposase, transposon sequences", + "rdfs:label": "TranspositionReaction", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { @@ -33110,33 +38878,39 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:SingleCell" + "@id": "bts:Tn5" }, { - "@id": "bts:BulkWholeCell" + "@id": "bts:EZ-Tn5" }, { - "@id": "bts:SingleNucleus" + "@id": "bts:Tn5-059" }, { - "@id": "bts:BulkNuclei" + "@id": "bts:NexteraTn5" }, { - "@id": "bts:Micro-region" + "@id": "bts:Diagenode-unloadedApex-Bio" + }, + { + "@id": "bts:Diagenode-loadedApex-Bio" + }, + { + "@id": "bts:In-House" } ], - "sms:displayName": "Nucleic Acid Source", + "sms:displayName": "Transposition Reaction", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:CryopreservedCellsinSample", + "@id": "bts:ScATACseqLibraryLayout", "@type": "rdfs:Class", - "rdfs:comment": "Indicate if library preparation was based on revived frozen cells.", - "rdfs:label": "CryopreservedCellsinSample", + "rdfs:comment": "Sequencing read type", + "rdfs:label": "ScATACseqLibraryLayout", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { @@ -33144,24 +38918,21 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" + "@id": "bts:ScATACseqPairedEnd" } ], - "sms:displayName": "Cryopreserved Cells in Sample", + "sms:displayName": "scATACseq Library Layout", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SingleCellIsolationMethod", + "@id": "bts:NucleusIdentifier", "@type": "rdfs:Class", - "rdfs:comment": "The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)", - "rdfs:label": "SingleCellIsolationMethod", + "rdfs:comment": "Unique nuclei barcode; added at transposition step. Determines which nucleus the reads originated from", + "rdfs:label": "NucleusIdentifier", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { @@ -33169,67 +38940,64 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:MicrofluidicsChip" - }, - { - "@id": "bts:Droplets" - }, - { - "@id": "bts:FACS" - }, - { - "@id": "bts:Plates" - }, - { - "@id": "bts:10x" - }, - { - "@id": "bts:NucleiIsolation" + "@id": "bts:NucleiBarcode" } ], - "sms:displayName": "Single Cell Isolation Method", + "sms:displayName": "Nucleus Identifier", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:DissociationMethod", + "@id": "bts:NucleiBarcodeLength", "@type": "rdfs:Class", - "rdfs:comment": "The tissue dissociation method used for scRNASeq or scATAC-seq assays", - "rdfs:label": "DissociationMethod", + "rdfs:comment": "Nuclei Barcode Length", + "rdfs:label": "NucleiBarcodeLength", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:ScATAC-seqLevel1" + }, + { + "@id": "bts:NucleiBarcode" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:GentleMACS" - }, - { - "@id": "bts:Dounce" - }, + "sms:displayName": "Nuclei Barcode Length", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:NucleiBarcodeRead", + "@type": "rdfs:Class", + "rdfs:comment": "Nuclei Barcode Read", + "rdfs:label": "NucleiBarcodeRead", + "rdfs:subClassOf": [ { - "@id": "bts:EnzymaticDigestion" + "@id": "bts:ScATAC-seqLevel1" }, { - "@id": "bts:NotApplicable" + "@id": "bts:NucleiBarcode" } ], - "sms:displayName": "Dissociation Method", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Nuclei Barcode Read", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LibraryConstructionMethod", + "@id": "bts:ScATACseqRead1", "@type": "rdfs:Class", - "rdfs:comment": "Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711]", - "rdfs:label": "LibraryConstructionMethod", + "rdfs:comment": "Read 1 content description", + "rdfs:label": "ScATACseqRead1", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel1" + }, + { + "@id": "bts:ScATACseqPairedEnd" } ], "schema:isPartOf": { @@ -33237,72 +39005,70 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Smart-seq2" - }, - { - "@id": "bts:Smart-SeqV4" - }, - { - "@id": "bts:10xV1.0" - }, - { - "@id": "bts:10xV1.1" - }, - { - "@id": "bts:10xV2" - }, - { - "@id": "bts:10xV3" - }, - { - "@id": "bts:10xV3.1" + "@id": "bts:CellBarcodeandDNAInsert" }, { - "@id": "bts:CEL-seq2" + "@id": "bts:SampleIndexandDNAInsert" }, { - "@id": "bts:Drop-seq" + "@id": "bts:DNAInsert" }, { - "@id": "bts:InDropsV2" + "@id": "bts:SampleIndex" }, { - "@id": "bts:InDropsV3" - }, + "@id": "bts:CellBarcode" + } + ], + "sms:displayName": "scATACseq Read1", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:ScATACseqRead2", + "@type": "rdfs:Class", + "rdfs:comment": "Read 2 content description", + "rdfs:label": "ScATACseqRead2", + "rdfs:subClassOf": [ { - "@id": "bts:TruDrop" + "@id": "bts:ScATAC-seqLevel1" }, { - "@id": "bts:Sci-ATAC-seq" - }, + "@id": "bts:ScATACseqPairedEnd" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:NexteraXT" + "@id": "bts:CellBarcodeandDNAInsert" }, { - "@id": "bts:10xMultiome" + "@id": "bts:SampleIndexandDNAInsert" }, { - "@id": "bts:10xFLEX" + "@id": "bts:DNAInsert" }, { - "@id": "bts:10xGEM3'" + "@id": "bts:SampleIndex" }, { - "@id": "bts:10xGEM5'" + "@id": "bts:CellBarcode" } ], - "sms:displayName": "Library Construction Method", + "sms:displayName": "scATACseq Read2", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ReadIndicator", + "@id": "bts:ScATACseqRead3", "@type": "rdfs:Class", - "rdfs:comment": "Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other", - "rdfs:label": "ReadIndicator", + "rdfs:comment": "Read 3 content description", + "rdfs:label": "ScATACseqRead3", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { @@ -33310,994 +39076,1081 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:R1" + "@id": "bts:CellBarcodeandDNAInsert" }, { - "@id": "bts:R2" + "@id": "bts:SampleIndexandDNAInsert" }, { - "@id": "bts:R1&R2" + "@id": "bts:DNAInsert" }, { - "@id": "bts:I1" + "@id": "bts:SampleIndex" }, { - "@id": "bts:Other" + "@id": "bts:CellBarcode" } ], - "sms:displayName": "Read Indicator", - "sms:required": "sms:true", + "sms:displayName": "scATACseq Read3", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Read1", + "@id": "bts:ThresholdforMinimumPassingReads", "@type": "rdfs:Class", - "rdfs:comment": "Read 1 content description", - "rdfs:label": "Read1", + "rdfs:comment": "Threshold for calling cells", + "rdfs:label": "ThresholdforMinimumPassingReads", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:CellBarcodeandUMI" - }, + "sms:displayName": "Threshold for Minimum Passing Reads", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:TotalNumberofPassingNuclei", + "@type": "rdfs:Class", + "rdfs:comment": "Number of nuclei sequenced", + "rdfs:label": "TotalNumberofPassingNuclei", + "rdfs:subClassOf": [ { - "@id": "bts:CDNA" + "@id": "bts:ScATAC-seqLevel1" } ], - "sms:displayName": "Read1", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Total Number of Passing Nuclei", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Read2", + "@id": "bts:MedianFractionofReadsinPeaks", "@type": "rdfs:Class", - "rdfs:comment": "Read 2 content description", - "rdfs:label": "Read2", + "rdfs:comment": "Median fraction of reads in peaks (FRIP)", + "rdfs:label": "MedianFractionofReadsinPeaks", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:CellBarcodeandUMI" - }, + "sms:displayName": "Median Fraction of Reads in Peaks", + "sms:required": "sms:true", + "sms:requiresDependency": [ { - "@id": "bts:CDNA" + "@id": "bts:PeaksCallingSoftware" } ], - "sms:displayName": "Read2", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:EndBias", + "@id": "bts:MedianFractionofReadsinAnnotatedcisDNAElements", "@type": "rdfs:Class", - "rdfs:comment": "The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript", - "rdfs:label": "EndBias", + "rdfs:comment": "Median fraction of reads in annotated cis-DNA elements (FRIADE)", + "rdfs:label": "MedianFractionofReadsinAnnotatedcisDNAElements", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:3Prime" - }, - { - "@id": "bts:5Prime" - }, + "sms:displayName": "Median Fraction of Reads in Annotated cis DNA Elements", + "sms:required": "sms:true", + "sms:requiresDependency": [ { - "@id": "bts:FullLengthTranscript" + "@id": "bts:PeaksCallingSoftware" } ], - "sms:displayName": "End Bias", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ReverseTranscriptionPrimer", + "@id": "bts:MedianPassingReadPercentage", "@type": "rdfs:Class", - "rdfs:comment": "An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA", - "rdfs:label": "ReverseTranscriptionPrimer", + "rdfs:comment": "Non-PCR duplicate nuclear genomic sequence reads not aligning to unanchored contigs out of total reads assigned to the nucleus barcode", + "rdfs:label": "MedianPassingReadPercentage", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Oligo-dT" - }, - { - "@id": "bts:Poly-dT" - }, - { - "@id": "bts:Featurebarcoding" - }, + "sms:displayName": "Median Passing Read Percentage", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus", + "@type": "rdfs:Class", + "rdfs:comment": "Contamination from mitochondrial sequences", + "rdfs:label": "MedianPercentageofMitochondrialReadsperNucleus", + "rdfs:subClassOf": [ { - "@id": "bts:Random" + "@id": "bts:ScATAC-seqLevel1" } ], - "sms:displayName": "Reverse Transcription Primer", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Median Percentage of Mitochondrial Reads per Nucleus", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SpikeIn", + "@id": "bts:ScATAC-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix", - "rdfs:label": "SpikeIn", + "rdfs:comment": "scATAC-seq files containing aligned sequence data, as a BAM file", + "rdfs:label": "ScATAC-seqLevel2", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "scATAC-seq Level 2", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:ERCC" + "@id": "bts:ScATAC-seqLevel1" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:OtherSpikeIn" + "@id": "bts:Filename" }, { - "@id": "bts:NoSpikeIn" + "@id": "bts:FileFormat" }, { - "@id": "bts:PhiX" + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:AlignmentWorkflowUrl" + }, + { + "@id": "bts:AlignmentWorkflowType" + }, + { + "@id": "bts:GenomicReference" + }, + { + "@id": "bts:GenomicReferenceURL" + }, + { + "@id": "bts:IndexFileName" + }, + { + "@id": "bts:AverageBaseQuality" + }, + { + "@id": "bts:AverageInsertSize" + }, + { + "@id": "bts:AverageReadLength" + }, + { + "@id": "bts:MeanCoverage" + }, + { + "@id": "bts:PairsOnDiffCHR" + }, + { + "@id": "bts:TotalReads" + }, + { + "@id": "bts:ProportionReadsMapped" + }, + { + "@id": "bts:MapQ30" + }, + { + "@id": "bts:TotalUniquelyMapped" + }, + { + "@id": "bts:TotalUnmappedreads" + }, + { + "@id": "bts:ProportionReadsDuplicated" + }, + { + "@id": "bts:ShortReads" + }, + { + "@id": "bts:ProportionCoverage10x" + }, + { + "@id": "bts:ProportionCoverage30X" + }, + { + "@id": "bts:ProportionTargetsNoCoverage" + }, + { + "@id": "bts:ProportionBaseMismatch" + }, + { + "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus" + }, + { + "@id": "bts:Contamination" + }, + { + "@id": "bts:ContaminationError" } ], - "sms:displayName": "Spike In", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SequencingPlatform", + "@id": "bts:MapQ30", "@type": "rdfs:Class", - "rdfs:comment": "A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.", - "rdfs:label": "SequencingPlatform", + "rdfs:comment": "Number of reads with Quality >= 30.", + "rdfs:label": "MapQ30", "rdfs:subClassOf": [ { - "@id": "bts:Device" + "@id": "bts:ScATAC-seqLevel1" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "MapQ30", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ScATAC-seqLevel3", + "@type": "rdfs:Class", + "rdfs:comment": "Processed data files containing peak information for cells", + "rdfs:label": "ScATAC-seqLevel3", + "rdfs:subClassOf": [ { - "@id": "bts:IlluminaNextSeq500" + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "scATAC-seq Level 3", + "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:ScATAC-seqLevel2" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:IlluminaNextSeq550" + "@id": "bts:Filename" }, { - "@id": "bts:IlluminaNextSeq2500" + "@id": "bts:FileFormat" }, { - "@id": "bts:IlluminaNovaSeq6000" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:IlluminaMiSeq" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:454GSFLXTitanium" + "@id": "bts:ScATAC-seqObjectID" }, { - "@id": "bts:ABSOLiD4" + "@id": "bts:NCountPeaks" }, { - "@id": "bts:ABSOLiD2" + "@id": "bts:NFeaturePeaks" }, { - "@id": "bts:ABSOLiD3" + "@id": "bts:TotalRead-Pairs" }, { - "@id": "bts:CompleteGenomics" + "@id": "bts:DuplicateRead-Pairs" }, { - "@id": "bts:IlluminaHiSeqXTen" + "@id": "bts:ChimericRead-Pairs" }, { - "@id": "bts:IlluminaHiSeqXFive" + "@id": "bts:UnmappedRead-Pairs" }, { - "@id": "bts:IlluminaGenomeAnalyzerII" + "@id": "bts:LowMapQ" }, { - "@id": "bts:IlluminaGenomeAnalyzerIIx" + "@id": "bts:MitochondrialRead-Pairs" }, { - "@id": "bts:IlluminaHiSeq2000" + "@id": "bts:PassedFilters" }, { - "@id": "bts:IlluminaHiSeq2500" + "@id": "bts:TSSFragments" }, { - "@id": "bts:IlluminaHiSeq4000" + "@id": "bts:DNaseSensitiveRegionFragments" }, { - "@id": "bts:IlluminaNextSeq" + "@id": "bts:EnhancerRegionFragments" }, { - "@id": "bts:IonTorrentPGM" + "@id": "bts:PromoterRegionFragments" }, { - "@id": "bts:IonTorrentProton" + "@id": "bts:OnTargetFragments" }, { - "@id": "bts:IonTorrentS5" + "@id": "bts:BlacklistRegionFragments" }, { - "@id": "bts:PacBioRS" + "@id": "bts:PeakRegionFragments" }, { - "@id": "bts:NovaSeq6000" + "@id": "bts:PeakRegionCutsites" }, { - "@id": "bts:NovaSeqS4" + "@id": "bts:NucleosomeSignal" }, { - "@id": "bts:UltimaGenomicsUG100" + "@id": "bts:NucleosomePercentile" }, { - "@id": "bts:OxfordNanoporeminION" + "@id": "bts:TSSEnrichment" }, { - "@id": "bts:GridION" + "@id": "bts:TSSPercentile" }, { - "@id": "bts:PromethION" + "@id": "bts:PctReadsinPeaks" }, { - "@id": "bts:PacBioSequel2" + "@id": "bts:BlacklistRatio" }, { - "@id": "bts:Revio" + "@id": "bts:SeuratClusters" }, { - "@id": "bts:IlluminaNextSeq1000" + "@id": "bts:NCountRNA" }, { - "@id": "bts:IlluminaNextSeq2000" + "@id": "bts:NFeatureRNA" }, { - "@id": "bts:Other" + "@id": "bts:MACS2Seqnames" }, { - "@id": "bts:Unknown" + "@id": "bts:MACS2Start" }, { - "@id": "bts:NotReported" + "@id": "bts:MACS2End" + }, + { + "@id": "bts:MACS2Width" + }, + { + "@id": "bts:MACS2Strand" + }, + { + "@id": "bts:MACS2Name" + }, + { + "@id": "bts:MACS2Score" + }, + { + "@id": "bts:MACS2FoldChange" + }, + { + "@id": "bts:MACS2NegLog10pvalueSummit" + }, + { + "@id": "bts:MACS2NegLog10qvalueSummit" + }, + { + "@id": "bts:MACS2RelativeSummitPosition" } ], - "sms:displayName": "Sequencing Platform", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TotalNumberofInputCells", + "@id": "bts:ScATAC-seqObjectID", "@type": "rdfs:Class", - "rdfs:comment": "Number of cells loaded/placed on plates", - "rdfs:label": "TotalNumberofInputCells", + "rdfs:comment": "Orig.Ident or scATAC-seq Object ID", + "rdfs:label": "ScATAC-seqObjectID", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total Number of Input Cells", - "sms:required": "sms:true", + "sms:displayName": "scATAC-seq Object ID", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:InputCellsandNuclei", + "@id": "bts:NCountPeaks", "@type": "rdfs:Class", - "rdfs:comment": "Number of cells and number of nuclei input; entry format: number, number", - "rdfs:label": "InputCellsandNuclei", + "rdfs:comment": "Total number of fragments in peaks", + "rdfs:label": "NCountPeaks", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Input Cells and Nuclei", - "sms:required": "sms:true", + "sms:displayName": "nCount Peaks", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LibraryPreparationDaysfromIndex", + "@id": "bts:NFeaturePeaks", "@type": "rdfs:Class", - "rdfs:comment": "Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable'", - "rdfs:label": "LibraryPreparationDaysfromIndex", + "rdfs:comment": "Number of peaks with at least one read", + "rdfs:label": "NFeaturePeaks", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Library Preparation Days from Index", + "sms:displayName": "nFeature Peaks", "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "sms:validationRules": [] }, { - "@id": "bts:SingleCellDissociationDaysfromIndex", + "@id": "bts:TotalRead-Pairs", "@type": "rdfs:Class", - "rdfs:comment": "Number of days between sample for single cell assay was received in lab and when the sample was dissociated and cells were isolated [number]. If not applicable please enter 'Not Applicable'", - "rdfs:label": "SingleCellDissociationDaysfromIndex", + "rdfs:comment": "Total read-pairs", + "rdfs:label": "TotalRead-Pairs", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Single Cell Dissociation Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "sms:displayName": "Total Read-Pairs", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:SequencingLibraryConstructionDaysfromIndex", + "@id": "bts:DuplicateRead-Pairs", "@type": "rdfs:Class", - "rdfs:comment": "Number of days between sample for assay was received in lab and day of sequencing library construction [number]. If not applicable please enter 'Not Applicable'", - "rdfs:label": "SequencingLibraryConstructionDaysfromIndex", + "rdfs:comment": "Number of duplicate read-pairs", + "rdfs:label": "DuplicateRead-Pairs", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Sequencing Library Construction Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "sms:displayName": "Duplicate Read-Pairs", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:NucleicAcidCaptureDaysfromIndex", + "@id": "bts:ChimericRead-Pairs", "@type": "rdfs:Class", - "rdfs:comment": "Number of days between sample for single cell assay was received in lab and day of nucleic acid capture part of library construction (in number of days since sample received in lab) [number]. If not applicable please enter 'Not Applicable'", - "rdfs:label": "NucleicAcidCaptureDaysfromIndex", + "rdfs:comment": "Number of chimerically mapped read-pairs", + "rdfs:label": "ChimericRead-Pairs", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Nucleic Acid Capture Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "sms:displayName": "Chimeric Read-Pairs", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:TechnicalReplicateGroup", + "@id": "bts:UnmappedRead-Pairs", "@type": "rdfs:Class", - "rdfs:comment": "A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch)", - "rdfs:label": "TechnicalReplicateGroup", + "rdfs:comment": "Number of read-pairs with at least one end not mapped", + "rdfs:label": "UnmappedRead-Pairs", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Technical Replicate Group", + "sms:displayName": "Unmapped Read-Pairs", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScRNA-seqLevel2", + "@id": "bts:LowMapQ", "@type": "rdfs:Class", - "rdfs:comment": "Alignment workflows downstream of scRNA-seq Level 1", - "rdfs:label": "ScRNA-seqLevel2", + "rdfs:comment": "Number of read-pairs with <30 mapq on at least one end", + "rdfs:label": "LowMapQ", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scRNA-seq Level 2", + "sms:displayName": "LowMapQ", "sms:required": "sms:false", - "sms:requiresComponent": [ + "sms:validationRules": [] + }, + { + "@id": "bts:MitochondrialRead-Pairs", + "@type": "rdfs:Class", + "rdfs:comment": "Number of read-pairs mapping to mitochondria and non-nuclear contigs", + "rdfs:label": "MitochondrialRead-Pairs", + "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:ScATAC-seqLevel2" } ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:ScRNAseqWorkflowType" - }, - { - "@id": "bts:WorkflowVersion" - }, - { - "@id": "bts:ScRNAseqWorkflowParametersDescription" - }, - { - "@id": "bts:WorkflowLink" - }, - { - "@id": "bts:GenomicReference" - }, - { - "@id": "bts:GenomicReferenceURL" - }, - { - "@id": "bts:GenomeAnnotationURL" - }, - { - "@id": "bts:Checksum" - }, - { - "@id": "bts:WhitelistCellBarcodeFileLink" - }, - { - "@id": "bts:CellBarcodeTag" - }, - { - "@id": "bts:UMITag" - }, + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Mitochondrial Read-Pairs", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PassedFilters", + "@type": "rdfs:Class", + "rdfs:comment": "Number of non-duplicate, usable read-pairs i.e. fragments", + "rdfs:label": "PassedFilters", + "rdfs:subClassOf": [ { - "@id": "bts:AppliedHardTrimming" + "@id": "bts:ScATAC-seqLevel2" } ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Passed Filters", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScRNAseqWorkflowType", + "@id": "bts:TSSFragments", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "ScRNAseqWorkflowType", + "rdfs:comment": "Number of fragments overlapping with TSS regions", + "rdfs:label": "TSSFragments", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:CellRanger" - }, - { - "@id": "bts:STARsolo" - }, - { - "@id": "bts:HCAOptimus" - }, - { - "@id": "bts:DropEST" - }, - { - "@id": "bts:SEQC" - }, - { - "@id": "bts:Cufflinks" - }, - { - "@id": "bts:DEXSeq" - }, - { - "@id": "bts:HTSeq-FPKM" - }, - { - "@id": "bts:Cellannotation" - }, - { - "@id": "bts:Differentiationtrajectoryanalysis" - }, + "sms:displayName": "TSS Fragments", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:DNaseSensitiveRegionFragments", + "@type": "rdfs:Class", + "rdfs:comment": "Number of fragments overlapping with DNase sensitive regions", + "rdfs:label": "DNaseSensitiveRegionFragments", + "rdfs:subClassOf": [ { - "@id": "bts:Other" + "@id": "bts:ScATAC-seqLevel2" } ], - "sms:displayName": "scRNAseq Workflow Type", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "DNase Sensitive Region Fragments", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:WorkflowVersion", + "@id": "bts:EnhancerRegionFragments", "@type": "rdfs:Class", - "rdfs:comment": "Major version of the workflow (e.g. Cell Ranger v3.1)", - "rdfs:label": "WorkflowVersion", + "rdfs:comment": "Number of fragments overlapping enhancer regions", + "rdfs:label": "EnhancerRegionFragments", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Workflow Version", - "sms:required": "sms:true", + "sms:displayName": "Enhancer Region Fragments", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScRNAseqWorkflowParametersDescription", + "@id": "bts:PromoterRegionFragments", "@type": "rdfs:Class", - "rdfs:comment": "Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion", - "rdfs:label": "ScRNAseqWorkflowParametersDescription", + "rdfs:comment": "Number of fragments overlapping promoter regions", + "rdfs:label": "PromoterRegionFragments", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scRNAseq Workflow Parameters Description", - "sms:required": "sms:true", + "sms:displayName": "Promoter Region Fragments", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:WorkflowLink", + "@id": "bts:OnTargetFragments", "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow or command. DockStore.org recommended. URL", - "rdfs:label": "WorkflowLink", + "rdfs:comment": "Number of fragments overlapping any of TSS, enhancer, promoter and DNase hypersensitivity sites (counted with multiplicity)", + "rdfs:label": "OnTargetFragments", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Workflow Link", - "sms:required": "sms:true", + "sms:displayName": "On Target Fragments", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GenomicReference", + "@id": "bts:BlacklistRegionFragments", "@type": "rdfs:Class", - "rdfs:comment": "Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39)", - "rdfs:label": "GenomicReference", + "rdfs:comment": "Number of fragments overlapping blacklisted regions", + "rdfs:label": "BlacklistRegionFragments", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Genomic Reference", - "sms:required": "sms:true", + "sms:displayName": "Blacklist Region Fragments", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GenomicReferenceURL", + "@id": "bts:PeakRegionFragments", "@type": "rdfs:Class", - "rdfs:comment": "Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz)", - "rdfs:label": "GenomicReferenceURL", + "rdfs:comment": "Number of fragments overlapping peaks", + "rdfs:label": "PeakRegionFragments", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Genomic Reference URL", - "sms:required": "sms:true", + "sms:displayName": "Peak Region Fragments", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GenomeAnnotationURL", + "@id": "bts:PeakRegionCutsites", "@type": "rdfs:Class", - "rdfs:comment": "Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz)", - "rdfs:label": "GenomeAnnotationURL", + "rdfs:comment": "Number of ends of fragments in peak regions", + "rdfs:label": "PeakRegionCutsites", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Genome Annotation URL", - "sms:required": "sms:true", + "sms:displayName": "Peak Region Cutsites", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:WhitelistCellBarcodeFileLink", + "@id": "bts:NucleosomeSignal", "@type": "rdfs:Class", - "rdfs:comment": "Link to file listing all possible cell barcodes. URL", - "rdfs:label": "WhitelistCellBarcodeFileLink", + "rdfs:comment": "Nucleosome signal score (strength of the nucleosome signal per cell, computed as the ratio of fragments between 147 bp and 294 bp (mononucleosome) to fragments < 147 bp (nucleosome-free))", + "rdfs:label": "NucleosomeSignal", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Whitelist Cell Barcode File Link", - "sms:required": "sms:true", + "sms:displayName": "Nucleosome Signal", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CellBarcodeTag", + "@id": "bts:NucleosomePercentile", "@type": "rdfs:Class", - "rdfs:comment": "SAM tag for cell barcode field; please provide a valid cell barcode tag (e.g. CB:Z)", - "rdfs:label": "CellBarcodeTag", + "rdfs:comment": "Percentile rank of nucleosome score", + "rdfs:label": "NucleosomePercentile", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cell Barcode Tag", - "sms:required": "sms:true", + "sms:displayName": "Nucleosome Percentile", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:UMITag", + "@id": "bts:TSSEnrichment", "@type": "rdfs:Class", - "rdfs:comment": "SAM tag for the UMI field; please provide a valid UB, UMI (e.g. UB:Z or UR:Z)", - "rdfs:label": "UMITag", + "rdfs:comment": "Transcription start site (TSS) enrichment score", + "rdfs:label": "TSSEnrichment", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "UMI Tag", - "sms:required": "sms:true", + "sms:displayName": "TSS Enrichment", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AppliedHardTrimming", + "@id": "bts:TSSPercentile", "@type": "rdfs:Class", - "rdfs:comment": "Was Hard Trimming applied", - "rdfs:label": "AppliedHardTrimming", + "rdfs:comment": "Percentile rank of TSS score", + "rdfs:label": "TSSPercentile", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes-AppliedHardTrimming" - }, + "sms:displayName": "TSS Percentile", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PctReadsinPeaks", + "@type": "rdfs:Class", + "rdfs:comment": "Percentage of reads in peaks", + "rdfs:label": "PctReadsinPeaks", + "rdfs:subClassOf": [ { - "@id": "bts:No" + "@id": "bts:ScATAC-seqLevel2" } ], - "sms:displayName": "Applied Hard Trimming", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Pct Reads in Peaks", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScRNA-seqLevel3", + "@id": "bts:BlacklistRatio", "@type": "rdfs:Class", - "rdfs:comment": "Gene and Isoform expression files", - "rdfs:label": "ScRNA-seqLevel3", + "rdfs:comment": "Ratio of reads in blacklist regions", + "rdfs:label": "BlacklistRatio", "rdfs:subClassOf": [ { - 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}, - { - "@id": "bts:CellTotal" - }, - { - "@id": "bts:ScRNAseqWorkflowType" - }, + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Seurat Clusters", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:NCountRNA", + "@type": "rdfs:Class", + "rdfs:comment": "Total number of fragments in genes", + "rdfs:label": "NCountRNA", + "rdfs:subClassOf": [ { - "@id": "bts:ScRNAseqWorkflowParametersDescription" - }, + "@id": "bts:ScATAC-seqLevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "nCount RNA", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:NFeatureRNA", + "@type": "rdfs:Class", + "rdfs:comment": "Number of genes detected in cell", + "rdfs:label": "NFeatureRNA", + "rdfs:subClassOf": [ { - "@id": "bts:WorkflowLink" - }, + "@id": "bts:ScATAC-seqLevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "nFeature RNA", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MACS2Seqnames", + "@type": "rdfs:Class", + "rdfs:comment": "Chromosome id", + "rdfs:label": "MACS2Seqnames", + "rdfs:subClassOf": [ { - "@id": "bts:WorkflowVersion" + "@id": "bts:ScATAC-seqLevel2" } ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "MACS2 Seqnames", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DataCategory", + "@id": "bts:MACS2Start", "@type": "rdfs:Class", - "rdfs:comment": "Specific content type of the data file.", - "rdfs:label": "DataCategory", + "rdfs:comment": "Genomic starting position in MACS2", + "rdfs:label": "MACS2Start", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:GeneExpression" - }, - { - "@id": "bts:TranscriptExpression" - }, - { - "@id": "bts:ExonExpressionQuantification" - }, - { - "@id": "bts:GeneExpressionQuantification" - }, - { - "@id": "bts:IsoformExpressionQuantification" - }, - { - "@id": "bts:SpliceJunctionQuantification" - }, - { - "@id": "bts:Other" - } - ], - "sms:displayName": "Data Category", - "sms:required": "sms:true", + "sms:displayName": "MACS2 Start", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MatrixType", + "@id": "bts:MACS2End", "@type": "rdfs:Class", - "rdfs:comment": "Type of data stored in matrix.", - "rdfs:label": "MatrixType", + "rdfs:comment": "Genomic ending position in MACS2", + "rdfs:label": "MACS2End", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:RawCounts" - }, - { - "@id": "bts:NormalizedCounts" - }, - { - "@id": "bts:ScaledCounts" - }, + "sms:displayName": "MACS2 End", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MACS2Width", + "@type": "rdfs:Class", + "rdfs:comment": "Width of the peak in bases in MACS2", + "rdfs:label": "MACS2Width", + "rdfs:subClassOf": [ { - "@id": "bts:BatchCorrectedCounts" + "@id": "bts:ScATAC-seqLevel2" } ], - "sms:displayName": "Matrix Type", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "MACS2 Width", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LinkedMatrices", + "@id": "bts:MACS2Strand", "@type": "rdfs:Class", - "rdfs:comment": "All matrices associated with every part of a SingleCellExperiment object. Comma-delimited list of filenames", - "rdfs:label": "LinkedMatrices", + "rdfs:comment": "DNA stand aligned with in MACS2", + "rdfs:label": "MACS2Strand", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Linked Matrices", + "sms:displayName": "MACS2 Strand", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CellMedianNumberReads", + "@id": "bts:MACS2Name", "@type": "rdfs:Class", - "rdfs:comment": "Median number of reads per cell. Number", - "rdfs:label": "CellMedianNumberReads", + "rdfs:comment": "Name of the peak in MACS2", + "rdfs:label": "MACS2Name", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel3" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cell Median Number Reads", - "sms:required": "sms:true", + "sms:displayName": "MACS2 Name", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CellMedianNumberGenes", + "@id": "bts:MACS2Score", "@type": "rdfs:Class", - "rdfs:comment": "Median number of genes detected per cell. Number", - "rdfs:label": "CellMedianNumberGenes", + "rdfs:comment": "Peak score (proportional to q-value) in MACS2", + "rdfs:label": "MACS2Score", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel3" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cell Median Number Genes", - "sms:required": "sms:true", + "sms:displayName": "MACS2 Score", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CellTotal", + "@id": "bts:MACS2FoldChange", "@type": "rdfs:Class", - "rdfs:comment": "Number of sequenced cells. Applies to raw counts matrix only.", - "rdfs:label": "CellTotal", + "rdfs:comment": "Fold enrichment for this peak summit against random Poisson distribution with local lambda in MACS2", + "rdfs:label": "MACS2FoldChange", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel3" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cell Total", - "sms:required": "sms:true", + "sms:displayName": "MACS2 Fold Change", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScRNA-seqLevel4", + "@id": "bts:MACS2NegLog10pvalueSummit", "@type": "rdfs:Class", - "rdfs:comment": "Data represents the relationships between cells derived from Level 3 expression data and shown as tSNE or UMAP coordinates per cell, plus all other cell-specific meta information (e.g., cell type)", - "rdfs:label": "ScRNA-seqLevel4", + "rdfs:comment": "Negative log10 p-value for the peak summit in MACS2", + "rdfs:label": "MACS2NegLog10pvalueSummit", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ScATAC-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scRNA-seq Level 4", + "sms:displayName": "MACS2 Neg Log10 pvalue Summit", "sms:required": "sms:false", - "sms:requiresComponent": [ + "sms:validationRules": [] + }, + { + "@id": "bts:MACS2NegLog10qvalueSummit", + "@type": "rdfs:Class", + "rdfs:comment": "Negative log10 q-value for the peak summit in MACS2", + "rdfs:label": "MACS2NegLog10qvalueSummit", + "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel3" + "@id": "bts:ScATAC-seqLevel2" } ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:ScRNAseqWorkflowType" - }, - { - "@id": "bts:ScRNAseqWorkflowParametersDescription" - }, - { - "@id": "bts:WorkflowVersion" - }, + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "MACS2 Neg Log10 qvalue Summit", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MACS2RelativeSummitPosition", + "@type": "rdfs:Class", + "rdfs:comment": "Position of the peak summit related to the start position in MACS2", + "rdfs:label": "MACS2RelativeSummitPosition", + "rdfs:subClassOf": [ { - "@id": "bts:WorkflowLink" + "@id": "bts:ScATAC-seqLevel2" } ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "MACS2 Relative Summit Position", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Slide-seqLevel1", + "@id": "bts:ScmC-seqLevel1", "@type": "rdfs:Class", - "rdfs:comment": "Raw sequencing files for the Slide-seq assay.", - "rdfs:label": "Slide-seqLevel1", + "rdfs:comment": "Files contain raw scmC-seq data.", + "rdfs:label": "ScmC-seqLevel1", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Slide-seq Level 1", + "sms:displayName": "scmC-seq Level 1", "sms:required": "sms:false", "sms:requiresComponent": [ { @@ -34324,28 +40177,31 @@ "@id": "bts:NucleicAcidSource" }, { - "@id": "bts:ReadIndicator" + "@id": "bts:ScmCseqRead1" }, { - "@id": "bts:SpatialRead1" + "@id": "bts:ScmCseqRead2" }, { - "@id": "bts:SpatialRead2" + "@id": "bts:ScmCseqRead3" }, { - "@id": "bts:EndBias" + "@id": "bts:SingleCellIsolationMethod" }, { - "@id": "bts:ReverseTranscriptionPrimer" + "@id": "bts:SingleNucleusBuffer" }, { - "@id": "bts:SpatialBarcodeOffset" + "@id": "bts:SingleNucleusCapture" }, { - "@id": "bts:SpatialBarcodeandUMI" + "@id": "bts:BisulfiteConversion" }, { - "@id": "bts:SpikeIn" + "@id": "bts:LibraryLayout" + }, + { + "@id": "bts:NucleusIdentifier" }, { "@id": "bts:SequencingPlatform" @@ -34354,31 +40210,37 @@ "@id": "bts:TechnicalReplicateGroup" }, { - "@id": "bts:ProtocolLink" + "@id": "bts:MedianFractionofReadsinPeaks" }, { - "@id": "bts:SpatialLibraryConstructionMethod" + "@id": "bts:MedianPassingReadPercentage" }, { - "@id": "bts:LibraryPreparationDaysfromIndex" + "@id": "bts:PeaksCallingSoftware" }, { - "@id": "bts:SequencingLibraryConstructionDaysfromIndex" + "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus" }, { - "@id": "bts:NucleicAcidCaptureDaysfromIndex" + "@id": "bts:ThresholdforMinimumPassingReads" + }, + { + "@id": "bts:TotalNumberofPassingNuclei" + }, + { + "@id": "bts:TotalReads" } ], "sms:validationRules": [] }, { - "@id": "bts:SpatialRead1", + "@id": "bts:ScmCseqRead1", "@type": "rdfs:Class", "rdfs:comment": "Read 1 content description", - "rdfs:label": "SpatialRead1", + "rdfs:label": "ScmCseqRead1", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:ScmC-seqLevel1" } ], "schema:isPartOf": { @@ -34386,24 +40248,24 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CDNA" + "@id": "bts:CellBarcodeandUMI" }, { - "@id": "bts:SpatialBarcodeandUMI" + "@id": "bts:CDNA" } ], - "sms:displayName": "Spatial Read1", + "sms:displayName": "scmCseq Read1", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SpatialRead2", + "@id": "bts:ScmCseqRead2", "@type": "rdfs:Class", "rdfs:comment": "Read 2 content description", - "rdfs:label": "SpatialRead2", + "rdfs:label": "ScmCseqRead2", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:ScmC-seqLevel1" } ], "schema:isPartOf": { @@ -34411,80 +40273,77 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CDNA" + "@id": "bts:CellBarcodeandUMI" }, { - "@id": "bts:SpatialBarcodeandUMI" + "@id": "bts:CDNA" } ], - "sms:displayName": "Spatial Read2", + "sms:displayName": "scmCseq Read2", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SpatialBarcodeOffset", + "@id": "bts:ScmCseqRead3", "@type": "rdfs:Class", - "rdfs:comment": "Offset in sequence for spot barcode read (in bp): number", - "rdfs:label": "SpatialBarcodeOffset", + "rdfs:comment": "Read 3 content description", + "rdfs:label": "ScmCseqRead3", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:ScmC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Spatial Barcode Offset", + "schema:rangeIncludes": [ + { + "@id": "bts:CellBarcodeandUMI" + }, + { + "@id": "bts:CDNA" + } + ], + "sms:displayName": "scmCseq Read3", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SpatialBarcodeandUMI", + "@id": "bts:SingleNucleusCapture", "@type": "rdfs:Class", - "rdfs:comment": "Spot and transcript identifiers", - "rdfs:label": "SpatialBarcodeandUMI", + "rdfs:comment": "Nuclei isolation method", + "rdfs:label": "SingleNucleusCapture", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" - }, - { - "@id": "bts:SpatialRead1" - }, - { - "@id": "bts:SpatialRead2" + "@id": "bts:ScmC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Spatial Barcode and UMI", - "sms:required": "sms:true", - "sms:requiresDependency": [ - { - "@id": "bts:SpatialBarcodeOffset" - }, + "schema:rangeIncludes": [ { - "@id": "bts:SpatialBarcodeLength" + "@id": "bts:Plates" }, { - "@id": "bts:UMIBarcodeOffset" + "@id": "bts:10x" }, { - "@id": "bts:UMIBarcodeLength" + "@id": "bts:Droplet" } ], - "sms:validationRules": [ - "num" - ] + "sms:displayName": "Single Nucleus Capture", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:SpatialLibraryConstructionMethod", + "@id": "bts:BisulfiteConversion", "@type": "rdfs:Class", - "rdfs:comment": "Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711]", - "rdfs:label": "SpatialLibraryConstructionMethod", + "rdfs:comment": "Name of the kit used in bisulfite conversion.", + "rdfs:label": "BisulfiteConversion", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:BulkMethylation-seqLevel1" } ], "schema:isPartOf": { @@ -34492,81 +40351,60 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Smart-seq2" - }, - { - "@id": "bts:Smart-SeqV4" - }, - { - "@id": "bts:10xV1.0" - }, - { - "@id": "bts:10xV1.1" - }, - { - "@id": "bts:10xV2" - }, - { - "@id": "bts:10xV3" - }, - { - "@id": "bts:10xV3.1" - }, - { - "@id": "bts:Drop-seq" + "@id": "bts:ZimoEZDNAMethylationKit" }, { - "@id": "bts:InDropsV2" + "@id": "bts:ZimoEZ-96DNAMethylationShallowKit" }, { - "@id": "bts:InDropsV3" + "@id": "bts:ZimoEZ-96DNAMethylationDeepKit" }, { - "@id": "bts:TruDrop" + "@id": "bts:NEBNextEnzymaticMethyl-seqKit" }, { - "@id": "bts:NexteraXT" + "@id": "bts:AgilentSureSelectXTMethyl-Seq" } ], - "sms:displayName": "Spatial Library Construction Method", + "sms:displayName": "Bisulfite Conversion", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SpatialTranscriptomics", + "@id": "bts:PeaksCallingSoftware", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "SpatialTranscriptomics", + "rdfs:comment": "Generic name of peaks calling tool", + "rdfs:label": "PeaksCallingSoftware", "rdfs:subClassOf": [ { - "@id": "bts:Thing" + "@id": "bts:ScATAC-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Spatial Transcriptomics", - "sms:required": "sms:false", + "sms:displayName": "Peaks Calling Software", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Slide-seqLevel2", + "@id": "bts:ScmC-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Aligned sequencing files and QC for the Slide-seq assay.", - "rdfs:label": "Slide-seqLevel2", + "rdfs:comment": "Files contain scmC-seq files containing aligned sequence data, as a BAM file.", + "rdfs:label": "ScmC-seqLevel2", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Slide-seq Level 2", + "sms:displayName": "scmC-seq Level 2", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:Slide-seqLevel1" + "@id": "bts:ScmC-seqLevel1" } ], "sms:requiresDependency": [ @@ -34586,130 +40424,171 @@ "@id": "bts:HTANDataFileID" }, { - "@id": "bts:Slide-seqWorkflowType" + "@id": "bts:AlignmentWorkflowUrl" }, { - "@id": "bts:WorkflowVersion" + "@id": "bts:AlignmentWorkflowType" }, { - "@id": "bts:Slide-seqWorkflowParameterDescription" + "@id": "bts:GenomicReference" }, { - "@id": "bts:WorkflowLink" + "@id": "bts:GenomicReferenceURL" }, { - "@id": "bts:GenomicReference" + "@id": "bts:IndexFileName" }, { - "@id": "bts:GenomicReferenceURL" + "@id": "bts:AverageBaseQuality" }, { - "@id": "bts:GenomeAnnotationURL" + "@id": "bts:AverageInsertSize" }, { - "@id": "bts:Checksum" + "@id": "bts:AverageReadLength" }, { - "@id": "bts:SpatialBarcodeTag" + "@id": "bts:Contamination" }, { - "@id": "bts:MatchedSpatialBarcodeTag" + "@id": "bts:ContaminationError" }, { - "@id": "bts:UMITag" + "@id": "bts:MeanCoverage" }, { - "@id": "bts:AppliedHardTrimming" + "@id": "bts:PairsOnDiffCHR" + }, + { + "@id": "bts:TotalReads" + }, + { + "@id": "bts:TotalUniquelyMapped" + }, + { + "@id": "bts:TotalUnmappedreads" + }, + { + "@id": "bts:ProportionReadsDuplicated" + }, + { + "@id": "bts:ProportionReadsMapped" + }, + { + "@id": "bts:ProportionTargetsNoCoverage" + }, + { + "@id": "bts:ProportionBaseMismatch" + }, + { + "@id": "bts:ShortReads" } ], "sms:validationRules": [] }, { - "@id": "bts:Slide-seqWorkflowType", + "@id": "bts:ScATAC-seqLevel4", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze the Slide-seq data set. String", - "rdfs:label": "Slide-seqWorkflowType", + "rdfs:comment": "Data represents the relationships between cells derived from Level 3 expression data and shown as tSNE or UMAP coordinates per cell, plus all other cell-specific meta information (e.g., cell type)", + "rdfs:label": "ScATAC-seqLevel4", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Slide-seq Workflow Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Slide-seqWorkflowParameterDescription", - "@type": "rdfs:Class", - "rdfs:comment": "Parameters used to run the Slide-seq workflow. String", - "rdfs:label": "Slide-seqWorkflowParameterDescription", - "rdfs:subClassOf": [ + "sms:displayName": "scATAC-seq Level 4", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:ScATAC-seqLevel3" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:ScATACseqWorkflowType" + }, + { + "@id": "bts:ScATACseqWorkflowParametersDescription" + }, + { + "@id": "bts:WorkflowVersion" + }, + { + "@id": "bts:WorkflowLink" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Slide-seq Workflow Parameter Description", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SpatialBarcodeTag", + "@id": "bts:ScATACseqWorkflowType", "@type": "rdfs:Class", - "rdfs:comment": "SAM tag for spot barcode field; please provide a valid spot barcode tag (e.g. CB:Z)", - "rdfs:label": "SpatialBarcodeTag", + "rdfs:comment": "Generic name for the workflow used to analyze a data set.", + "rdfs:label": "ScATACseqWorkflowType", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Spatial Barcode Tag", + "sms:displayName": "scATACseq Workflow Type", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MatchedSpatialBarcodeTag", + "@id": "bts:ScATACseqWorkflowParametersDescription", "@type": "rdfs:Class", - "rdfs:comment": "SAM tag for matched spot barcode field; please provide a valid spot barcode tag (e.g. CB:Z) (Slide-seq specific)", - "rdfs:label": "MatchedSpatialBarcodeTag", + "rdfs:comment": "Parameters used to run the scATAC-seq workflow.", + "rdfs:label": "ScATACseqWorkflowParametersDescription", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Matched Spatial Barcode Tag", + "sms:displayName": "scATACseq Workflow Parameters Description", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Slide-seqLevel3", + "@id": "bts:ScDNA-seqLevel1", "@type": "rdfs:Class", - "rdfs:comment": "Gene matrices with features and barcodes for Slide-seq as well as spatial information (bead location files).", - "rdfs:label": "Slide-seqLevel3", + "rdfs:comment": "Single-cell DNA-seq", + "rdfs:label": "ScDNA-seqLevel1", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Slide-seq Level 3", + "sms:displayName": "scDNA-seq Level 1", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:Slide-seqLevel2" + "@id": "bts:Biospecimen" } ], "sms:requiresDependency": [ @@ -34723,464 +40602,408 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:HTANParentBiospecimenID" }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:RunID" + "@id": "bts:SequencingBatchID" }, { - "@id": "bts:SequencingBatchID" + "@id": "bts:LibraryLayout" }, { - "@id": "bts:DataCategory" + "@id": "bts:NucleicAcidSource" }, { - "@id": "bts:MatrixType" + "@id": "bts:LibrarySelectionMethod" }, { - "@id": "bts:Slide-seqWorkflowType" + "@id": "bts:ReadLength" }, { - "@id": "bts:WorkflowVersion" + "@id": "bts:LibraryPreparationKitName" }, { - "@id": "bts:Slide-seqWorkflowParameterDescription" + "@id": "bts:LibraryPreparationKitVendor" }, { - "@id": "bts:WorkflowLink" + "@id": "bts:LibraryPreparationKitVersion" }, { - "@id": "bts:BeadsTotal" + "@id": "bts:AdapterName" }, { - "@id": "bts:MedianUMICountsperSpot" + "@id": "bts:AdapterSequence" }, { - "@id": "bts:MedianNumberGenesperSpatialSpot" + "@id": "bts:BaseCallerName" }, { - "@id": "bts:Slide-seqBeadFileType" + "@id": "bts:BaseCallerVersion" }, { - "@id": "bts:Slide-seqFragmentSize" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:RunID", - "@type": "rdfs:Class", - "rdfs:comment": "A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.", - "rdfs:label": "RunID", - "rdfs:subClassOf": [ + "@id": "bts:FlowCellBarcode" + }, { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Run ID", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SequencingBatchID", - "@type": "rdfs:Class", - "rdfs:comment": "Links samples to a specific local sequencer run. Can be string or 'null'", - "rdfs:label": "SequencingBatchID", - "rdfs:subClassOf": [ + "@id": "bts:FragmentMaximumLength" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Sequencing Batch ID", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:BeadsTotal", - "@type": "rdfs:Class", - "rdfs:comment": "Number of sequenced beads. Applies to raw counts matrix only. Integer", - "rdfs:label": "BeadsTotal", - "rdfs:subClassOf": [ + "@id": "bts:FragmentMeanLength" + }, { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Beads Total", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MedianUMICountsperSpot", - "@type": "rdfs:Class", - "rdfs:comment": "The median number of UMI counts per tissue covered spot.", - "rdfs:label": "MedianUMICountsperSpot", - "rdfs:subClassOf": [ + "@id": "bts:FragmentMinimumLength" + }, { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Median UMI Counts per Spot", - "sms:required": "sms:true", - "sms:validationRules": [ - "num" - ] - }, - { - "@id": "bts:MedianNumberGenesperSpatialSpot", - "@type": "rdfs:Class", - "rdfs:comment": "The median number of genes detected per spot under tissue-associated barcode. Detection is defined as the presence of at least 1 UMI count.", - "rdfs:label": "MedianNumberGenesperSpatialSpot", - "rdfs:subClassOf": [ + "@id": "bts:FragmentStandardDeviationLength" + }, { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Median Number Genes per Spatial Spot", - "sms:required": "sms:true", - "sms:validationRules": [ - "num" - ] - }, - { - "@id": "bts:Slide-seqBeadFileType", - "@type": "rdfs:Class", - "rdfs:comment": "The type of Level 3 file submitted as part of the Slide-seq workflow.", - "rdfs:label": "Slide-seqBeadFileType", - "rdfs:subClassOf": [ + "@id": "bts:LaneNumber" + }, { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:LibraryStrand" + }, { - "@id": "bts:MatrixFeatures" + "@id": "bts:MultiplexBarcode" }, { - "@id": "bts:MatrixBarcodes" + "@id": "bts:SizeSelectionRange" }, { - "@id": "bts:AllBeadLocations" + "@id": "bts:TargetDepth" }, { - "@id": "bts:AllBeadBarcodes" + "@id": "bts:ToTrimAdapterSequence" }, { - "@id": "bts:MatchedBeadBarcodes" + "@id": "bts:AdapterContent" }, { - "@id": "bts:MatchedBeadLocations" + "@id": "bts:BasicStatistics" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Slide-seq Bead File Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Slide-seqFragmentSize", - "@type": "rdfs:Class", - "rdfs:comment": "Average cDNA length associated with the experiemtn. Integer", - "rdfs:label": "Slide-seqFragmentSize", - "rdfs:subClassOf": [ + "@id": "bts:Encoding" + }, { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Slide-seq Fragment Size", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MatrixFeatures", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "MatrixFeatures", - "rdfs:subClassOf": [ + "@id": "bts:KmerContent" + }, { - "@id": "bts:Slide-seqBeadFileType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Matrix Features", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MatrixBarcodes", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "MatrixBarcodes", - "rdfs:subClassOf": [ + "@id": "bts:OverrepresentedSequences" + }, { - "@id": "bts:Slide-seqBeadFileType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Matrix Barcodes", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AllBeadLocations", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "AllBeadLocations", - "rdfs:subClassOf": [ + "@id": "bts:PerBaseNContent" + }, { - "@id": "bts:Slide-seqBeadFileType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "All Bead Locations", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AllBeadBarcodes", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "AllBeadBarcodes", - "rdfs:subClassOf": [ + "@id": "bts:PerBaseSequenceContent" + }, { - "@id": "bts:Slide-seqBeadFileType" + "@id": "bts:PerBaseSequenceQuality" + }, + { + "@id": "bts:PerSequenceGCContent" + }, + { + "@id": "bts:PerSequenceQualityScore" + }, + { + "@id": "bts:PerTileSequenceQuality" + }, + { + "@id": "bts:PercentGCContent" + }, + { + "@id": "bts:SequenceDuplicationLevels" + }, + { + "@id": "bts:SequenceLengthDistribution" + }, + { + "@id": "bts:TotalReads" + }, + { + "@id": "bts:QCWorkflowType" + }, + { + "@id": "bts:QCWorkflowVersion" + }, + { + "@id": "bts:QCWorkflowLink" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "All Bead Barcodes", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MatchedBeadBarcodes", + "@id": "bts:ScDNA-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "MatchedBeadBarcodes", + "rdfs:comment": "Alignment workflows downstream of scDNA-seq Level 1", + "rdfs:label": "ScDNA-seqLevel2", "rdfs:subClassOf": [ { - "@id": "bts:Slide-seqBeadFileType" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Matched Bead Barcodes", + "sms:displayName": "scDNA-seq Level 2", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MatchedBeadLocations", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "MatchedBeadLocations", - "rdfs:subClassOf": [ + "sms:requiresComponent": [ { - "@id": "bts:Slide-seqBeadFileType" + "@id": "bts:ScDNA-seqLevel1" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Matched Bead Locations", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:NotApplicable", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "NotApplicable", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:TargetCaptureKit" + "@id": "bts:Component" }, { - "@id": "bts:SomaticVariantsSampleType" + "@id": "bts:Filename" }, { - "@id": "bts:HistoryofPriorColonPolyps" + "@id": "bts:FileFormat" }, { - "@id": "bts:FamilyColonCancerHistoryIndicator" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:FamilyMedicalHistoryColorectalPolypDiagnosis" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:PatientColonoscopyPerformedIndicator" + "@id": "bts:AlignmentWorkflowUrl" }, { - "@id": "bts:ReplicateType" + "@id": "bts:AlignmentWorkflowType" }, { - "@id": "bts:DissociationMethod" + "@id": "bts:GenomicReference" }, { - "@id": "bts:LibraryStrand" + "@id": "bts:GenomicReferenceURL" }, { - "@id": "bts:Immunosuppression" + "@id": "bts:IndexFileName" }, { - "@id": "bts:COVID19OccurrenceIndicator" + "@id": "bts:AverageBaseQuality" }, { - "@id": "bts:COVID19PositiveLabTestIndicator" + "@id": "bts:AverageInsertSize" }, { - "@id": "bts:COVID19CancerTreatmentFollowup" + "@id": "bts:AverageReadLength" }, { - "@id": "bts:ImmediateFamilyHistoryEndometrialCancer" + "@id": "bts:MeanCoverage" }, { - "@id": "bts:ImmediateFamilyHistoryOvarianCancer" + "@id": "bts:PairsOnDiffCHR" }, { - "@id": "bts:ColorectalCancerKRASIndicator" + "@id": "bts:TotalReads" }, { - "@id": "bts:ColonPolypOccurenceIndicator" + "@id": "bts:ProportionReadsMapped" }, { - "@id": "bts:FamilyHistoryColorectalPolyp" + "@id": "bts:MapQ30" }, { - "@id": "bts:ColorectalPolypNewIndicator" + "@id": "bts:TotalUniquelyMapped" }, { - "@id": "bts:HormoneTherapyBreastCancerPreventionIndicator" + "@id": "bts:TotalUnmappedreads" }, { - "@id": "bts:GliomaSpecificRadiationField" + "@id": "bts:ProportionReadsDuplicated" }, { - "@id": "bts:SupraTentorialEpendymomaMolecularSubgroup" + "@id": "bts:ShortReads" }, { - "@id": "bts:RefluxTreatmentType" + "@id": "bts:ProportionCoverage10x" }, { - "@id": "bts:COVID19ComplicationsSeverity" + "@id": "bts:ProportionCoverage30X" }, { - "@id": "bts:PatientInflammatoryBowelDiseasePersonalMedicaHistory" + "@id": "bts:ProportionTargetsNoCoverage" }, { - "@id": "bts:ColorectalCancerTumorBorderConfiguration" + "@id": "bts:ProportionBaseMismatch" }, { - "@id": "bts:ColorectalPolypShape" + "@id": "bts:ProportionMitochondrialReads" }, { - "@id": "bts:InfraTentorialEpendymomaMolecularSubgroup" + "@id": "bts:Contamination" }, { - "@id": "bts:SpecimenLaterality" - }, + "@id": "bts:ContaminationError" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:ProportionMitochondrialReads", + "@type": "rdfs:Class", + "rdfs:comment": "Proportion of reads mapping to mitochondria.", + "rdfs:label": "ProportionMitochondrialReads", + "rdfs:subClassOf": [ { - "@id": "bts:LabTestsforMMRStatus" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Proportion Mitochondrial Reads", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BulkMethylation-seqLevel1", + "@type": "rdfs:Class", + "rdfs:comment": "Raw data for bulk methylation sequencing, such as FASTQs and unaligned BAMs", + "rdfs:label": "BulkMethylation-seqLevel1", + "rdfs:subClassOf": [ { - "@id": "bts:Slide-seqBeadFileType" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Bulk Methylation-seq Level 1", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:GliomaSpecificMetastasisSites" - }, + "@id": "bts:Biospecimen" + } + ], + "sms:requiresDependency": [ { - "@id": "bts:COVID19AntibodyTesting" + "@id": "bts:Component" }, { - "@id": "bts:ColorectalPolypAdenomaType" + "@id": "bts:Filename" }, { - "@id": "bts:LastKnownDiseaseStatus" + "@id": "bts:FileFormat" }, { - "@id": "bts:CutaneousMelanomaAdditionalFindings" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:CauseofDeath" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:TumorGrade" + "@id": "bts:NucleicAcidSource" }, { - "@id": "bts:ImagingAssayType" + "@id": "bts:BisulfiteConversion" }, { - "@id": "bts:ExtentofTumorResection" + "@id": "bts:SequencingPlatform" }, { - "@id": "bts:TestResult" + "@id": "bts:ReplicateType" }, { - "@id": "bts:StorageMethod" + "@id": "bts:BulkMethylationAssayType" }, { - "@id": "bts:MolecularAnalysisMethod" + "@id": "bts:TotalDNAInput" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:ReplicateType", + "@type": "rdfs:Class", + "rdfs:comment": "A common term for all files belonging to the same sample. We suggest using a stable sample accession from a biosample archive like BioSamples.", + "rdfs:label": "ReplicateType", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Technicalreplicate" }, { - "@id": "bts:ConcomitantMedicationReceivedType" + "@id": "bts:Biologicalreplicate" }, { - "@id": "bts:HereditaryCancerPredispositionSyndrome" + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Replicate Type", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:BulkMethylationAssayType", + "@type": "rdfs:Class", + "rdfs:comment": "Assay types normally determine genomic coverage", + "rdfs:label": "BulkMethylationAssayType", + "rdfs:subClassOf": [ + { + "@id": "bts:BulkMethylation-seqLevel1" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Wholegenome" }, { - "@id": "bts:CancerAssociatedGeneMutations" + "@id": "bts:TargetedGenome" }, { - "@id": "bts:MutationalSignatures" + "@id": "bts:BeadchipArray" + } + ], + "sms:displayName": "Bulk Methylation Assay Type", + "sms:required": "sms:true", + "sms:requiresDependency": [ + { + "@id": "bts:TargetedGenome" }, { - "@id": "bts:PrecancerousConditionType" + "@id": "bts:BeadchipArray" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:TotalDNAInput", + "@type": "rdfs:Class", + "rdfs:comment": "Overall number of reads for a given sample in digits (microgram, nanogram).", + "rdfs:label": "TotalDNAInput", + "rdfs:subClassOf": [ + { + "@id": "bts:BulkMethylationAssayType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Not Applicable", + "sms:displayName": "Total DNA Input", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BulkRNA-seqLevel1", + "@id": "bts:BulkMethylation-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Bulk RNA-seq [EFO_0003738]", - "rdfs:label": "BulkRNA-seqLevel1", + "rdfs:comment": "Aligned primary data for bulk methylation sequencing, such as gene expression matrix files, VCFs, etc.", + "rdfs:label": "BulkMethylation-seqLevel2", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -35189,9 +41012,12 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk RNA-seq Level 1", + "sms:displayName": "Bulk Methylation-seq Level 2", "sms:required": "sms:false", "sms:requiresComponent": [ + { + "@id": "bts:BulkMethylation-seqLevel1" + }, { "@id": "bts:Biospecimen" } @@ -35207,172 +41033,149 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:HTANParentDataFileID" }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:LibraryLayout" - }, - { - "@id": "bts:ReadIndicator" - }, - { - "@id": "bts:NucleicAcidSource" - }, - { - "@id": "bts:Micro-regionSeqPlatform" - }, - { - "@id": "bts:ROITag" - }, - { - "@id": "bts:SequencingPlatform" - }, - { - "@id": "bts:SequencingBatchID" - }, - { - "@id": "bts:ReadLength" - }, - { - "@id": "bts:LibrarySelectionMethod" - }, - { - "@id": "bts:LibraryPreparationKitName" - }, - { - "@id": "bts:LibraryPreparationKitVendor" - }, - { - "@id": "bts:LibraryPreparationKitVersion" - }, - { - "@id": "bts:LibraryPreparationDaysfromIndex" - }, - { - "@id": "bts:SpikeIn" + "@id": "bts:AlignmentWorkflowUrl" }, { - "@id": "bts:AdapterName" + "@id": "bts:Trimmer" }, { - "@id": "bts:AdapterSequence" + "@id": "bts:BulkMethylationGenomicReference" }, { - "@id": "bts:BaseCallerName" + "@id": "bts:GenomicReferenceURL" }, { - "@id": "bts:BaseCallerVersion" + "@id": "bts:IndexFileName" }, { - "@id": "bts:FlowCellBarcode" + "@id": "bts:AlignmentWorkflowType" }, { - "@id": "bts:FragmentMaximumLength" + "@id": "bts:DuplicateRemovalSoftware" }, { - "@id": "bts:FragmentMeanLength" + "@id": "bts:MeanCoverage" }, { - "@id": "bts:FragmentMinimumLength" + "@id": "bts:LibraryLayout" }, { - "@id": "bts:FragmentStandardDeviationLength" + "@id": "bts:AverageBaseQuality" }, { - "@id": "bts:LaneNumber" + "@id": "bts:AverageInsertSize" }, { - "@id": "bts:LibraryStrand" + "@id": "bts:AverageReadLength" }, { - "@id": "bts:MultiplexBarcode" + "@id": "bts:Contamination" }, { - "@id": "bts:SizeSelectionRange" + "@id": "bts:ContaminationError" }, { - "@id": "bts:TargetDepth" + "@id": "bts:PairsOnDiffCHR" }, { - "@id": "bts:ToTrimAdapterSequence" + "@id": "bts:TotalReads" }, { - "@id": "bts:TranscriptIntegrityNumber" + "@id": "bts:TotalUniquelyMapped" }, { - "@id": "bts:RIN" + "@id": "bts:TotalUnmappedreads" }, { - "@id": "bts:DV200" + "@id": "bts:ProportionReadsDuplicated" }, { - "@id": "bts:AdapterContent" + "@id": "bts:ProportionReadsMapped" }, { - "@id": "bts:BasicStatistics" + "@id": "bts:ProportionTargetsNoCoverage" }, { - "@id": "bts:Encoding" + "@id": "bts:ProportionBaseMismatch" }, { - "@id": "bts:KmerContent" + "@id": "bts:ShortReads" }, { - "@id": "bts:OverrepresentedSequences" + "@id": "bts:ProportionofMinimumCpGCoverage10X" }, { - "@id": "bts:PerBaseNContent" - }, + "@id": "bts:ProportionCoverage30X" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:Trimmer", + "@type": "rdfs:Class", + "rdfs:comment": "Software used for trimming", + "rdfs:label": "Trimmer", + "rdfs:subClassOf": [ { - "@id": "bts:PerBaseSequenceContent" - }, + "@id": "bts:BulkMethylation-seqLevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:PerBaseSequenceQuality" + "@id": "bts:FASTXtoolkit" }, { - "@id": "bts:PerSequenceGCContent" + "@id": "bts:SolexaQA" }, { - "@id": "bts:PerSequenceQualityScore" + "@id": "bts:Btrim" }, { - "@id": "bts:PerTileSequenceQuality" + "@id": "bts:Cutadapt" }, { - "@id": "bts:PercentGCContent" + "@id": "bts:Kraken" }, { - "@id": "bts:SequenceDuplicationLevels" + "@id": "bts:PRINSEQ" }, { - "@id": "bts:SequenceLengthDistribution" + "@id": "bts:Adapterremoval" }, { - "@id": "bts:TotalReads" + "@id": "bts:TrimGalore!" }, { - "@id": "bts:QCWorkflowType" + "@id": "bts:ConDeTri" }, { - "@id": "bts:QCWorkflowVersion" + "@id": "bts:ERNE-FILTER" }, { - "@id": "bts:QCWorkflowLink" + "@id": "bts:Trimmo-matic" } ], + "sms:displayName": "Trimmer", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LibraryLayout", + "@id": "bts:BulkMethylationGenomicReference", "@type": "rdfs:Class", - "rdfs:comment": "Sequencing read type", - "rdfs:label": "LibraryLayout", + "rdfs:comment": "The human genome reference used in the alignment of reads", + "rdfs:label": "BulkMethylationGenomicReference", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:BulkMethylation-seqLevel2" } ], "schema:isPartOf": { @@ -35380,30 +41183,27 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:PairedEnd" - }, - { - "@id": "bts:SingleRead" + "@id": "bts:HG19" }, { - "@id": "bts:Mid-length" + "@id": "bts:HG38" }, { - "@id": "bts:LongRead" + "@id": "bts:T2TCHM13" } ], - "sms:displayName": "Library Layout", + "sms:displayName": "Bulk Methylation Genomic Reference", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Micro-regionSeqPlatform", + "@id": "bts:DuplicateRemovalSoftware", "@type": "rdfs:Class", - "rdfs:comment": "The platform used for micro-regional RNA sequencing (if applicable)", - "rdfs:label": "Micro-regionSeqPlatform", + "rdfs:comment": "Software used for remove duplicate reads", + "rdfs:label": "DuplicateRemovalSoftware", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:BulkMethylation-seqLevel2" } ], "schema:isPartOf": { @@ -35411,38 +41211,38 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:RarecytePick-Seq" + "@id": "bts:Samtoolssort" }, { - "@id": "bts:LaserCaptureMicrodissection" + "@id": "bts:PicardMarkDuplicates" } ], - "sms:displayName": "Micro-region Seq Platform", - "sms:required": "sms:false", + "sms:displayName": "Duplicate Removal Software", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ROITag", + "@id": "bts:ProportionofMinimumCpGCoverage10X", "@type": "rdfs:Class", - "rdfs:comment": "The tag or grouping used to identify the ROI in micro-regional RNA sequencing (if applicable). Must match the ROI tag within the count matrix in level 3.", - "rdfs:label": "ROITag", + "rdfs:comment": "Proportion of all reference bases for whole genome sequencing, or targeted sequencing, that achieves 10X or greater coverage per CpG.", + "rdfs:label": "ProportionofMinimumCpGCoverage10X", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:BulkMethylation-seqLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "ROI Tag", + "sms:displayName": "Proportion of Minimum CpG Coverage 10X", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ReadLength", + "@id": "bts:BulkMethylation-seqLevel3", "@type": "rdfs:Class", - "rdfs:comment": "The length of the sequencing reads. Can be integer, null", - "rdfs:label": "ReadLength", + "rdfs:comment": "Sample level summary data for bulk methylation sequencing, such as t-SNE plot coordinates, etc.", + "rdfs:label": "BulkMethylation-seqLevel3", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -35451,282 +41251,135 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Read Length", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:LibrarySelectionMethod", - "@type": "rdfs:Class", - "rdfs:comment": "How RNA molecules are isolated.", - "rdfs:label": "LibrarySelectionMethod", - "rdfs:subClassOf": [ + "sms:displayName": "Bulk Methylation-seq Level 3", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:Sequencing" + "@id": "bts:BulkMethylation-seqLevel2" + }, + { + "@id": "bts:Biospecimen" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "sms:requiresDependency": [ { - "@id": "bts:HybridSelection" + "@id": "bts:Component" }, { - "@id": "bts:PCR" + "@id": "bts:Filename" }, { - "@id": "bts:AffinityEnrichment" + "@id": "bts:FileFormat" }, { - "@id": "bts:Poly-TEnrichment" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:Random" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:RRNADepletion" + "@id": "bts:DMCCallingTool" }, { - "@id": "bts:MiRNASizeFractionation" + "@id": "bts:DMCCallingWorkflowURL" }, { - "@id": "bts:Other" - } - ], - "sms:displayName": "Library Selection Method", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:LibraryPreparationKitName", - "@type": "rdfs:Class", - "rdfs:comment": "Name of Library Preparation Kit. String", - "rdfs:label": "LibraryPreparationKitName", - "rdfs:subClassOf": [ + "@id": "bts:DMRCallingTool" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Library Preparation Kit Name", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:LibraryPreparationKitVendor", - "@type": "rdfs:Class", - "rdfs:comment": "Vendor of Library Preparation Kit. String", - "rdfs:label": "LibraryPreparationKitVendor", - "rdfs:subClassOf": [ + "@id": "bts:DMRCallingWorkflowURL" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Library Preparation Kit Vendor", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:LibraryPreparationKitVersion", - "@type": "rdfs:Class", - "rdfs:comment": "Version of Library Preparation Kit. String", - "rdfs:label": "LibraryPreparationKitVersion", - "rdfs:subClassOf": [ + "@id": "bts:PUC19methylationratio" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Library Preparation Kit Version", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:AdapterName", - "@type": "rdfs:Class", - "rdfs:comment": "Name of the sequencing adapter. String", - "rdfs:label": "AdapterName", - "rdfs:subClassOf": [ + "@id": "bts:Lambdamethylationratio" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Adapter Name", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AdapterSequence", - "@type": "rdfs:Class", - "rdfs:comment": "Base sequence of the sequencing adapter. String", - "rdfs:label": "AdapterSequence", - "rdfs:subClassOf": [ + "@id": "bts:DMCdatafileformat" + }, { - "@id": "bts:Sequencing" + "@id": "bts:DMRdatafileFormat" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Adapter Sequence", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BaseCallerName", + "@id": "bts:DMCCallingTool", "@type": "rdfs:Class", - "rdfs:comment": "Name of the base caller. String", - "rdfs:label": "BaseCallerName", + "rdfs:comment": "Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR)", + "rdfs:label": "DMCCallingTool", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:BulkMethylation-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Base Caller Name", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BaseCallerVersion", - "@type": "rdfs:Class", - "rdfs:comment": "Version of the base caller. String", - "rdfs:label": "BaseCallerVersion", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Base Caller Version", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FlowCellBarcode", - "@type": "rdfs:Class", - "rdfs:comment": "Flow cell barcode. Wrong or missing information may affect analysis results. String", - "rdfs:label": "FlowCellBarcode", - "rdfs:subClassOf": [ + "@id": "bts:MethylKit" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Flow Cell Barcode", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FragmentMaximumLength", - "@type": "rdfs:Class", - "rdfs:comment": "Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer", - "rdfs:label": "FragmentMaximumLength", - "rdfs:subClassOf": [ + "@id": "bts:BSmooth" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Fragment Maximum Length", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FragmentMeanLength", - "@type": "rdfs:Class", - "rdfs:comment": "Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number", - "rdfs:label": "FragmentMeanLength", - "rdfs:subClassOf": [ + "@id": "bts:BiSeq" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Fragment Mean Length", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FragmentMinimumLength", - "@type": "rdfs:Class", - "rdfs:comment": "Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer", - "rdfs:label": "FragmentMinimumLength", - "rdfs:subClassOf": [ + "@id": "bts:MethylSig" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Fragment Minimum Length", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FragmentStandardDeviationLength", - "@type": "rdfs:Class", - "rdfs:comment": "Standard deviation of the sequenced fragments length (e.g., as predicted by Agilent Bioanalyzer). Number", - "rdfs:label": "FragmentStandardDeviationLength", - "rdfs:subClassOf": [ + "@id": "bts:DSS" + }, { - "@id": "bts:Sequencing" + "@id": "bts:MOABS" + }, + { + "@id": "bts:DSS-single" + }, + { + "@id": "bts:Metilene" + }, + { + "@id": "bts:MACAU" + }, + { + "@id": "bts:MethylDackel" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Fragment Standard Deviation Length", - "sms:required": "sms:false", + "sms:displayName": "DMC Calling Tool", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LaneNumber", + "@id": "bts:DMCCallingWorkflowURL", "@type": "rdfs:Class", - "rdfs:comment": "The basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer", - "rdfs:label": "LaneNumber", + "rdfs:comment": "Generic name for the workflow used to analyze a data set", + "rdfs:label": "DMCCallingWorkflowURL", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:BulkMethylation-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Lane Number", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "DMC Calling Workflow URL", + "sms:required": "sms:true", + "sms:validationRules": [ + "url" + ] }, { - "@id": "bts:LibraryStrand", + "@id": "bts:DMRCallingTool", "@type": "rdfs:Class", - "rdfs:comment": "Library stranded-ness.", - "rdfs:label": "LibraryStrand", + "rdfs:comment": "Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR)", + "rdfs:label": "DMRCallingTool", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:BulkMethylation-seqLevel3" } ], "schema:isPartOf": { @@ -35734,157 +41387,98 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Unstranded" + "@id": "bts:MethylKit" }, { - "@id": "bts:FirstStranded" + "@id": "bts:BSmooth" }, { - "@id": "bts:SecondStranded" + "@id": "bts:BiSeq" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Library Strand", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MultiplexBarcode", - "@type": "rdfs:Class", - "rdfs:comment": "The barcode/index sequence used. Wrong or missing information may affect analysis results. String", - "rdfs:label": "MultiplexBarcode", - "rdfs:subClassOf": [ - { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Multiplex Barcode", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SizeSelectionRange", - "@type": "rdfs:Class", - "rdfs:comment": "Range of size selection. String", - "rdfs:label": "SizeSelectionRange", - "rdfs:subClassOf": [ + "@id": "bts:MethylSig" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Size Selection Range", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TargetDepth", - "@type": "rdfs:Class", - "rdfs:comment": "The targeted read depth prior to sequencing. Integer", - "rdfs:label": "TargetDepth", - "rdfs:subClassOf": [ + "@id": "bts:DSS" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Target Depth", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ToTrimAdapterSequence", - "@type": "rdfs:Class", - "rdfs:comment": "Does the user suggest adapter trimming?", - "rdfs:label": "ToTrimAdapterSequence", - "rdfs:subClassOf": [ + "@id": "bts:MOABS" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:DSS-single" + }, { - "@id": "bts:Yes-TrimAdapterSequence" + "@id": "bts:Metilene" }, { - "@id": "bts:No" + "@id": "bts:MACAU" } ], - "sms:displayName": "To Trim Adapter Sequence", - "sms:required": "sms:false", + "sms:displayName": "DMR Calling Tool", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TranscriptIntegrityNumber", + "@id": "bts:DMRCallingWorkflowURL", "@type": "rdfs:Class", - "rdfs:comment": "Used to describe the quality of the starting material, esp. in regards to FFPE samples. Number", - "rdfs:label": "TranscriptIntegrityNumber", + "rdfs:comment": "Generic name for the workflow used to analyze a data set", + "rdfs:label": "DMRCallingWorkflowURL", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:BulkMethylation-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Transcript Integrity Number", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "DMR Calling Workflow URL", + "sms:required": "sms:true", + "sms:validationRules": [ + "url" + ] }, { - "@id": "bts:RIN", + "@id": "bts:PUC19methylationratio", "@type": "rdfs:Class", - "rdfs:comment": "A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products. Number", - "rdfs:label": "RIN", + "rdfs:comment": "Methylation ratio of mostly methylated pUC19 control, as a percentage", + "rdfs:label": "PUC19methylationratio", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:BulkMethylation-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "RIN", - "sms:required": "sms:false", + "sms:displayName": "pUC19 methylation ratio", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:DV200", + "@id": "bts:Lambdamethylationratio", "@type": "rdfs:Class", - "rdfs:comment": "Represents the percentage of RNA fragments that are >200 nucleotides in size. Number", - "rdfs:label": "DV200", + "rdfs:comment": "Methylation ratio of mostly unmethylated lambda control, as a percentage", + "rdfs:label": "Lambdamethylationratio", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:BulkMethylation-seqLevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "DV200", - "sms:required": "sms:false", + "sms:displayName": "Lambda methylation ratio", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AdapterContent", + "@id": "bts:DMCdatafileformat", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "AdapterContent", + "rdfs:comment": "Format of the data files", + "rdfs:label": "DMCdatafileformat", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:BulkMethylation-seqLevel3" } ], "schema:isPartOf": { @@ -35892,33 +41486,24 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:FAIL" - }, - { - "@id": "bts:PASS" - }, - { - "@id": "bts:WARN" - }, - { - "@id": "bts:Unknown" + "@id": "bts:BED" }, { - "@id": "bts:NotReported" + "@id": "bts:BedGraph" } ], - "sms:displayName": "Adapter Content", - "sms:required": "sms:false", + "sms:displayName": "DMC data file format", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BasicStatistics", + "@id": "bts:DMRdatafileFormat", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "BasicStatistics", + "rdfs:comment": "Format of the data files.", + "rdfs:label": "DMRdatafileFormat", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:BulkMethylation-seqLevel3" } ], "schema:isPartOf": { @@ -35926,152 +41511,84 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:FAIL" - }, - { - "@id": "bts:PASS" - }, - { - "@id": "bts:WARN" - }, - { - "@id": "bts:Unknown" + "@id": "bts:BED" }, { - "@id": "bts:NotReported" + "@id": "bts:BedGraph" } ], - "sms:displayName": "Basic Statistics", - "sms:required": "sms:false", + "sms:displayName": "DMR data file Format", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Encoding", + "@id": "bts:ImagingLevel1", "@type": "rdfs:Class", - "rdfs:comment": "Version of ASCII encoding of quality values found in the file. String", - "rdfs:label": "Encoding", + "rdfs:comment": "Raw imaging data", + "rdfs:label": "ImagingLevel1", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Encoding", + "sms:displayName": "Imaging Level 1", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:KmerContent", - "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "KmerContent", - "rdfs:subClassOf": [ + "sms:requiresComponent": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:FAIL" - }, + "sms:requiresDependency": [ { - "@id": "bts:PASS" + "@id": "bts:Component" }, { - "@id": "bts:WARN" + "@id": "bts:Filename" }, { - "@id": "bts:Unknown" + "@id": "bts:FileFormat" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Kmer Content", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:OverrepresentedSequences", - "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "OverrepresentedSequences", - "rdfs:subClassOf": [ - { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:FAIL" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:PASS" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:WARN" + "@id": "bts:ImagingAssayType" }, { - "@id": "bts:Unknown" + "@id": "bts:ProtocolLink" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Overrepresented Sequences", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PerBaseNContent", - "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerBaseNContent", - "rdfs:subClassOf": [ - { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:FAIL" + "@id": "bts:SoftwareandVersion" }, { - "@id": "bts:PASS" + "@id": "bts:CommitSHA" }, { - "@id": "bts:WARN" + "@id": "bts:Pre-processingCompleted" }, { - "@id": "bts:Unknown" + "@id": "bts:Pre-processingRequired" }, { - "@id": "bts:NotReported" + "@id": "bts:Comment" } ], - "sms:displayName": "Per Base N Content", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PerBaseSequenceContent", + "@id": "bts:ImagingAssayType", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerBaseSequenceContent", + "rdfs:comment": "Type of imaging assay", + "rdfs:label": "ImagingAssayType", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Imaging" } ], "schema:isPartOf": { @@ -36079,132 +41596,60 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:FAIL" - }, - { - "@id": "bts:PASS" - }, - { - "@id": "bts:WARN" + "@id": "bts:H&E" }, { - "@id": "bts:Unknown" + "@id": "bts:CyCIF" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Per Base Sequence Content", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PerBaseSequenceQuality", - "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerBaseSequenceQuality", - "rdfs:subClassOf": [ - { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:FAIL" + "@id": "bts:T-CyCIF" }, { - "@id": "bts:PASS" + "@id": "bts:IHC" }, { - "@id": "bts:WARN" + "@id": "bts:MIHC" }, { - "@id": "bts:Unknown" + "@id": "bts:MxIF" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Per Base Sequence Quality", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PerSequenceGCContent", - "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerSequenceGCContent", - "rdfs:subClassOf": [ - { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:FAIL" + "@id": "bts:SABER" }, { - "@id": "bts:PASS" + "@id": "bts:IMC" }, { - "@id": "bts:WARN" + "@id": "bts:CODEX" }, { - "@id": "bts:Unknown" + "@id": "bts:GeoMX-DSP" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Per Sequence GC Content", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PerSequenceQualityScore", - "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerSequenceQualityScore", - "rdfs:subClassOf": [ - { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:FAIL" + "@id": "bts:MIBI" }, { - "@id": "bts:PASS" + "@id": "bts:MERFISH" }, { - "@id": "bts:WARN" + "@id": "bts:ExSeq" }, { - "@id": "bts:Unknown" + "@id": "bts:RareCyteOrion" }, { - "@id": "bts:NotReported" + "@id": "bts:NotApplicable" } ], - "sms:displayName": "Per Sequence Quality Score", - "sms:required": "sms:false", + "sms:displayName": "Imaging Assay Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PerTileSequenceQuality", + "@id": "bts:SoftwareandVersion", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerTileSequenceQuality", + "rdfs:comment": "Name of software used to generate expression values. String", + "rdfs:label": "SoftwareandVersion", "rdfs:subClassOf": [ { "@id": "bts:Sequencing" @@ -36213,52 +41658,35 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:FAIL" - }, - { - "@id": "bts:PASS" - }, - { - "@id": "bts:WARN" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Per Tile Sequence Quality", - "sms:required": "sms:false", + "sms:displayName": "Software and Version", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PercentGCContent", + "@id": "bts:CommitSHA", "@type": "rdfs:Class", - "rdfs:comment": "The overall %GC of all bases in all sequences. Integer", - "rdfs:label": "PercentGCContent", + "rdfs:comment": "Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]", + "rdfs:label": "CommitSHA", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent GC Content", + "sms:displayName": "Commit SHA", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SequenceDuplicationLevels", + "@id": "bts:Pre-processingCompleted", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "SequenceDuplicationLevels", + "rdfs:comment": "Pre-processing steps completed to convert level 1 raw data to a single level 2 image", + "rdfs:label": "Pre-processingCompleted", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Imaging" } ], "schema:isPartOf": { @@ -36266,33 +41694,36 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:FAIL" + "@id": "bts:Illuminationcorrection" }, { - "@id": "bts:PASS" + "@id": "bts:TileStitching" }, { - "@id": "bts:WARN" + "@id": "bts:Channel/CycleRegistration" }, { - "@id": "bts:Unknown" + "@id": "bts:TMAde-arraying" }, { - "@id": "bts:NotReported" + "@id": "bts:None" + }, + { + "@id": "bts:Other" } ], - "sms:displayName": "Sequence Duplication Levels", - "sms:required": "sms:false", + "sms:displayName": "Pre-processing Completed", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SequenceLengthDistribution", + "@id": "bts:Pre-processingRequired", "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "SequenceLengthDistribution", + "rdfs:comment": "Pre-processing steps required to convert level 1 raw data to a single level 2 image", + "rdfs:label": "Pre-processingRequired", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Imaging" } ], "schema:isPartOf": { @@ -36300,111 +41731,63 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:FAIL" + "@id": "bts:Illuminationcorrection" }, { - "@id": "bts:PASS" + "@id": "bts:TileStitching" }, { - "@id": "bts:WARN" + "@id": "bts:Channel/CycleRegistration" }, { - "@id": "bts:Unknown" + "@id": "bts:TMAde-arraying" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Sequence Length Distribution", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TotalReads", - "@type": "rdfs:Class", - "rdfs:comment": "Total number of reads per sample. Integer", - "rdfs:label": "TotalReads", - "rdfs:subClassOf": [ - { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Total Reads", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:QCWorkflowType", - "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set. String", - "rdfs:label": "QCWorkflowType", - "rdfs:subClassOf": [ - { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "QC Workflow Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:QCWorkflowVersion", - "@type": "rdfs:Class", - "rdfs:comment": "Major version for a workflow. String", - "rdfs:label": "QCWorkflowVersion", - "rdfs:subClassOf": [ + "@id": "bts:None" + }, { - "@id": "bts:Sequencing" + "@id": "bts:Other" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "QC Workflow Version", - "sms:required": "sms:false", + "sms:displayName": "Pre-processing Required", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:QCWorkflowLink", + "@id": "bts:Comment", "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow used. String", - "rdfs:label": "QCWorkflowLink", + "rdfs:comment": "Free text field (generally for QC comment)", + "rdfs:label": "Comment", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "QC Workflow Link", + "sms:displayName": "Comment", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BulkRNA-seqLevel2", + "@id": "bts:ImagingLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Bulk RNA-seq alignment protocol description", - "rdfs:label": "BulkRNA-seqLevel2", + "rdfs:comment": "Raw and pre-processed image data", + "rdfs:label": "ImagingLevel2", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk RNA-seq Level 2", + "sms:displayName": "Imaging Level 2", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:BulkRNA-seqLevel1" + "@id": "bts:ImagingLevel1" } ], "sms:requiresDependency": [ @@ -36418,373 +41801,290 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:AlignmentWorkflowUrl" - }, - { - "@id": "bts:AlignmentWorkflowType" - }, - { - "@id": "bts:GenomicReference" - }, - { - "@id": "bts:GenomicReferenceURL" - }, - { - "@id": "bts:IndexFileName" - }, - { - "@id": "bts:AverageBaseQuality" - }, - { - "@id": "bts:AverageInsertSize" - }, - { - "@id": "bts:AverageReadLength" - }, - { - "@id": "bts:Contamination" - }, - { - "@id": "bts:ContaminationError" - }, - { - "@id": "bts:MeanCoverage" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:MSIWorkflowLink" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:MSIScore" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:MSIStatus" + "@id": "bts:ChannelMetadataFilename" }, { - "@id": "bts:PairsOnDiffCHR" + "@id": "bts:ImagingAssayType" }, { - "@id": "bts:TotalReads" + "@id": "bts:ProtocolLink" }, { - "@id": "bts:TotalUniquelyMapped" + "@id": "bts:SoftwareandVersion" }, { - "@id": "bts:TotalUnmappedreads" + "@id": "bts:Microscope" }, { - "@id": "bts:ProportionReadsDuplicated" + "@id": "bts:Objective" }, { - "@id": "bts:ProportionReadsMapped" + "@id": "bts:NominalMagnification" }, { - "@id": "bts:ProportionTargetsNoCoverage" + "@id": "bts:LensNA" }, { - "@id": "bts:ProportionBaseMismatch" + "@id": "bts:WorkingDistance" }, { - "@id": "bts:ShortReads" + "@id": "bts:WorkingDistanceUnit" }, { - "@id": "bts:Islowestlevel" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:AlignmentWorkflowUrl", - "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow used for read alignment. DockStore.org recommended. String", - "rdfs:label": "AlignmentWorkflowUrl", - "rdfs:subClassOf": [ - { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Alignment Workflow Url", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:AlignmentWorkflowType", - "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "AlignmentWorkflowType", - "rdfs:subClassOf": [ - { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:BWA" + "@id": "bts:Immersion" }, { - "@id": "bts:BWAwithBQSR" + "@id": "bts:Pyramid" }, { - "@id": "bts:BWA-aln" + "@id": "bts:Zstack" }, { - "@id": "bts:BWA-mem" + "@id": "bts:Tseries" }, { - "@id": "bts:BWAwithMarkDuplicatesandBQSR" + "@id": "bts:PassedQC" }, { - "@id": "bts:STAR2-Pass" + "@id": "bts:Comment" }, { - "@id": "bts:STAR2-PassChimeric" + "@id": "bts:FOVnumber" }, { - "@id": "bts:STAR2-PassGenome" + "@id": "bts:FOVX" }, { - "@id": "bts:STAR2-PassTranscriptome" + "@id": "bts:FOVXUnit" }, { - "@id": "bts:Bowtie" + "@id": "bts:FOVY" }, { - "@id": "bts:Bismark" + "@id": "bts:FOVYUnit" }, { - "@id": "bts:GSNAP" + "@id": "bts:FrameAveraging" }, { - "@id": "bts:BSMAP" + "@id": "bts:ImageID" }, { - "@id": "bts:BSmooth" + "@id": "bts:DimensionOrder" }, { - "@id": "bts:BS-Seeker2" + "@id": "bts:PhysicalSizeX" }, { - "@id": "bts:BS-Seeker" + "@id": "bts:PhysicalSizeXUnit" }, { - "@id": "bts:RMAP" + "@id": "bts:PhysicalSizeY" }, { - "@id": "bts:MethylCoder" + "@id": "bts:PhysicalSizeYUnit" }, { - "@id": "bts:BRAT-BW" + "@id": "bts:PhysicalSizeZ" }, { - "@id": "bts:Pash" + "@id": "bts:PhysicalSizeZUnit" }, { - "@id": "bts:Segemehl" + "@id": "bts:PixelsBigEndian" }, { - "@id": "bts:Bisulfighter" + "@id": "bts:PlaneCount" }, { - "@id": "bts:BatMeth" + "@id": "bts:SizeC" }, { - "@id": "bts:LAST" + "@id": "bts:SizeT" }, { - "@id": "bts:ERNE-BS5" + "@id": "bts:SizeX" }, { - "@id": "bts:B-SOLANA" + "@id": "bts:SizeY" }, { - "@id": "bts:SOCS-B" + "@id": "bts:SizeZ" }, { - "@id": "bts:BWA-meth" + "@id": "bts:PixelType" }, { - "@id": "bts:OtherAlignmentWorkflow" + "@id": "bts:MERFISHPositionsFile" }, { - "@id": "bts:None" + "@id": "bts:MERFISHCodebookFile" } ], - "sms:displayName": "Alignment Workflow Type", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:IndexFileName", + "@id": "bts:ChannelMetadataFilename", "@type": "rdfs:Class", - "rdfs:comment": "The name (or part of a name) of a file (of any type). String", - "rdfs:label": "IndexFileName", + "rdfs:comment": "Full path within Synapse project of uploaded companion CSV file containing channel-level metadata details", + "rdfs:label": "ChannelMetadataFilename", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Index File Name", + "sms:displayName": "Channel Metadata Filename", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AverageBaseQuality", + "@id": "bts:Microscope", "@type": "rdfs:Class", - "rdfs:comment": "Average base quality collected from samtools. Number", - "rdfs:label": "AverageBaseQuality", + "rdfs:comment": "Microscope type (manufacturer, model, etc) used for this experiment", + "rdfs:label": "Microscope", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Average Base Quality", - "sms:required": "sms:false", + "sms:displayName": "Microscope", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AverageInsertSize", + "@id": "bts:Objective", "@type": "rdfs:Class", - "rdfs:comment": "Average insert size collected from samtools. Integer", - "rdfs:label": "AverageInsertSize", + "rdfs:comment": "Objective", + "rdfs:label": "Objective", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Average Insert Size", + "sms:displayName": "Objective", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AverageReadLength", + "@id": "bts:NominalMagnification", "@type": "rdfs:Class", - "rdfs:comment": "Average read length collected from samtools. Integer", - "rdfs:label": "AverageReadLength", + "rdfs:comment": "The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units)", + "rdfs:label": "NominalMagnification", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Average Read Length", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "NominalMagnification", + "sms:required": "sms:true", + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:Contamination", + "@id": "bts:LensNA", "@type": "rdfs:Class", - "rdfs:comment": "Fraction of reads coming from cross-sample contamination collected from GATK4. Number", - "rdfs:label": "Contamination", + "rdfs:comment": "The numerical aperture of the lens. Floating point value > 0.", + "rdfs:label": "LensNA", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Contamination", + "sms:displayName": "LensNA", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:ContaminationError", + "@id": "bts:WorkingDistance", "@type": "rdfs:Class", - "rdfs:comment": "Estimation error of cross-sample contamination collected from GATK4. Number", - "rdfs:label": "ContaminationError", + "rdfs:comment": "The working distance of the lens, expressed as a floating point number. Floating point > 0.", + "rdfs:label": "WorkingDistance", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Contamination Error", + "sms:displayName": "WorkingDistance", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MeanCoverage", - "@type": "rdfs:Class", - "rdfs:comment": "Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number", - "rdfs:label": "MeanCoverage", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:Sequencing" + "@id": "bts:WorkingDistanceUnit" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Mean Coverage", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MSIWorkflowLink", + "@id": "bts:WorkingDistanceUnit", "@type": "rdfs:Class", - "rdfs:comment": "Link to method workflow (or command) used in estimating the MSI. URL", - "rdfs:label": "MSIWorkflowLink", + "rdfs:comment": "The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "WorkingDistanceUnit", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MSI Workflow Link", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MSIScore", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric score denoting the aligned reads file's MSI score from MSIsensor. Number", - "rdfs:label": "MSIScore", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:Sequencing" + "@id": "bts:Cm" + }, + { + "@id": "bts:Mm" + }, + { + "@id": "bts:Μm" + }, + { + "@id": "bts:Nm" + }, + { + "@id": "bts:Å" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "MSI Score", + "sms:displayName": "WorkingDistanceUnit", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MSIStatus", + "@id": "bts:Immersion", "@type": "rdfs:Class", - "rdfs:comment": "MSIsensor determination of either microsatellite stability or instability.", - "rdfs:label": "MSIStatus", + "rdfs:comment": "Immersion medium", + "rdfs:label": "Immersion", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Imaging" } ], "schema:isPartOf": { @@ -36792,273 +42092,231 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:MSI" + "@id": "bts:Air" }, { - "@id": "bts:MSI-low" + "@id": "bts:Oil" }, { - "@id": "bts:MSI-high" + "@id": "bts:Water" }, { - "@id": "bts:MSS" + "@id": "bts:Other" } ], - "sms:displayName": "MSI Status", + "sms:displayName": "Immersion", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PairsOnDiffCHR", + "@id": "bts:Pyramid", "@type": "rdfs:Class", - "rdfs:comment": "Pairs on different chromosomes collected from samtools. Integer", - "rdfs:label": "PairsOnDiffCHR", + "rdfs:comment": "Does data file contain pyramid of images", + "rdfs:label": "Pyramid", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Pairs On Diff CHR", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TotalUniquelyMapped", - "@type": "rdfs:Class", - "rdfs:comment": "Number of reads that map to genome. Integer", - "rdfs:label": "TotalUniquelyMapped", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:Sequencing" + "@id": "bts:Yes" + }, + { + "@id": "bts:No" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Total Uniquely Mapped", - "sms:required": "sms:false", + "sms:displayName": "Pyramid", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TotalUnmappedreads", + "@id": "bts:Zstack", "@type": "rdfs:Class", - "rdfs:comment": "Number of reads that did not map to genome. Integer", - "rdfs:label": "TotalUnmappedreads", + "rdfs:comment": "Does data file contain a Z-stack of images", + "rdfs:label": "Zstack", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total Unmapped reads", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ProportionReadsDuplicated", - "@type": "rdfs:Class", - "rdfs:comment": "Proportion of duplicated reads collected from samtools. Number", - "rdfs:label": "ProportionReadsDuplicated", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:Sequencing" + "@id": "bts:Yes" + }, + { + "@id": "bts:No" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Proportion Reads Duplicated", - "sms:required": "sms:false", + "sms:displayName": "Zstack", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ProportionReadsMapped", + "@id": "bts:Tseries", "@type": "rdfs:Class", - "rdfs:comment": "Proportion of mapped reads collected from samtools. Number", - "rdfs:label": "ProportionReadsMapped", + "rdfs:comment": "Does data file contain a time-series of images", + "rdfs:label": "Tseries", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion Reads Mapped", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ProportionTargetsNoCoverage", - "@type": "rdfs:Class", - "rdfs:comment": "Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number", - "rdfs:label": "ProportionTargetsNoCoverage", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:Sequencing" + "@id": "bts:Yes" + }, + { + "@id": "bts:No" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Proportion Targets No Coverage", - "sms:required": "sms:false", + "sms:displayName": "Tseries", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ProportionBaseMismatch", + "@id": "bts:PassedQC", "@type": "rdfs:Class", - "rdfs:comment": "Proportion of mismatched bases collected from samtools. Number", - "rdfs:label": "ProportionBaseMismatch", + "rdfs:comment": "Did all channels pass QC (if not add free text Comment)", + "rdfs:label": "PassedQC", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion Base Mismatch", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No-ChannelsQC" + } + ], + "sms:displayName": "Passed QC", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ShortReads", + "@id": "bts:FOVnumber", "@type": "rdfs:Class", - "rdfs:comment": "Number of reads that were too short. Integer", - "rdfs:label": "ShortReads", + "rdfs:comment": "Index of FOV (as it pertains to its sequence order). Integer >= 1", + "rdfs:label": "FOVnumber", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Short Reads", + "sms:displayName": "FOV number", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:Islowestlevel", + "@id": "bts:FOVX", "@type": "rdfs:Class", - "rdfs:comment": "Denotes that the manifest represents the lowest data level submitted. Use when L1 data is missing", - "rdfs:label": "Islowestlevel", + "rdfs:comment": "Field of view X dimension. Floating point", + "rdfs:label": "FOVX", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel2" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes-Islowestlevel" - }, + "sms:displayName": "FOVX", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:No" + "@id": "bts:FOVXUnit" } ], - "sms:displayName": "Is lowest level", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:BulkRNA-seqLevel3", + "@id": "bts:FOVXUnit", "@type": "rdfs:Class", - "rdfs:comment": "Bulk RNA-seq gene expression matrices", - "rdfs:label": "BulkRNA-seqLevel3", + "rdfs:comment": "Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "FOVXUnit", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk RNA-seq Level 3", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:BulkRNA-seqLevel2" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:PseudoAlignmentUsed" - }, + "schema:rangeIncludes": [ { - "@id": "bts:DataCategory" + "@id": "bts:Cm" }, { - "@id": "bts:ExpressionUnits" + "@id": "bts:Mm" }, { - "@id": "bts:MatrixType" + "@id": "bts:Μm" }, { - "@id": "bts:FusionGeneDetected" + "@id": "bts:Nm" }, { - "@id": "bts:FusionGeneIdentity" + "@id": "bts:Å" } ], + "sms:displayName": "FOVXUnit", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PseudoAlignmentUsed", + "@id": "bts:FOVY", "@type": "rdfs:Class", - "rdfs:comment": "Pseudo aligners such as Kallisto or Salmon do not produce aligned reads BAM files. True indicates pseudoalignment was used.", - "rdfs:label": "PseudoAlignmentUsed", + "rdfs:comment": "Field of view Y dimension. Floating point value", + "rdfs:label": "FOVY", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes-PseudoAlignmentUsed" - }, + "sms:displayName": "FOVY", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:No" + "@id": "bts:FOVYUnit" } ], - "sms:displayName": "Pseudo Alignment Used", - "sms:required": "sms:true", - "sms:validationRules": [] + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:ExpressionUnits", + "@id": "bts:FOVYUnit", "@type": "rdfs:Class", - "rdfs:comment": "How quantities are corrected for gene length", - "rdfs:label": "ExpressionUnits", + "rdfs:comment": "Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "FOVYUnit", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Imaging" } ], "schema:isPartOf": { @@ -37066,64 +42324,67 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:TPM" - }, - { - "@id": "bts:RPKM" + "@id": "bts:Cm" }, { - "@id": "bts:FPKM" + "@id": "bts:Mm" }, { - "@id": "bts:Counts" + "@id": "bts:Μm" }, { - "@id": "bts:Other" + "@id": "bts:Nm" }, { - "@id": "bts:NA" + "@id": "bts:Å" } ], - "sms:displayName": "Expression Units", - "sms:required": "sms:true", + "sms:displayName": "FOVYUnit", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FusionGeneDetected", + "@id": "bts:FrameAveraging", "@type": "rdfs:Class", - "rdfs:comment": "Was a fusion gene identified?", - "rdfs:label": "FusionGeneDetected", + "rdfs:comment": "Number of frames averaged together (if no averaging, set to 1). Integer >= 1", + "rdfs:label": "FrameAveraging", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes-FusionGeneDetected" - }, - { - "@id": "bts:No" - }, + "sms:displayName": "Frame Averaging", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ImageID", + "@type": "rdfs:Class", + "rdfs:comment": "Unique internal image identifier. eg \"Image:0\". (To be extracted from OME-XML)", + "rdfs:label": "ImageID", + "rdfs:subClassOf": [ { - "@id": "bts:Unknown" + "@id": "bts:Imaging" } ], - "sms:displayName": "Fusion Gene Detected", - "sms:required": "sms:false", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Image ID", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:FusionGeneIdentity", + "@id": "bts:DimensionOrder", "@type": "rdfs:Class", - "rdfs:comment": "The gene symbols of fused genes.", - "rdfs:label": "FusionGeneIdentity", + "rdfs:comment": "The order in which the individual planes of data are interleaved.", + "rdfs:label": "DimensionOrder", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Imaging" } ], "schema:isPartOf": { @@ -37131,152 +42392,58 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:EWS-FLI" + "@id": "bts:XYZCT" }, { - "@id": "bts:EWS-ERG" + "@id": "bts:XYZTC" }, { - "@id": "bts:SYT-SSX1" + "@id": "bts:XYCTZ" }, { - "@id": "bts:SYT-SSX2" + "@id": "bts:XYCZT" }, { - "@id": "bts:EWS-WT1" + "@id": "bts:XYTZC" }, { - "@id": "bts:OtherFusionGene" + "@id": "bts:ZYX" } ], - "sms:displayName": "Fusion Gene Identity", - "sms:required": "sms:false", - "sms:validationRules": [ - "list like" - ] + "sms:displayName": "DimensionOrder", + "sms:required": "sms:true", + "sms:validationRules": [] }, { - "@id": "bts:BulkWESLevel1", + "@id": "bts:PhysicalSizeX", "@type": "rdfs:Class", - "rdfs:comment": "Bulk Whole Exome Sequencing raw files", - "rdfs:label": "BulkWESLevel1", + "rdfs:comment": "Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.", + "rdfs:label": "PhysicalSizeX", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk WES Level 1", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Biospecimen" - } - ], + "sms:displayName": "PhysicalSizeX", + "sms:required": "sms:true", "sms:requiresDependency": [ { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:SequencingBatchID" - }, - { - "@id": "bts:LibraryLayout" - }, - { - "@id": "bts:ReadIndicator" - }, - { - "@id": "bts:LibrarySelectionMethod" - }, - { - "@id": "bts:ReadLength" - }, - { - "@id": "bts:TargetCaptureKit" - }, - { - "@id": "bts:LibraryPreparationKitName" - }, - { - "@id": "bts:LibraryPreparationKitVendor" - }, - { - "@id": "bts:LibraryPreparationKitVersion" - }, - { - "@id": "bts:SequencingPlatform" - }, - { - "@id": "bts:AdapterName" - }, - { - "@id": "bts:AdapterSequence" - }, - { - "@id": "bts:BaseCallerName" - }, - { - "@id": "bts:BaseCallerVersion" - }, - { - "@id": "bts:FlowCellBarcode" - }, - { - "@id": "bts:FragmentMaximumLength" - }, - { - "@id": "bts:FragmentMeanLength" - }, - { - "@id": "bts:FragmentMinimumLength" - }, - { - "@id": "bts:FragmentStandardDeviationLength" - }, - { - "@id": "bts:LaneNumber" - }, - { - "@id": "bts:MultiplexBarcode" - }, - { - "@id": "bts:LibraryPreparationDaysfromIndex" - }, - { - "@id": "bts:SizeSelectionRange" - }, - { - "@id": "bts:TargetDepth" - }, - { - "@id": "bts:ToTrimAdapterSequence" + "@id": "bts:PhysicalSizeXUnit" } ], "sms:validationRules": [] }, { - "@id": "bts:TargetCaptureKit", + "@id": "bts:PhysicalSizeXUnit", "@type": "rdfs:Class", - "rdfs:comment": "Description that can uniquely identify a target capture kit. Suggested value is a combination of vendor, kit name, and kit version.", - "rdfs:label": "TargetCaptureKit", + "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "PhysicalSizeXUnit", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Imaging" } ], "schema:isPartOf": { @@ -37284,492 +42451,282 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:NotApplicable" - }, - { - "@id": "bts:CustomTargetsFileProvided" - }, - { - "@id": "bts:CustomAmpliSeqCancerHotspotGENIE-MDAAugmentedPanelv1-46Genes" - }, - { - "@id": "bts:CustomGENIE-DFCIOncoPanel-275Genes" - }, - { - "@id": "bts:CustomGENIE-DFCIOncopanel-300Genes" - }, - { - "@id": "bts:CustomGENIE-DFCIOncopanel-447Genes" - }, - { - "@id": "bts:CustomHaloPlexDLBCLPanel-370Genes" - }, - { - "@id": "bts:CustomIonAmpliSeqHotspotGENIE-MOSC3AugmentedPanel-74Genes" - }, - { - "@id": "bts:CustomLargeConstructCaptureTARGET-OSPanel-8Genes" - }, - { - "@id": "bts:CustomMSKIMPACTPanel-341Genes" - }, - { - "@id": "bts:CustomMSKIMPACTPanel-410Genes" - }, - { - "@id": "bts:CustomMSKIMPACTPanel-468Genes" - }, - { - "@id": "bts:CustomMyeloidGENIE-VICCPanel-37Genes" - }, - { - "@id": "bts:CustomPersonalisACEcpVAREPOP-APOLLOPanelv2" - }, - { - "@id": "bts:CustomPGDXSureSelectCancerSelectVAREPOP-APOLLOPanel-203Genes" - }, - { - "@id": "bts:CustomPGDXSureSelectCancerSelectVAREPOP-APOLLOPanel-88Genes" - }, - { - "@id": "bts:CustomSeqCapEZHGSCVCRomev2.1ERAugmentedv1" - }, - { - "@id": "bts:CustomSeqCapEZHGSCVCRomev2.1ERAugmentedv2" - }, - { - "@id": "bts:CustomSeqCapEZTARGET-OSPanel-7.0Mb" - }, - { - "@id": "bts:CustomSolidTumorGENIE-VICCPanel-34Genes" - }, - { - "@id": "bts:CustomSureSelectCGCI-BLGSPPanel-4.6Mb" - }, - { - "@id": "bts:CustomSureSelectCGCI-HTMCP-CCKMT2DAndHotspotPanel-37.0Kb" - }, - { - "@id": "bts:CustomSureSelectCGCI-HTMCP-CCPanel-19.7Mb" - }, - { - "@id": "bts:CustomSureSelectGENIE-UHNPanel-555Genes" - }, - { - "@id": "bts:CustomSureSelectHumanAllExonv1.1Plus3Boosters" - }, - { - "@id": "bts:CustomSureSelectTARGET-AMLNBLWTPanel-2.8Mb" - }, - { - "@id": "bts:CustomTwistBroadExomev1.0-35.0Mb" - }, - { - "@id": "bts:CustomTwistBroadPanCancerPanel-396Genes" - }, - { - "@id": "bts:FoundationMedicineT5aPanel-322Genes" - }, - { - "@id": "bts:FoundationMedicineT7Panel-429Genes" - }, - { - "@id": "bts:IonAmpliSeqCancerHotspotPanelv2" - }, - { - "@id": "bts:IonAmpliSeqComprehensiveCancerPanel" - }, - { - "@id": "bts:NexteraDNAExome" - }, - { - "@id": "bts:NexteraRapidCaptureExomev1.2" - }, - { - "@id": "bts:SeqCapEZHGSCVCRomev2.1" - }, - { - "@id": "bts:SeqCapEZHumanExomev2.0" - }, - { - "@id": "bts:SeqCapEZHumanExomev3.0" - }, - { - "@id": "bts:SureSelectHumanAllExonv3" - }, - { - "@id": "bts:SureSelectHumanAllExonv4" - }, - { - "@id": "bts:SureSelectHumanAllExonv5" - }, - { - "@id": "bts:SureSelectHumanAllExonv5+UTR" - }, - { - "@id": "bts:TruSeqAmpliconCancerPanel" - }, - { - "@id": "bts:TruSeqExomeEnrichment-62Mb" - }, - { - "@id": "bts:TruSeqRNAExome" - }, - { - "@id": "bts:TruSightMyeloidSequencingPanel" - }, - { - "@id": "bts:XGenExomeResearchPanelv1.0" + "@id": "bts:Cm" }, { - "@id": "bts:XGenUniversalBlockingOligo–TSHT-i5-25rxn" + "@id": "bts:Mm" }, { - "@id": "bts:25rxnxGenUniversalBlockingOligo–TSHT-i7" + "@id": "bts:Μm" }, { - "@id": "bts:SureSelectHumanAllExonv6" + "@id": "bts:Nm" }, { - "@id": "bts:Unknown" + "@id": "bts:Å" } ], - "sms:displayName": "Target Capture Kit", + "sms:displayName": "PhysicalSizeXUnit", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BulkWESLevel2", + "@id": "bts:PhysicalSizeY", "@type": "rdfs:Class", - "rdfs:comment": "Bulk Whole Exome Sequencing aligned files and QC", - "rdfs:label": "BulkWESLevel2", + "rdfs:comment": "Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.", + "rdfs:label": "PhysicalSizeY", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk WES Level 2", - "sms:required": "sms:false", - "sms:requiresComponent": [ + "sms:displayName": "PhysicalSizeY", + "sms:required": "sms:true", + "sms:requiresDependency": [ { - "@id": "bts:BulkWESLevel1" + "@id": "bts:PhysicalSizeYUnit" } ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:AlignmentWorkflowType" - }, - { - "@id": "bts:GenomicReference" - }, - { - "@id": "bts:GenomicReferenceURL" - }, - { - "@id": "bts:IndexFileName" - }, - { - "@id": "bts:AverageBaseQuality" - }, - { - "@id": "bts:AverageInsertSize" - }, - { - "@id": "bts:AverageReadLength" - }, - { - "@id": "bts:Contamination" - }, - { - "@id": "bts:ContaminationError" - }, - { - "@id": "bts:MeanCoverage" - }, - { - "@id": "bts:AdapterContent" - }, - { - "@id": "bts:BasicStatistics" - }, - { - "@id": "bts:Encoding" - }, - { - "@id": "bts:OverrepresentedSequences" - }, - { - "@id": "bts:PerBaseNContent" - }, - { - "@id": "bts:PerBaseSequenceContent" - }, - { - "@id": "bts:PerBaseSequenceQuality" - }, - { - "@id": "bts:PerSequenceGCContent" - }, - { - "@id": "bts:PerSequenceQualityScore" - }, - { - "@id": "bts:PerTileSequenceQuality" - }, - { - "@id": "bts:PercentGCContent" - }, - { - "@id": "bts:SequenceDuplicationLevels" - }, - { - "@id": "bts:SequenceLengthDistribution" - }, - { - "@id": "bts:QCWorkflowType" - }, - { - "@id": "bts:QCWorkflowVersion" - }, - { - "@id": "bts:QCWorkflowLink" - }, - { - "@id": "bts:MSIWorkflowLink" - }, - { - "@id": "bts:MSIScore" - }, - { - "@id": "bts:MSIStatus" - }, - { - "@id": "bts:PairsOnDiffCHR" - }, - { - "@id": "bts:TotalReads" - }, - { - "@id": "bts:TotalUniquelyMapped" - }, - { - "@id": "bts:TotalUnmappedreads" - }, - { - "@id": "bts:ProportionReadsDuplicated" - }, - { - "@id": "bts:ProportionReadsMapped" - }, + "sms:validationRules": [] + }, + { + "@id": "bts:PhysicalSizeYUnit", + "@type": "rdfs:Class", + "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "PhysicalSizeYUnit", + "rdfs:subClassOf": [ { - "@id": "bts:ProportionTargetsNoCoverage" - }, + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:ProportionBaseMismatch" + "@id": "bts:Cm" }, { - "@id": "bts:ShortReads" + "@id": "bts:Mm" }, { - "@id": "bts:ProportionCoverage10x" + "@id": "bts:Μm" }, { - "@id": "bts:ProportionCoverage30X" + "@id": "bts:Nm" }, { - "@id": "bts:Islowestlevel" + "@id": "bts:Å" } ], + "sms:displayName": "PhysicalSizeYUnit", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ProportionCoverage10x", + "@id": "bts:PhysicalSizeZ", "@type": "rdfs:Class", - "rdfs:comment": "Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 10X or greater coverage from Picard Tools.", - "rdfs:label": "ProportionCoverage10x", + "rdfs:comment": "Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.", + "rdfs:label": "PhysicalSizeZ", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion Coverage 10x", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ProportionCoverage30X", - "@type": "rdfs:Class", - "rdfs:comment": "Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools.", - "rdfs:label": "ProportionCoverage30X", - "rdfs:subClassOf": [ + "sms:displayName": "PhysicalSizeZ", + "sms:required": "sms:true", + "sms:requiresDependency": [ { - "@id": "bts:Sequencing" + "@id": "bts:PhysicalSizeZUnit" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Proportion Coverage 30X", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BulkWESLevel3", + "@id": "bts:PhysicalSizeZUnit", "@type": "rdfs:Class", - "rdfs:comment": "Bulk Whole Exome Sequencing called variants", - "rdfs:label": "BulkWESLevel3", + "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "PhysicalSizeZUnit", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk WES Level 3", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:BulkWESLevel2" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:GenomicReference" - }, + "schema:rangeIncludes": [ { - "@id": "bts:GenomicReferenceURL" + "@id": "bts:Cm" }, { - "@id": "bts:GermlineVariantsWorkflowURL" + "@id": "bts:Mm" }, { - "@id": "bts:GermlineVariantsWorkflowType" + "@id": "bts:Μm" }, { - "@id": "bts:SomaticVariantsWorkflowURL" + "@id": "bts:Nm" }, { - "@id": "bts:SomaticVariantsWorkflowType" - }, + "@id": "bts:Å" + } + ], + "sms:displayName": "PhysicalSizeZUnit", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:PixelsBigEndian", + "@type": "rdfs:Class", + "rdfs:comment": "Boolean (True/False)", + "rdfs:label": "PixelsBigEndian", + "rdfs:subClassOf": [ { - "@id": "bts:SomaticVariantsSampleType" - }, + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:StructuralVariantWorkflowURL" + "@id": "bts:True" }, { - "@id": "bts:StructuralVariantWorkflowType" + "@id": "bts:False" } ], + "sms:displayName": "Pixels BigEndian", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:GermlineVariantsWorkflowURL", + "@id": "bts:PlaneCount", "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow document, e.g. Github, DockStore.org recommended", - "rdfs:label": "GermlineVariantsWorkflowURL", + "rdfs:comment": "Number of Z-planes (not to be confused with downsampled \"pyramid\"). Integer >=1", + "rdfs:label": "PlaneCount", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Germline Variants Workflow URL", + "sms:displayName": "PlaneCount", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:GermlineVariantsWorkflowType", + "@id": "bts:SizeC", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set", - "rdfs:label": "GermlineVariantsWorkflowType", + "rdfs:comment": "Number of channels. Integer >= 1", + "rdfs:label": "SizeC", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "SizeC", + "sms:required": "sms:true", + "sms:validationRules": [ + "int" + ] + }, + { + "@id": "bts:SizeT", + "@type": "rdfs:Class", + "rdfs:comment": "Number of time points. Integer >= 1", + "rdfs:label": "SizeT", + "rdfs:subClassOf": [ { - "@id": "bts:GATK4" - }, + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "SizeT", + "sms:required": "sms:true", + "sms:validationRules": [ + "int" + ] + }, + { + "@id": "bts:SizeX", + "@type": "rdfs:Class", + "rdfs:comment": "Size of image: X dimension (in pixels). Integer >= 1", + "rdfs:label": "SizeX", + "rdfs:subClassOf": [ { - "@id": "bts:OtherGermlineVariantsWorkflowType" - }, + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "SizeX", + "sms:required": "sms:true", + "sms:validationRules": [ + "int" + ] + }, + { + "@id": "bts:SizeY", + "@type": "rdfs:Class", + "rdfs:comment": "Size of image: Y dimension (in pixels). Integer >= 1", + "rdfs:label": "SizeY", + "rdfs:subClassOf": [ { - "@id": "bts:None" + "@id": "bts:Imaging" } ], - "sms:displayName": "Germline Variants Workflow Type", - "sms:required": "sms:false", - "sms:validationRules": [] + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "SizeY", + "sms:required": "sms:true", + "sms:validationRules": [ + "int" + ] }, { - "@id": "bts:SomaticVariantsWorkflowURL", + "@id": "bts:SizeZ", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "SomaticVariantsWorkflowURL", + "rdfs:comment": "Size of image: Z dimension (in pixels). Integer >= 1", + "rdfs:label": "SizeZ", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Somatic Variants Workflow URL", + "sms:displayName": "SizeZ", "sms:required": "sms:true", - "sms:validationRules": [] + "sms:validationRules": [ + "int" + ] }, { - "@id": "bts:SomaticVariantsWorkflowType", + "@id": "bts:PixelType", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "SomaticVariantsWorkflowType", + "rdfs:comment": "Data type for each pixel value. E.g. \"uint16\"", + "rdfs:label": "PixelType", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Imaging" } ], "schema:isPartOf": { @@ -37777,124 +42734,76 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CaVEMan" - }, - { - "@id": "bts:GATK4" - }, - { - "@id": "bts:MuTect2" + "@id": "bts:Int8" }, { - "@id": "bts:MuSE" + "@id": "bts:Int16" }, { - "@id": "bts:Pindel" + "@id": "bts:Int32" }, { - "@id": "bts:SomaticSniper" + "@id": "bts:Uint8" }, { - "@id": "bts:VarScan2" + "@id": "bts:Uint16" }, { - "@id": "bts:OtherSomaticVariantsWorkflowType" + "@id": "bts:Uint32" }, { - "@id": "bts:None" - } - ], - "sms:displayName": "Somatic Variants Workflow Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SomaticVariantsSampleType", - "@type": "rdfs:Class", - "rdfs:comment": "Is the sample case or control in somatic variant analysis", - "rdfs:label": "SomaticVariantsSampleType", - "rdfs:subClassOf": [ - { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:CaseSample" + "@id": "bts:Float" }, { - "@id": "bts:ControlSample" + "@id": "bts:Double" }, { - "@id": "bts:NotApplicable" + "@id": "bts:Bit" } ], - "sms:displayName": "Somatic Variants Sample Type", + "sms:displayName": "PixelType", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:StructuralVariantWorkflowURL", + "@id": "bts:MERFISHPositionsFile", "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow document. DockStore.org recommended. URL", - "rdfs:label": "StructuralVariantWorkflowURL", + "rdfs:comment": "The positions file is an auxiliary MERFISH file that describes the location of bead positions in the assay.", + "rdfs:label": "MERFISHPositionsFile", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Structural Variant Workflow URL", - "sms:required": "sms:true", + "sms:displayName": "MERFISH Positions File", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:StructuralVariantWorkflowType", + "@id": "bts:MERFISHCodebookFile", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "StructuralVariantWorkflowType", + "rdfs:comment": "The codebook is an auxiliary MERFISH file that describes how each grouping of bits is converted to a gene name.", + "rdfs:label": "MERFISHCodebookFile", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:BRASS" - }, - { - "@id": "bts:GATK4" - }, - { - "@id": "bts:CNV" - }, - { - "@id": "bts:CNVkit" - }, - { - "@id": "bts:OtherStructuralVariantWorkflowType" - }, - { - "@id": "bts:None" - } - ], - "sms:displayName": "Structural Variant Workflow Type", + "sms:displayName": "MERFISH Codebook File", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MicroarrayLevel1", + "@id": "bts:ImagingLevel3Segmentation", "@type": "rdfs:Class", - "rdfs:comment": "Microarray Level 1 refers to the raw text table of probe level intensities", - "rdfs:label": "MicroarrayLevel1", + "rdfs:comment": "Object segmentations", + "rdfs:label": "ImagingLevel3Segmentation", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -37903,11 +42812,11 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Microarray Level 1", + "sms:displayName": "Imaging Level 3 Segmentation", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ImagingLevel2" } ], "sms:requiresDependency": [ @@ -37921,62 +42830,40 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:HTANParticipantID" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:NucleicAcidSource" + "@id": "bts:ImagingSegmentationDataType" }, { - "@id": "bts:MicroarrayPlatformID" + "@id": "bts:Parameterfile" }, { - "@id": "bts:MicroarrayMolecule" + "@id": "bts:SoftwareandVersion" }, { - "@id": "bts:MicroarrayLabel" + "@id": "bts:CommitSHA" }, { - "@id": "bts:MicroarrayValueDefinition" + "@id": "bts:ImagingObjectClass" }, { - "@id": "bts:MicroarrayProtocolAuxiliaryFile" + "@id": "bts:NumberofObjects" } ], "sms:validationRules": [] }, { - "@id": "bts:MicroarrayPlatformID", - "@type": "rdfs:Class", - "rdfs:comment": "The NCBI GEO Microarray Platform ID that links to the table containing the array definition", - "rdfs:label": "MicroarrayPlatformID", - "rdfs:subClassOf": [ - { - "@id": "bts:MicroarrayLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Microarray Platform ID", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match GPL\\d+" - ] - }, - { - "@id": "bts:MicroarrayMolecule", + "@id": "bts:ImagingSegmentationDataType", "@type": "rdfs:Class", - "rdfs:comment": "Microarray is measuring this kind of molecule", - "rdfs:label": "MicroarrayMolecule", + "rdfs:comment": "Specifies how the segmentation is stored", + "rdfs:label": "ImagingSegmentationDataType", "rdfs:subClassOf": [ { - "@id": "bts:MicroarrayLevel1" + "@id": "bts:Imaging" } ], "schema:isPartOf": { @@ -37984,74 +42871,105 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:DNA" + "@id": "bts:Mask" }, { - "@id": "bts:RNA" + "@id": "bts:Outline" + }, + { + "@id": "bts:Polygon" + }, + { + "@id": "bts:ProbabilityMap" + }, + { + "@id": "bts:Point" } ], - "sms:displayName": "Microarray Molecule", + "sms:displayName": "Imaging Segmentation Data Type", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MicroarrayLabel", + "@id": "bts:Parameterfile", "@type": "rdfs:Class", - "rdfs:comment": "Microarray used this kind of label", - "rdfs:label": "MicroarrayLabel", + "rdfs:comment": "Path in Syanpse to a text file listing algorithm version numbers and relevant parameters needed to reproduce the analysis", + "rdfs:label": "Parameterfile", "rdfs:subClassOf": [ { - "@id": "bts:MicroarrayLevel1" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Microarray Label", - "sms:required": "sms:true", + "sms:displayName": "Parameter file", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MicroarrayValueDefinition", + "@id": "bts:ImagingObjectClass", "@type": "rdfs:Class", - "rdfs:comment": "What the provided value signifies", - "rdfs:label": "MicroarrayValueDefinition", + "rdfs:comment": "Defines the structure that the mask delineates", + "rdfs:label": "ImagingObjectClass", "rdfs:subClassOf": [ { - "@id": "bts:MicroarrayLevel1" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Microarray Value Definition", + "schema:rangeIncludes": [ + { + "@id": "bts:Nucleus" + }, + { + "@id": "bts:Cytoplasm" + }, + { + "@id": "bts:Plasmamembrane" + }, + { + "@id": "bts:Wholecell" + }, + { + "@id": "bts:Spot" + }, + { + "@id": "bts:ImagingObjectClassOther" + } + ], + "sms:displayName": "Imaging Object Class", "sms:required": "sms:true", - "sms:validationRules": [] + "sms:validationRules": [ + "list like" + ] }, { - "@id": "bts:MicroarrayProtocolAuxiliaryFile", + "@id": "bts:NumberofObjects", "@type": "rdfs:Class", - "rdfs:comment": "Auxiliary file describing the experimental protocols used, as described in the NCBI GEO microarray template, recorded as synapse ID (syn12345).", - "rdfs:label": "MicroarrayProtocolAuxiliaryFile", + "rdfs:comment": "The number of objects (eg cells) described", + "rdfs:label": "NumberofObjects", "rdfs:subClassOf": [ { - "@id": "bts:MicroarrayLevel1" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Microarray Protocol Auxiliary File", + "sms:displayName": "Number of Objects", "sms:required": "sms:true", "sms:validationRules": [ - "regex match syn\\d+" + "int" ] }, { - "@id": "bts:MicroarrayLevel2", + "@id": "bts:ImagingLevel3Image", "@type": "rdfs:Class", - "rdfs:comment": "Microarray Level 2 provides a normalized matrix of values.", - "rdfs:label": "MicroarrayLevel2", + "rdfs:comment": "Quality controlled imaging data", + "rdfs:label": "ImagingLevel3Image", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -38060,11 +42978,14 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Microarray Level 2", + "sms:displayName": "Imaging Level 3 Image", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:MicroarrayLevel1" + "@id": "bts:ImagingLevel3Channels" + }, + { + "@id": "bts:ImagingLevel2" } ], "sms:requiresDependency": [ @@ -38077,355 +42998,287 @@ { "@id": "bts:FileFormat" }, - { - "@id": "bts:HTANParticipantID" - }, { "@id": "bts:HTANParentBiospecimenID" }, { "@id": "bts:HTANParentDataFileID" }, + { + "@id": "bts:HTANParentChannelMetadataID" + }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:MicroarrayPlatformID" + "@id": "bts:ImagingAssayType" }, { - "@id": "bts:NormalizationMethod" + "@id": "bts:ProtocolLink" + }, + { + "@id": "bts:SoftwareandVersion" + }, + { + "@id": "bts:Microscope" + }, + { + "@id": "bts:Objective" + }, + { + "@id": "bts:NominalMagnification" + }, + { + "@id": "bts:LensNA" + }, + { + "@id": "bts:WorkingDistance" + }, + { + "@id": "bts:Immersion" + }, + { + "@id": "bts:Pyramid" + }, + { + "@id": "bts:Zstack" + }, + { + "@id": "bts:Tseries" + }, + { + "@id": "bts:PassedQC" + }, + { + "@id": "bts:Comment" + }, + { + "@id": "bts:FOVnumber" + }, + { + "@id": "bts:FOVX" + }, + { + "@id": "bts:FOVY" + }, + { + "@id": "bts:FrameAveraging" } ], "sms:validationRules": [] }, { - "@id": "bts:NormalizationMethod", + "@id": "bts:HTANParentChannelMetadataID", "@type": "rdfs:Class", - "rdfs:comment": "Description of Normalization Process", - "rdfs:label": "NormalizationMethod", + "rdfs:comment": "HTAN ID for a level 3 channels table.", + "rdfs:label": "HTANParentChannelMetadataID", "rdfs:subClassOf": [ { - "@id": "bts:RPPALevel2" + "@id": "bts:ImagingLevel4" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Normalization Method", - "sms:required": "sms:false", + "sms:displayName": "HTAN Parent Channel Metadata ID", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ScATAC-seqLevel1", + "@id": "bts:ImagingLevel3Channels", "@type": "rdfs:Class", - "rdfs:comment": "scATAC-seq files containing sequence read information, with or without alignment, as FASTQ or BAM files", - "rdfs:label": "ScATAC-seqLevel1", + "rdfs:comment": "Channel-level Metadata Attributes", + "rdfs:label": "ImagingLevel3Channels", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scATAC-seq Level 1", + "sms:displayName": "Imaging Level 3 Channels", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Biospecimen" - } - ], "sms:requiresDependency": [ { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:HTANChannelMetadataID" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:ChannelID" }, { - "@id": "bts:NucleicAcidSource" + "@id": "bts:ChannelName" }, { - "@id": "bts:DissociationMethod" + "@id": "bts:ChannelPassedQC" }, { - "@id": "bts:SingleNucleusBuffer" + "@id": "bts:CycleNumber" }, { - "@id": "bts:SingleCellIsolationMethod" + "@id": "bts:SubCycleNumber" }, { - "@id": "bts:TranspositionReaction" + "@id": "bts:AntibodyRole" }, { - "@id": "bts:ScATACseqLibraryLayout" + "@id": "bts:TargetName" }, { - "@id": "bts:NucleusIdentifier" + "@id": "bts:AntibodyName" }, { - "@id": "bts:NucleiBarcodeLength" + "@id": "bts:RRIDidentifier" }, { - "@id": "bts:NucleiBarcodeRead" + "@id": "bts:Fluorophore" }, { - "@id": "bts:ScATACseqRead1" + "@id": "bts:Clone" }, { - "@id": "bts:ScATACseqRead2" + "@id": "bts:Lot" }, { - "@id": "bts:ScATACseqRead3" + "@id": "bts:Vendor" }, { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:CatalogNumber" }, { - "@id": "bts:SequencingPlatform" + "@id": "bts:ExcitationWavelength" }, { - "@id": "bts:ThresholdforMinimumPassingReads" + "@id": "bts:EmissionWavelength" }, { - "@id": "bts:TotalNumberofPassingNuclei" + "@id": "bts:ExcitationBandwidth" }, { - "@id": "bts:MedianFractionofReadsinPeaks" + "@id": "bts:EmissionBandwidth" }, { - "@id": "bts:MedianFractionofReadsinAnnotatedcisDNAElements" + "@id": "bts:MetalIsotopeElement" }, { - "@id": "bts:MedianPassingReadPercentage" + "@id": "bts:MetalIsotopeMass" }, { - "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus" + "@id": "bts:OligoBarcodeUpperStrand" }, { - "@id": "bts:TechnicalReplicateGroup" + "@id": "bts:OligoBarcodeLowerStrand" }, { - "@id": "bts:TotalReads" + "@id": "bts:Dilution" }, { - "@id": "bts:ProtocolLink" + "@id": "bts:Concentration" } ], "sms:validationRules": [] }, { - "@id": "bts:SingleNucleusBuffer", + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel1", "@type": "rdfs:Class", - "rdfs:comment": "Nuclei isolation buffer", - "rdfs:label": "SingleNucleusBuffer", + "rdfs:comment": "Files contain raw RNA-seq data associated with spot/slide data.", + "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel1", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:NIB" - }, - { - "@id": "bts:10x" - }, - { - "@id": "bts:Omni" - }, + "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 1", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:TST" + "@id": "bts:Biospecimen" } ], - "sms:displayName": "Single Nucleus Buffer", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:TranspositionReaction", - "@type": "rdfs:Class", - "rdfs:comment": "Name of the transposase, transposon sequences", - "rdfs:label": "TranspositionReaction", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:ScATAC-seqLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Component" + }, { - "@id": "bts:Tn5" + "@id": "bts:Filename" }, { - "@id": "bts:EZ-Tn5" + "@id": "bts:RunID" }, { - "@id": "bts:Tn5-059" + "@id": "bts:FileFormat" }, { - "@id": "bts:NexteraTn5" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:Diagenode-unloadedApex-Bio" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:Diagenode-loadedApex-Bio" + "@id": "bts:ReadIndicator" }, { - "@id": "bts:In-House" - } - ], - "sms:displayName": "Transposition Reaction", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ScATACseqLibraryLayout", - "@type": "rdfs:Class", - "rdfs:comment": "Sequencing read type", - "rdfs:label": "ScATACseqLibraryLayout", - "rdfs:subClassOf": [ + "@id": "bts:SpatialRead1" + }, { - "@id": "bts:ScATAC-seqLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:SpatialRead2" + }, { - "@id": "bts:ScATACseqPairedEnd" - } - ], - "sms:displayName": "scATACseq Library Layout", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:NucleusIdentifier", - "@type": "rdfs:Class", - "rdfs:comment": "Unique nuclei barcode; added at transposition step. Determines which nucleus the reads originated from", - "rdfs:label": "NucleusIdentifier", - "rdfs:subClassOf": [ + "@id": "bts:SpatialLibraryConstructionMethod" + }, { - "@id": "bts:ScATAC-seqLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:LibraryPreparationDaysfromIndex" + }, { - "@id": "bts:NucleiBarcode" - } - ], - "sms:displayName": "Nucleus Identifier", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:NucleiBarcodeLength", - "@type": "rdfs:Class", - "rdfs:comment": "Nuclei Barcode Length", - "rdfs:label": "NucleiBarcodeLength", - "rdfs:subClassOf": [ + "@id": "bts:SequencingLibraryConstructionDaysfromIndex" + }, { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:EndBias" }, { - "@id": "bts:NucleiBarcode" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Nuclei Barcode Length", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:NucleiBarcodeRead", - "@type": "rdfs:Class", - "rdfs:comment": "Nuclei Barcode Read", - "rdfs:label": "NucleiBarcodeRead", - "rdfs:subClassOf": [ + "@id": "bts:ReverseTranscriptionPrimer" + }, { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:SequencingPlatform" }, { - "@id": "bts:NucleiBarcode" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Nuclei Barcode Read", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ScATACseqRead1", - "@type": "rdfs:Class", - "rdfs:comment": "Read 1 content description", - "rdfs:label": "ScATACseqRead1", - "rdfs:subClassOf": [ + "@id": "bts:CaptureArea" + }, { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:ProtocolLink" }, { - "@id": "bts:ScATACseqPairedEnd" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:SlideVersion" + }, { - "@id": "bts:CellBarcodeandDNAInsert" + "@id": "bts:SlideID" }, { - "@id": "bts:SampleIndexandDNAInsert" + "@id": "bts:ImageRe-orientation" }, { - "@id": "bts:DNAInsert" + "@id": "bts:PermeabilizationTime" }, { - "@id": "bts:SampleIndex" + "@id": "bts:RIN" }, { - "@id": "bts:CellBarcode" + "@id": "bts:DV200" } ], - "sms:displayName": "scATACseq Read1", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ScATACseqRead2", + "@id": "bts:CaptureArea", "@type": "rdfs:Class", - "rdfs:comment": "Read 2 content description", - "rdfs:label": "ScATACseqRead2", + "rdfs:comment": "Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.", + "rdfs:label": "CaptureArea", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" - }, - { - "@id": "bts:ScATACseqPairedEnd" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { @@ -38433,33 +43286,42 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CellBarcodeandDNAInsert" + "@id": "bts:A" }, { - "@id": "bts:SampleIndexandDNAInsert" + "@id": "bts:B" }, { - "@id": "bts:DNAInsert" + "@id": "bts:C" }, { - "@id": "bts:SampleIndex" + "@id": "bts:D" }, { - "@id": "bts:CellBarcode" + "@id": "bts:A1" + }, + { + "@id": "bts:B1" + }, + { + "@id": "bts:C1" + }, + { + "@id": "bts:D1" } ], - "sms:displayName": "scATACseq Read2", - "sms:required": "sms:true", + "sms:displayName": "Capture Area", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScATACseqRead3", + "@id": "bts:SlideVersion", "@type": "rdfs:Class", - "rdfs:comment": "Read 3 content description", - "rdfs:label": "ScATACseqRead3", + "rdfs:comment": "Version of imaging slide used. Slide version is critical for the analysis of the sequencing data as different slides have different capture area layouts.", + "rdfs:label": "SlideVersion", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { @@ -38467,155 +43329,99 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CellBarcodeandDNAInsert" - }, - { - "@id": "bts:SampleIndexandDNAInsert" + "@id": "bts:V1" }, { - "@id": "bts:DNAInsert" + "@id": "bts:V2" }, { - "@id": "bts:SampleIndex" + "@id": "bts:V3" }, { - "@id": "bts:CellBarcode" + "@id": "bts:V4" } ], - "sms:displayName": "scATACseq Read3", + "sms:displayName": "Slide Version", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ThresholdforMinimumPassingReads", - "@type": "rdfs:Class", - "rdfs:comment": "Threshold for calling cells", - "rdfs:label": "ThresholdforMinimumPassingReads", - "rdfs:subClassOf": [ - { - "@id": "bts:ScATAC-seqLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Threshold for Minimum Passing Reads", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:TotalNumberofPassingNuclei", - "@type": "rdfs:Class", - "rdfs:comment": "Number of nuclei sequenced", - "rdfs:label": "TotalNumberofPassingNuclei", - "rdfs:subClassOf": [ - { - "@id": "bts:ScATAC-seqLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Total Number of Passing Nuclei", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:MedianFractionofReadsinPeaks", + "@id": "bts:SlideID", "@type": "rdfs:Class", - "rdfs:comment": "Median fraction of reads in peaks (FRIP)", - "rdfs:label": "MedianFractionofReadsinPeaks", + "rdfs:comment": "For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide.", + "rdfs:label": "SlideID", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Median Fraction of Reads in Peaks", - "sms:required": "sms:true", - "sms:requiresDependency": [ - { - "@id": "bts:PeaksCallingSoftware" - } - ], + "sms:displayName": "Slide ID", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MedianFractionofReadsinAnnotatedcisDNAElements", + "@id": "bts:ImageRe-orientation", "@type": "rdfs:Class", - "rdfs:comment": "Median fraction of reads in annotated cis-DNA elements (FRIADE)", - "rdfs:label": "MedianFractionofReadsinAnnotatedcisDNAElements", + "rdfs:comment": "To ensure good fiducial alignment and tissue spots detection, it is important to correct for this shift in orientation.", + "rdfs:label": "ImageRe-orientation", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Median Fraction of Reads in Annotated cis DNA Elements", - "sms:required": "sms:true", - "sms:requiresDependency": [ + "schema:rangeIncludes": [ { - "@id": "bts:PeaksCallingSoftware" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:MedianPassingReadPercentage", - "@type": "rdfs:Class", - "rdfs:comment": "Non-PCR duplicate nuclear genomic sequence reads not aligning to unanchored contigs out of total reads assigned to the nucleus barcode", - "rdfs:label": "MedianPassingReadPercentage", - "rdfs:subClassOf": [ + "@id": "bts:TRUE" + }, { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:FALSE" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Median Passing Read Percentage", - "sms:required": "sms:true", + "sms:displayName": "Image Re-orientation", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus", + "@id": "bts:PermeabilizationTime", "@type": "rdfs:Class", - "rdfs:comment": "Contamination from mitochondrial sequences", - "rdfs:label": "MedianPercentageofMitochondrialReadsperNucleus", + "rdfs:comment": "Fixed and stained tissue sections are permeabilized for different times. Each Capture Area captures polyadenylated mRNA from the attached tissue section. Measure is provided in minutes.", + "rdfs:label": "PermeabilizationTime", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Median Percentage of Mitochondrial Reads per Nucleus", - "sms:required": "sms:true", + "sms:displayName": "Permeabilization Time", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ScATAC-seqLevel2", + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "scATAC-seq files containing aligned sequence data, as a BAM file", - "rdfs:label": "ScATAC-seqLevel2", + "rdfs:comment": "Alignment workflows downstream of Spatial Transcriptomics RNA-seq Level 1.", + "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel2", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scATAC-seq Level 2", + "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 2", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:ScATAC-seqLevel1" + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel1" } ], "sms:requiresDependency": [ @@ -38629,124 +43435,91 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:AlignmentWorkflowUrl" - }, - { - "@id": "bts:AlignmentWorkflowType" - }, - { - "@id": "bts:GenomicReference" - }, - { - "@id": "bts:GenomicReferenceURL" - }, - { - "@id": "bts:IndexFileName" - }, - { - "@id": "bts:AverageBaseQuality" - }, - { - "@id": "bts:AverageInsertSize" - }, - { - "@id": "bts:AverageReadLength" - }, - { - "@id": "bts:MeanCoverage" - }, - { - "@id": "bts:PairsOnDiffCHR" + "@id": "bts:Checksum" }, { - "@id": "bts:TotalReads" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:ProportionReadsMapped" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:MapQ30" + "@id": "bts:UMITag" }, { - "@id": "bts:TotalUniquelyMapped" + "@id": "bts:WhitelistSpatialBarcodeFileLink" }, { - "@id": "bts:TotalUnmappedreads" + "@id": "bts:SpatialBarcodeTag" }, { - "@id": "bts:ProportionReadsDuplicated" + "@id": "bts:AppliedHardTrimming" }, { - "@id": "bts:ShortReads" + "@id": "bts:WorkflowVersion" }, { - "@id": "bts:ProportionCoverage10x" + "@id": "bts:WorkflowLink" }, { - "@id": "bts:ProportionCoverage30X" + "@id": "bts:GenomicReference" }, { - "@id": "bts:ProportionTargetsNoCoverage" + "@id": "bts:GenomicReferenceURL" }, { - "@id": "bts:ProportionBaseMismatch" + "@id": "bts:GenomeAnnotationURL" }, { - "@id": "bts:MedianPercentageofMitochondrialReadsperNucleus" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:Contamination" + "@id": "bts:RunID" }, { - "@id": "bts:ContaminationError" + "@id": "bts:CaptureArea" } ], "sms:validationRules": [] }, { - "@id": "bts:MapQ30", - "@type": "rdfs:Class", - "rdfs:comment": "Number of reads with Quality >= 30.", - "rdfs:label": "MapQ30", + "@id": "bts:WhitelistSpatialBarcodeFileLink", + "@type": "rdfs:Class", + "rdfs:comment": "Link to file listing all possible spatial barcodes. URL", + "rdfs:label": "WhitelistSpatialBarcodeFileLink", "rdfs:subClassOf": [ { - "@id": "bts:ScATAC-seqLevel1" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MapQ30", - "sms:required": "sms:false", + "sms:displayName": "Whitelist Spatial Barcode File Link", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ScATAC-seqLevel3", + "@id": "bts:10xVisiumSpatialTranscriptomics-AuxiliaryFiles", "@type": "rdfs:Class", - "rdfs:comment": "Processed data files containing peak information for cells", - "rdfs:label": "ScATAC-seqLevel3", + "rdfs:comment": "Auxiliary data associated with spot/slide analysis (aligned Images, quality control files, etc) from Spatial Transcriptomics.", + "rdfs:label": "10xVisiumSpatialTranscriptomics-AuxiliaryFiles", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scATAC-seq Level 3", + "sms:displayName": "10x Visium Spatial Transcriptomics - Auxiliary Files", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:ScATAC-seqLevel2" + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel1" + }, + { + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel2" } ], "sms:requiresDependency": [ @@ -38759,6 +43532,9 @@ { "@id": "bts:FileFormat" }, + { + "@id": "bts:HTANParentBiospecimenID" + }, { "@id": "bts:HTANParentDataFileID" }, @@ -38766,1890 +43542,1168 @@ "@id": "bts:HTANDataFileID" }, { - "@id": "bts:ScATAC-seqObjectID" + "@id": "bts:RunID" }, { - "@id": "bts:NCountPeaks" + "@id": "bts:VisiumFileType" }, { - "@id": "bts:NFeaturePeaks" + "@id": "bts:SlideID" }, { - "@id": "bts:TotalRead-Pairs" + "@id": "bts:CaptureArea" }, { - "@id": "bts:DuplicateRead-Pairs" + "@id": "bts:WorkflowVersion" }, { - "@id": "bts:ChimericRead-Pairs" - }, + "@id": "bts:WorkflowLink" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:VisiumFileType", + "@type": "rdfs:Class", + "rdfs:comment": "The file type generated for the visium experiment.", + "rdfs:label": "VisiumFileType", + "rdfs:subClassOf": [ { - "@id": "bts:UnmappedRead-Pairs" - }, + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:LowMapQ" + "@id": "bts:Referencepng" }, { - "@id": "bts:MitochondrialRead-Pairs" + "@id": "bts:Referencejpg" }, { - "@id": "bts:PassedFilters" + "@id": "bts:Jsonscalefactors" }, { - "@id": "bts:TSSFragments" + "@id": "bts:Probedatasetcsv" }, { - "@id": "bts:DNaseSensitiveRegionFragments" + "@id": "bts:Qcresulthtml" }, { - "@id": "bts:EnhancerRegionFragments" + "@id": "bts:Filteredmex" }, { - "@id": "bts:PromoterRegionFragments" + "@id": "bts:Unfilteredmex" }, { - "@id": "bts:OnTargetFragments" + "@id": "bts:TissuePositions" }, { - "@id": "bts:BlacklistRegionFragments" + "@id": "bts:Barcodes" }, { - "@id": "bts:PeakRegionFragments" + "@id": "bts:Features" }, { - "@id": "bts:PeakRegionCutsites" + "@id": "bts:Fiducialimagepng" }, { - "@id": "bts:NucleosomeSignal" + "@id": "bts:Fiducialimagejpg" }, { - "@id": "bts:NucleosomePercentile" + "@id": "bts:Detectedimagepng" }, { - "@id": "bts:TSSEnrichment" + "@id": "bts:Detectedjpg" }, { - "@id": "bts:TSSPercentile" + "@id": "bts:Highresimage" }, { - "@id": "bts:PctReadsinPeaks" + "@id": "bts:Lowresimage" + } + ], + "sms:displayName": "Visium File Type", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel3", + "@type": "rdfs:Class", + "rdfs:comment": "Processed data files based on Spatial Transcriptomics RNA-seq Level 2 and Spatial Transcriptomics Auxiliary files.", + "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel3", + "rdfs:subClassOf": [ + { + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 3", + "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel2" }, { - "@id": "bts:BlacklistRatio" + "@id": "bts:10xVisiumSpatialTranscriptomics-AuxiliaryFiles" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:SeuratClusters" + "@id": "bts:Filename" }, { - "@id": "bts:NCountRNA" + "@id": "bts:FileFormat" }, { - "@id": "bts:NFeatureRNA" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:MACS2Seqnames" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:MACS2Start" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:MACS2End" + "@id": "bts:RunID" }, { - "@id": "bts:MACS2Width" + "@id": "bts:VisiumFileType" }, { - "@id": "bts:MACS2Strand" + "@id": "bts:WorkflowVersion" }, { - "@id": "bts:MACS2Name" + "@id": "bts:WorkflowLink" }, { - "@id": "bts:MACS2Score" + "@id": "bts:CaptureArea" }, { - "@id": "bts:MACS2FoldChange" + "@id": "bts:Spotsundertissue" }, { - "@id": "bts:MACS2NegLog10pvalueSummit" + "@id": "bts:MeanReadsperSpatialSpot" }, { - "@id": "bts:MACS2NegLog10qvalueSummit" + "@id": "bts:MedianNumberGenesperSpatialSpot" }, { - 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{ - "@id": "bts:AlignmentWorkflowUrl" - }, - { - "@id": "bts:AlignmentWorkflowType" - }, - { - "@id": "bts:GenomicReference" - }, - { - "@id": "bts:GenomicReferenceURL" - }, - { - "@id": "bts:IndexFileName" - }, - { - "@id": "bts:AverageBaseQuality" - }, - { - "@id": "bts:AverageInsertSize" - }, - { - "@id": "bts:AverageReadLength" - }, - { - "@id": "bts:MeanCoverage" - }, - { - "@id": "bts:PairsOnDiffCHR" - }, - { - "@id": "bts:TotalReads" - }, - { - "@id": "bts:ProportionReadsMapped" - }, - { - "@id": "bts:MapQ30" - }, - { - "@id": "bts:TotalUniquelyMapped" - }, - { - "@id": "bts:TotalUnmappedreads" - }, - { - "@id": "bts:ProportionReadsDuplicated" - }, - { - "@id": "bts:ShortReads" - }, - { - "@id": "bts:ProportionCoverage10x" - }, - { - "@id": "bts:ProportionCoverage30X" - }, - { - "@id": "bts:ProportionTargetsNoCoverage" - }, - { - "@id": "bts:ProportionBaseMismatch" - }, - { - "@id": "bts:ProportionMitochondrialReads" - }, - { - "@id": "bts:Contamination" - }, - { - "@id": "bts:ContaminationError" - } - ], "sms:validationRules": [] }, { - "@id": "bts:ProportionMitochondrialReads", + "@id": "bts:V4", "@type": "rdfs:Class", - "rdfs:comment": "Proportion of reads mapping to mitochondria.", - "rdfs:label": "ProportionMitochondrialReads", + "rdfs:comment": "TBD", + "rdfs:label": "V4", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:SlideVersion" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion Mitochondrial Reads", + "sms:displayName": "V4", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BulkMethylation-seqLevel1", + "@id": "bts:TRUE", "@type": "rdfs:Class", - "rdfs:comment": "Raw data for bulk methylation sequencing, such as FASTQs and unaligned BAMs", - "rdfs:label": "BulkMethylation-seqLevel1", + "rdfs:comment": "TBD", + "rdfs:label": "TRUE", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ImageRe-orientation" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk Methylation-seq Level 1", + "sms:displayName": "TRUE", "sms:required": "sms:false", - 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We suggest using a stable sample accession from a biosample archive like BioSamples.", - "rdfs:label": "ReplicateType", + "rdfs:comment": "Length of spot barcode read (in bp): number", + "rdfs:label": "SpatialBarcodeLength", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Technicalreplicate" - }, + "sms:displayName": "Spatial Barcode Length", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Smart-seq2", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Smart-seq2", + "rdfs:subClassOf": [ { - "@id": "bts:Biologicalreplicate" + "@id": "bts:SpatialLibraryConstructionMethod" }, { - "@id": "bts:NotApplicable" + "@id": "bts:LibraryConstructionMethod" } ], - "sms:displayName": "Replicate Type", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Smart-seq2", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BulkMethylationAssayType", + "@id": "bts:Smart-SeqV4", "@type": "rdfs:Class", - "rdfs:comment": "Assay types normally determine genomic coverage", - "rdfs:label": "BulkMethylationAssayType", + "rdfs:comment": "TBD", + "rdfs:label": "Smart-SeqV4", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel1" + "@id": "bts:SpatialLibraryConstructionMethod" + }, + { + "@id": "bts:LibraryConstructionMethod" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Wholegenome" - }, + "sms:displayName": "Smart-SeqV4", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:10xV1.0", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "10xV1.0", + "rdfs:subClassOf": [ { - "@id": "bts:TargetedGenome" + "@id": "bts:SpatialLibraryConstructionMethod" }, { - "@id": "bts:BeadchipArray" + "@id": "bts:LibraryConstructionMethod" } ], - "sms:displayName": "Bulk Methylation Assay Type", - "sms:required": "sms:true", - "sms:requiresDependency": [ + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "10xV1.0", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:10xV1.1", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "10xV1.1", + "rdfs:subClassOf": [ { - "@id": "bts:TargetedGenome" + "@id": "bts:SpatialLibraryConstructionMethod" }, { - "@id": "bts:BeadchipArray" + "@id": "bts:LibraryConstructionMethod" } ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "10xV1.1", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TotalDNAInput", + "@id": "bts:10xV2", "@type": "rdfs:Class", - "rdfs:comment": "Overall number of reads for a given sample in digits (microgram, nanogram).", - "rdfs:label": "TotalDNAInput", + "rdfs:comment": "TBD", + "rdfs:label": "10xV2", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylationAssayType" + "@id": "bts:SpatialLibraryConstructionMethod" + }, + { + "@id": "bts:LibraryConstructionMethod" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total DNA Input", + "sms:displayName": "10xV2", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BulkMethylation-seqLevel2", + "@id": "bts:10xV3", "@type": "rdfs:Class", - "rdfs:comment": "Aligned primary data for bulk methylation sequencing, such as gene expression matrix files, VCFs, etc.", - "rdfs:label": "BulkMethylation-seqLevel2", + "rdfs:comment": "TBD", + "rdfs:label": "10xV3", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:SpatialLibraryConstructionMethod" + }, + { + "@id": "bts:LibraryConstructionMethod" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk Methylation-seq Level 2", + "sms:displayName": "10xV3", "sms:required": "sms:false", - "sms:requiresComponent": [ + "sms:validationRules": [] + }, + { + "@id": "bts:10xV3.1", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "10xV3.1", + "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel1" + "@id": "bts:SpatialLibraryConstructionMethod" }, { - "@id": "bts:Biospecimen" + "@id": "bts:LibraryConstructionMethod" } ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:AlignmentWorkflowUrl" - }, - { - "@id": "bts:Trimmer" - }, - { - "@id": "bts:BulkMethylationGenomicReference" - }, - { - "@id": "bts:GenomicReferenceURL" - }, - { - "@id": "bts:IndexFileName" - }, - { - "@id": "bts:AlignmentWorkflowType" - }, - { - "@id": "bts:DuplicateRemovalSoftware" - }, - { - "@id": "bts:MeanCoverage" - }, - { - "@id": "bts:LibraryLayout" - }, - { - "@id": "bts:AverageBaseQuality" - }, - { - "@id": "bts:AverageInsertSize" - }, - { - "@id": "bts:AverageReadLength" - }, - { - "@id": "bts:Contamination" - }, - { - "@id": "bts:ContaminationError" - }, - { - "@id": "bts:PairsOnDiffCHR" - }, - { - "@id": "bts:TotalReads" - }, - { - "@id": "bts:TotalUniquelyMapped" - }, - { - "@id": "bts:TotalUnmappedreads" - }, - { - "@id": "bts:ProportionReadsDuplicated" - }, - { - "@id": "bts:ProportionReadsMapped" - }, - { - "@id": "bts:ProportionTargetsNoCoverage" - }, - { - "@id": "bts:ProportionBaseMismatch" - }, - { - "@id": "bts:ShortReads" - }, + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "10xV3.1", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Drop-seq", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Drop-seq", + "rdfs:subClassOf": [ { - "@id": "bts:ProportionofMinimumCpGCoverage10X" + "@id": "bts:SpatialLibraryConstructionMethod" }, { - "@id": "bts:ProportionCoverage30X" + "@id": "bts:LibraryConstructionMethod" } ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Drop-seq", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Trimmer", + "@id": "bts:InDropsV2", "@type": "rdfs:Class", - "rdfs:comment": "Software used for trimming", - "rdfs:label": "Trimmer", + "rdfs:comment": "TBD", + "rdfs:label": "InDropsV2", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel2" + "@id": "bts:SpatialLibraryConstructionMethod" + }, + { + "@id": "bts:LibraryConstructionMethod" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:FASTXtoolkit" - }, - { - "@id": "bts:SolexaQA" - }, - { - "@id": "bts:Btrim" - }, - { - "@id": "bts:Cutadapt" - }, - { - "@id": "bts:Kraken" - }, - { - "@id": "bts:PRINSEQ" - }, - { - "@id": "bts:Adapterremoval" - }, - { - "@id": "bts:TrimGalore!" - }, - { - "@id": "bts:ConDeTri" - }, + "sms:displayName": "inDropsV2", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:InDropsV3", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "InDropsV3", + "rdfs:subClassOf": [ { - "@id": "bts:ERNE-FILTER" + "@id": "bts:SpatialLibraryConstructionMethod" }, { - "@id": "bts:Trimmo-matic" + "@id": "bts:LibraryConstructionMethod" } ], - "sms:displayName": "Trimmer", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "inDropsV3", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BulkMethylationGenomicReference", + "@id": "bts:TruDrop", "@type": "rdfs:Class", - "rdfs:comment": "The human genome reference used in the alignment of reads", - "rdfs:label": "BulkMethylationGenomicReference", + "rdfs:comment": "TBD", + "rdfs:label": "TruDrop", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel2" + "@id": "bts:SpatialLibraryConstructionMethod" + }, + { + "@id": "bts:LibraryConstructionMethod" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:HG19" - }, + "sms:displayName": "TruDrop", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:NexteraXT", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "NexteraXT", + "rdfs:subClassOf": [ { - "@id": "bts:HG38" + "@id": "bts:SpatialLibraryConstructionMethod" }, { - "@id": "bts:T2TCHM13" + "@id": "bts:LibraryConstructionMethod" } ], - "sms:displayName": "Bulk Methylation Genomic Reference", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Nextera XT", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DuplicateRemovalSoftware", + "@id": "bts:UMIBarcodeOffset", "@type": "rdfs:Class", - "rdfs:comment": "Software used for remove duplicate reads", - "rdfs:label": "DuplicateRemovalSoftware", + "rdfs:comment": "Start position of UMI barcode in the sequence. Values: number, 0 for start of read", + "rdfs:label": "UMIBarcodeOffset", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel2" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Samtoolssort" - }, - { - "@id": "bts:PicardMarkDuplicates" - } - ], - "sms:displayName": "Duplicate Removal Software", + "sms:displayName": "UMI Barcode Offset", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ProportionofMinimumCpGCoverage10X", + "@id": "bts:UMIBarcodeLength", "@type": "rdfs:Class", - "rdfs:comment": "Proportion of all reference bases for whole genome sequencing, or targeted sequencing, that achieves 10X or greater coverage per CpG.", - "rdfs:label": "ProportionofMinimumCpGCoverage10X", + "rdfs:comment": "Length of UMI barcode read (in bp): number", + "rdfs:label": "UMIBarcodeLength", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel2" + "@id": "bts:ScRNA-seqLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Proportion of Minimum CpG Coverage 10X", - "sms:required": "sms:false", + "sms:displayName": "UMI Barcode Length", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BulkMethylation-seqLevel3", + "@id": "bts:NanoStringGeoMxDSPSpatialTranscriptomicsLevel1", "@type": "rdfs:Class", - "rdfs:comment": "Sample level summary data for bulk methylation sequencing, such as t-SNE plot coordinates, etc.", - "rdfs:label": "BulkMethylation-seqLevel3", + "rdfs:comment": "Files contain raw data output from the NanoString GeoMx DSP Pipeline. These can include RCC or DCC Files.", + "rdfs:label": "NanoStringGeoMxDSPSpatialTranscriptomicsLevel1", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk Methylation-seq Level 3", + "sms:displayName": "NanoString GeoMx DSP Spatial Transcriptomics Level 1", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:BulkMethylation-seqLevel2" + "@id": "bts:Biospecimen" }, { - "@id": "bts:Biospecimen" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "sms:requiresDependency": [ @@ -40663,260 +44717,168 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:HTANParentBiospecimenID" }, { "@id": "bts:HTANDataFileID" }, { - "@id": "bts:DMCCallingTool" - }, - { - "@id": "bts:DMCCallingWorkflowURL" - }, - { - "@id": "bts:DMRCallingTool" - }, - { - "@id": "bts:DMRCallingWorkflowURL" - }, - { - "@id": "bts:PUC19methylationratio" - }, - { - "@id": "bts:Lambdamethylationratio" - }, - { - "@id": "bts:DMCdatafileformat" - }, - { - "@id": "bts:DMRdatafileFormat" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:DMCCallingTool", - "@type": "rdfs:Class", - "rdfs:comment": "Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR)", - "rdfs:label": "DMCCallingTool", - "rdfs:subClassOf": [ - { - "@id": "bts:BulkMethylation-seqLevel3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:MethylKit" - }, - { - "@id": "bts:BSmooth" - }, - { - "@id": "bts:BiSeq" + "@id": "bts:SynapseIDofGeoMxDSPPKCFile" }, { - "@id": "bts:MethylSig" + "@id": "bts:GeoMxDSPNGSSequencingPlatform" }, { - "@id": "bts:DSS" + "@id": "bts:GeoMxDSPNGSLibrarySelectionMethod" }, { - "@id": "bts:MOABS" + "@id": "bts:GeoMxDSPNGSLibraryPreparationKitName" }, { - "@id": "bts:DSS-single" + "@id": "bts:GeoMxDSPLibraryPreparationKitVendor" }, { - "@id": "bts:Metilene" + "@id": "bts:GeoMxDSPLibraryPreparationKitVersion" }, { - "@id": "bts:MACAU" + "@id": "bts:SynapseIDofGeoMxLabWorksheetFile" }, { - "@id": "bts:MethylDackel" + "@id": "bts:SoftwareandVersion" } ], - "sms:displayName": "DMC Calling Tool", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:DMCCallingWorkflowURL", + "@id": "bts:SynapseIDofGeoMxDSPPKCFile", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set", - "rdfs:label": "DMCCallingWorkflowURL", + "rdfs:comment": "The Synapse ID(s) associated with the PKC mapping file for the assay. Multiple files are listed as comma separated values.", + "rdfs:label": "SynapseIDofGeoMxDSPPKCFile", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel3" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "DMC Calling Workflow URL", + "sms:displayName": "Synapse ID of GeoMx DSP PKC File", "sms:required": "sms:true", "sms:validationRules": [ - "url" + "list", + "regex match syn\\d+" ] }, { - "@id": "bts:DMRCallingTool", + "@id": "bts:GeoMxDSPNGSSequencingPlatform", "@type": "rdfs:Class", - "rdfs:comment": "Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR)", - "rdfs:label": "DMRCallingTool", + "rdfs:comment": "A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.", + "rdfs:label": "GeoMxDSPNGSSequencingPlatform", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel3" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:MethylKit" - }, - { - "@id": "bts:BSmooth" - }, - { - "@id": "bts:BiSeq" - }, - { - "@id": "bts:MethylSig" - }, - { - "@id": "bts:DSS" - }, - { - "@id": "bts:MOABS" - }, - { - "@id": "bts:DSS-single" - }, - { - "@id": "bts:Metilene" - }, - { - "@id": "bts:MACAU" - } - ], - "sms:displayName": "DMR Calling Tool", - "sms:required": "sms:true", + "sms:displayName": "GeoMx DSP NGS Sequencing Platform", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DMRCallingWorkflowURL", + "@id": "bts:GeoMxDSPNGSLibrarySelectionMethod", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set", - "rdfs:label": "DMRCallingWorkflowURL", + "rdfs:comment": "How RNA molecules are isolated.", + "rdfs:label": "GeoMxDSPNGSLibrarySelectionMethod", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel3" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "DMR Calling Workflow URL", - "sms:required": "sms:true", - "sms:validationRules": [ - "url" - ] + "sms:displayName": "GeoMx DSP NGS Library Selection Method", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:PUC19methylationratio", + "@id": "bts:GeoMxDSPNGSLibraryPreparationKitName", "@type": "rdfs:Class", - "rdfs:comment": "Methylation ratio of mostly methylated pUC19 control, as a percentage", - "rdfs:label": "PUC19methylationratio", + "rdfs:comment": "Name of Library Preparation Kit. String", + "rdfs:label": "GeoMxDSPNGSLibraryPreparationKitName", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel3" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "pUC19 methylation ratio", - "sms:required": "sms:true", + "sms:displayName": "GeoMx DSP NGS Library Preparation Kit Name", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Lambdamethylationratio", + "@id": "bts:GeoMxDSPLibraryPreparationKitVendor", "@type": "rdfs:Class", - "rdfs:comment": "Methylation ratio of mostly unmethylated lambda control, as a percentage", - "rdfs:label": "Lambdamethylationratio", + "rdfs:comment": "Vendor of Library Preparation Kit. String", + "rdfs:label": "GeoMxDSPLibraryPreparationKitVendor", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel3" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Lambda methylation ratio", - "sms:required": "sms:true", + "sms:displayName": "GeoMx DSP Library Preparation Kit Vendor", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DMCdatafileformat", + "@id": "bts:GeoMxDSPLibraryPreparationKitVersion", "@type": "rdfs:Class", - "rdfs:comment": "Format of the data files", - "rdfs:label": "DMCdatafileformat", + "rdfs:comment": "Version of Library Preparation Kit. String", + "rdfs:label": "GeoMxDSPLibraryPreparationKitVersion", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel3" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:BED" - }, - { - "@id": "bts:BedGraph" - } - ], - "sms:displayName": "DMC data file format", - "sms:required": "sms:true", + "sms:displayName": "GeoMx DSP Library Preparation Kit Version", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DMRdatafileFormat", + "@id": "bts:SynapseIDofGeoMxLabWorksheetFile", "@type": "rdfs:Class", - "rdfs:comment": "Format of the data files.", - "rdfs:label": "DMRdatafileFormat", + "rdfs:comment": "Synapse ID(s) of Lab Worksheet Files output from the GeoMx DSP workflow. Multiple files are listed as comma separated values.", + "rdfs:label": "SynapseIDofGeoMxLabWorksheetFile", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel3" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:BED" - }, - { - "@id": "bts:BedGraph" - } - ], - "sms:displayName": "DMR data file Format", - "sms:required": "sms:true", - "sms:validationRules": [] + "sms:displayName": "Synapse ID of GeoMx Lab Worksheet File", + "sms:required": "sms:false", + "sms:validationRules": [ + "list", + "regex match syn\\d+" + ] }, { - "@id": "bts:ImagingLevel1", + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata", "@type": "rdfs:Class", - "rdfs:comment": "Raw imaging data", - "rdfs:label": "ImagingLevel1", + "rdfs:comment": "GeoMx ROI and Segment Metadata Attributes. The assayed biospecimen should be reported one per row with the associated ROI coordinates.", + "rdfs:label": "NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -40925,260 +44887,274 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Imaging Level 1", + "sms:displayName": "NanoString GeoMx DSP ROI RCC Segment Annotation Metadata", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Biospecimen" - } - ], "sms:requiresDependency": [ { - "@id": "bts:Component" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:Filename" + "@id": "bts:Scanname" }, { - "@id": "bts:FileFormat" + "@id": "bts:ROIname" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:Segmentname" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:ROIXCoordinate" }, { - "@id": "bts:ImagingAssayType" + "@id": "bts:ROIYCoordinate" }, { - "@id": "bts:ProtocolLink" + "@id": "bts:Tags" }, { - "@id": "bts:SoftwareandVersion" + "@id": "bts:QCstatus" }, { - "@id": "bts:CommitSHA" + "@id": "bts:ScanHeight" }, { - "@id": "bts:Pre-processingCompleted" + "@id": "bts:ScanWidth" }, { - "@id": "bts:Pre-processingRequired" + "@id": "bts:ScanOffsetX" }, { - "@id": "bts:Comment" + "@id": "bts:ScanOffsetY" + }, + { + "@id": "bts:BindingDensity" + }, + { + "@id": "bts:Positivenormfactor" + }, + { + "@id": "bts:Surfacearea" + }, + { + "@id": "bts:Nucleicount" + }, + { + "@id": "bts:TissueStain" } ], "sms:validationRules": [] }, { - "@id": "bts:ImagingAssayType", + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata", "@type": "rdfs:Class", - "rdfs:comment": "Type of imaging assay", - "rdfs:label": "ImagingAssayType", + "rdfs:comment": "GeoMx ROI and Segment Metadata Attributes. The assayed biospecimen should be reported one per row with the associated ROI coordinates.", + "rdfs:label": "NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "NanoString GeoMx DSP ROI DCC Segment Annotation Metadata", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:H&E" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:CyCIF" + "@id": "bts:Scanname" + }, + { + "@id": "bts:Slidename" + }, + { + "@id": "bts:ROIname" + }, + { + "@id": "bts:Segmentname" + }, + { + "@id": "bts:ROIXCoordinate" + }, + { + "@id": "bts:ROIYCoordinate" + }, + { + "@id": "bts:Tags" + }, + { + "@id": "bts:ScanHeight" }, { - "@id": "bts:T-CyCIF" + "@id": "bts:ScanWidth" }, { - "@id": "bts:IHC" + "@id": "bts:ScanOffsetX" }, { - "@id": "bts:MIHC" + "@id": "bts:ScanOffsetY" }, { - "@id": "bts:MxIF" + "@id": "bts:Surfacearea" }, { - "@id": "bts:SABER" + "@id": "bts:Nucleicount" }, { - "@id": "bts:IMC" + "@id": "bts:SequencingSaturation" }, { - "@id": "bts:CODEX" + "@id": "bts:MapQ30" }, { - "@id": "bts:GeoMX-DSP" + "@id": "bts:Rawreads" }, { - "@id": "bts:MIBI" + "@id": "bts:Stitchedreads" }, { - "@id": "bts:MERFISH" + "@id": "bts:Alignedreads" }, { - "@id": "bts:ExSeq" + "@id": "bts:Deduplicatedreads" }, { - "@id": "bts:RareCyteOrion" + "@id": "bts:InSituNegativemedian" }, { - "@id": "bts:NotApplicable" + "@id": "bts:Biologicalprobemedian" } ], - "sms:displayName": "Imaging Assay Type", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SoftwareandVersion", + "@id": "bts:GeoMxDSPAssayType", "@type": "rdfs:Class", - "rdfs:comment": "Name of software used to generate expression values. String", - "rdfs:label": "SoftwareandVersion", + "rdfs:comment": "The assay type which was used for the GeoMx DSP pipeline.", + "rdfs:label": "GeoMxDSPAssayType", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Software and Version", + "schema:rangeIncludes": [ + { + "@id": "bts:RNAnCounter" + }, + { + "@id": "bts:ProteinnCounter" + }, + { + "@id": "bts:ProteinNGS" + }, + { + "@id": "bts:RNANGS" + } + ], + "sms:displayName": "GeoMx DSP Assay Type", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:CommitSHA", + "@id": "bts:RNAnCounter", "@type": "rdfs:Class", - "rdfs:comment": "Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]", - "rdfs:label": "CommitSHA", + "rdfs:comment": "TBD", + "rdfs:label": "RNAnCounter", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:GeoMxDSPAssayType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Commit SHA", + "sms:displayName": "RNA nCounter", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Pre-processingCompleted", + "@id": "bts:ProteinnCounter", "@type": "rdfs:Class", - "rdfs:comment": "Pre-processing steps completed to convert level 1 raw data to a single level 2 image", - "rdfs:label": "Pre-processingCompleted", + "rdfs:comment": "TBD", + "rdfs:label": "ProteinnCounter", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:GeoMxDSPAssayType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Illuminationcorrection" - }, - { - "@id": "bts:TileStitching" - }, - { - "@id": "bts:Channel/CycleRegistration" - }, - { - "@id": "bts:TMAde-arraying" - }, - { - "@id": "bts:None" - }, - { - "@id": "bts:Other" - } - ], - "sms:displayName": "Pre-processing Completed", - "sms:required": "sms:true", + "sms:displayName": "Protein nCounter", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Pre-processingRequired", + "@id": "bts:ProteinNGS", "@type": "rdfs:Class", - "rdfs:comment": "Pre-processing steps required to convert level 1 raw data to a single level 2 image", - "rdfs:label": "Pre-processingRequired", + "rdfs:comment": "TBD", + "rdfs:label": "ProteinNGS", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:GeoMxDSPAssayType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Illuminationcorrection" - }, - { - "@id": "bts:TileStitching" - }, - { - "@id": "bts:Channel/CycleRegistration" - }, - { - "@id": "bts:TMAde-arraying" - }, - { - "@id": "bts:None" - }, - { - "@id": "bts:Other" - } - ], - "sms:displayName": "Pre-processing Required", - "sms:required": "sms:true", + "sms:displayName": "Protein NGS", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Comment", + "@id": "bts:RNANGS", "@type": "rdfs:Class", - "rdfs:comment": "Free text field (generally for QC comment)", - "rdfs:label": "Comment", + "rdfs:comment": "TBD", + "rdfs:label": "RNANGS", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:GeoMxDSPAssayType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Comment", + "sms:displayName": "RNA NGS", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ImagingLevel2", + "@id": "bts:NanoStringGeoMxDSPSpatialTranscriptomicsLevel3", "@type": "rdfs:Class", - "rdfs:comment": "Raw and pre-processed image data", - "rdfs:label": "ImagingLevel2", + "rdfs:comment": "Files contain processed data from the NanoString GeoMx DSP Pipeline. This level depends on GeoMx Level 1 and Imaging Level 2.", + "rdfs:label": "NanoStringGeoMxDSPSpatialTranscriptomicsLevel3", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Imaging Level 2", + "sms:displayName": "NanoString GeoMx DSP Spatial Transcriptomics Level 3", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:ImagingLevel1" + "@id": "bts:NanoStringGeoMxDSPSpatialTranscriptomicsLevel1" + }, + { + "@id": "bts:ImagingLevel2" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "sms:requiresDependency": [ @@ -41191,9 +45167,6 @@ { "@id": "bts:FileFormat" }, - { - "@id": "bts:HTANParticipantID" - }, { "@id": "bts:HTANParentBiospecimenID" }, @@ -41201,1025 +45174,905 @@ "@id": "bts:HTANDataFileID" }, { - "@id": "bts:ChannelMetadataFilename" - }, - { - "@id": "bts:ImagingAssayType" - }, - { - "@id": "bts:ProtocolLink" - }, - { - "@id": "bts:SoftwareandVersion" - }, - { - "@id": "bts:Microscope" - }, - { - "@id": "bts:Objective" - }, - { - "@id": "bts:NominalMagnification" - }, - { - "@id": "bts:LensNA" - }, - { - "@id": "bts:WorkingDistance" - }, - { - "@id": "bts:WorkingDistanceUnit" - }, - { - "@id": "bts:Immersion" - }, - { - "@id": "bts:Pyramid" - }, - { - "@id": "bts:Zstack" - }, - { - "@id": "bts:Tseries" - }, - { - "@id": "bts:PassedQC" - }, - { - "@id": "bts:Comment" - }, - { - "@id": "bts:FOVnumber" - }, - { - "@id": "bts:FOVX" - }, - { - "@id": "bts:FOVXUnit" - }, - { - "@id": "bts:FOVY" - }, - { - "@id": "bts:FOVYUnit" - }, - { - "@id": "bts:FrameAveraging" - }, - { - "@id": "bts:ImageID" - }, - { - "@id": "bts:DimensionOrder" - }, - { - "@id": "bts:PhysicalSizeX" - }, - { - "@id": "bts:PhysicalSizeXUnit" - }, - { - "@id": "bts:PhysicalSizeY" - }, - { - "@id": "bts:PhysicalSizeYUnit" - }, - { - "@id": "bts:PhysicalSizeZ" - }, - { - "@id": "bts:PhysicalSizeZUnit" - }, - { - "@id": "bts:PixelsBigEndian" - }, - { - "@id": "bts:PlaneCount" + "@id": "bts:GeoMxDSPAssayType" }, { - "@id": "bts:SizeC" + "@id": "bts:SynapseIDofGeoMxDSPROISegmentAnnotationFile" }, { - "@id": "bts:SizeT" + "@id": "bts:GeoMxDSPUniqueProbeCount" }, { - "@id": "bts:SizeX" + "@id": "bts:GeoMxDSPUniqueTargetCount" }, { - "@id": "bts:SizeY" + "@id": "bts:GeoMxDSPGenomicReference" }, { - "@id": "bts:SizeZ" + "@id": "bts:MatrixType" }, { - "@id": "bts:PixelType" + "@id": "bts:GeoMxDSPWorkflowType" }, { - "@id": "bts:MERFISHPositionsFile" + "@id": "bts:GeoMxDSPWorkflowParameterDescription" }, { - "@id": "bts:MERFISHCodebookFile" + "@id": "bts:GeoMxDSPWorkflowLink" } ], "sms:validationRules": [] }, { - "@id": "bts:ChannelMetadataFilename", + "@id": "bts:SynapseIDofGeoMxDSPROISegmentAnnotationFile", "@type": "rdfs:Class", - "rdfs:comment": "Full path within Synapse project of uploaded companion CSV file containing channel-level metadata details", - "rdfs:label": "ChannelMetadataFilename", + "rdfs:comment": "Synapse ID(s) for ROI/Segmentation annotations in the GeoMx DSP experiment.", + "rdfs:label": "SynapseIDofGeoMxDSPROISegmentAnnotationFile", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel2" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Channel Metadata Filename", + "sms:displayName": "Synapse ID of GeoMx DSP ROI Segment Annotation File", "sms:required": "sms:true", - "sms:validationRules": [] + "sms:validationRules": [ + "list", + "regex match syn\\d+" + ] }, { - "@id": "bts:Microscope", + "@id": "bts:GeoMxDSPUniqueProbeCount", "@type": "rdfs:Class", - "rdfs:comment": "Microscope type (manufacturer, model, etc) used for this experiment", - "rdfs:label": "Microscope", + "rdfs:comment": "Total number of unique probes reported.", + "rdfs:label": "GeoMxDSPUniqueProbeCount", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Microscope", - "sms:required": "sms:true", - "sms:validationRules": [] + "sms:displayName": "GeoMx DSP Unique Probe Count", + "sms:required": "sms:false", + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:Objective", + "@id": "bts:GeoMxDSPUniqueTargetCount", "@type": "rdfs:Class", - "rdfs:comment": "Objective", - "rdfs:label": "Objective", + "rdfs:comment": "Total number of unique genes reported.", + "rdfs:label": "GeoMxDSPUniqueTargetCount", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Objective", + "sms:displayName": "GeoMx DSP Unique Target Count", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:NominalMagnification", + "@id": "bts:GeoMxDSPGenomicReference", "@type": "rdfs:Class", - "rdfs:comment": "The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units)", - "rdfs:label": "NominalMagnification", + "rdfs:comment": "Exact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/). Only applicable to some applications in GeoMx", + "rdfs:label": "GeoMxDSPGenomicReference", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "NominalMagnification", - "sms:required": "sms:true", + "sms:displayName": "GeoMx DSP Genomic Reference", + "sms:required": "sms:false", "sms:validationRules": [ "num" ] }, { - "@id": "bts:LensNA", + "@id": "bts:GeoMxDSPWorkflowType", "@type": "rdfs:Class", - "rdfs:comment": "The numerical aperture of the lens. Floating point value > 0.", - "rdfs:label": "LensNA", + "rdfs:comment": "Generic name for the workflow used to analyze the GeoMx DSP data set.", + "rdfs:label": "GeoMxDSPWorkflowType", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "LensNA", + "sms:displayName": "GeoMx DSP Workflow Type", "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] + "sms:validationRules": [] }, { - "@id": "bts:WorkingDistance", + "@id": "bts:GeoMxDSPWorkflowParameterDescription", "@type": "rdfs:Class", - "rdfs:comment": "The working distance of the lens, expressed as a floating point number. Floating point > 0.", - "rdfs:label": "WorkingDistance", + "rdfs:comment": "Parameters used to run the GeoMx DSP workflow.", + "rdfs:label": "GeoMxDSPWorkflowParameterDescription", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "WorkingDistance", + "sms:displayName": "GeoMx DSP Workflow Parameter Description", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:WorkingDistanceUnit" - } - ], "sms:validationRules": [] }, { - "@id": "bts:WorkingDistanceUnit", + "@id": "bts:GeoMxDSPWorkflowLink", "@type": "rdfs:Class", - "rdfs:comment": "The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "WorkingDistanceUnit", + "rdfs:comment": "Link to workflow or command. DockStore.org recommended. URL", + "rdfs:label": "GeoMxDSPWorkflowLink", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Cm" - }, - { - "@id": "bts:Mm" - }, - { - "@id": "bts:Μm" - }, - { - "@id": "bts:Nm" - }, - { - "@id": "bts:Å" - } - ], - "sms:displayName": "WorkingDistanceUnit", + "sms:displayName": "GeoMx DSP Workflow Link", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Immersion", + "@id": "bts:Scanname", "@type": "rdfs:Class", - "rdfs:comment": "Immersion medium", - "rdfs:label": "Immersion", + "rdfs:comment": "GeoMx Scan name (as appears in Segment Summary)", + "rdfs:label": "Scanname", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Air" - }, - { - "@id": "bts:Oil" - }, + "sms:displayName": "Scan name", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:ROIname", + "@type": "rdfs:Class", + "rdfs:comment": "ROI name (application generated). For Xenium this is referred to as the “region name”", + "rdfs:label": "ROIname", + "rdfs:subClassOf": [ { - "@id": "bts:Water" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" }, { - "@id": "bts:Other" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], - "sms:displayName": "Immersion", - "sms:required": "sms:false", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "ROI name", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Pyramid", + "@id": "bts:Segmentname", "@type": "rdfs:Class", - "rdfs:comment": "Does data file contain pyramid of images", - "rdfs:label": "Pyramid", + "rdfs:comment": "Name given to segment at time of generation", + "rdfs:label": "Segmentname", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Segment name", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:ROIXCoordinate", + "@type": "rdfs:Class", + "rdfs:comment": "X location within the image", + "rdfs:label": "ROIXCoordinate", + "rdfs:subClassOf": [ { - "@id": "bts:Yes" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" }, { - "@id": "bts:No" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], - "sms:displayName": "Pyramid", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "ROI X Coordinate", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Zstack", + "@id": "bts:ROIYCoordinate", "@type": "rdfs:Class", - "rdfs:comment": "Does data file contain a Z-stack of images", - "rdfs:label": "Zstack", + "rdfs:comment": "Y location within the image", + "rdfs:label": "ROIYCoordinate", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "ROI Y Coordinate", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Tags", + "@type": "rdfs:Class", + "rdfs:comment": "Unique descriptor of a variable group (ie. MAPK+)", + "rdfs:label": "Tags", + "rdfs:subClassOf": [ { - "@id": "bts:Yes" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" }, { - "@id": "bts:No" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], - "sms:displayName": "Zstack", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Tags", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Tseries", + "@id": "bts:QCstatus", "@type": "rdfs:Class", - "rdfs:comment": "Does data file contain a time-series of images", - "rdfs:label": "Tseries", + "rdfs:comment": "ROI quality control flag as reported by the application", + "rdfs:label": "QCstatus", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, + "sms:displayName": "QC status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ScanHeight", + "@type": "rdfs:Class", + "rdfs:comment": "Height of the scan for GeoMx Analysis", + "rdfs:label": "ScanHeight", + "rdfs:subClassOf": [ { - "@id": "bts:No" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" } ], - "sms:displayName": "Tseries", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Scan Height", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PassedQC", + "@id": "bts:ScanWidth", "@type": "rdfs:Class", - "rdfs:comment": "Did all channels pass QC (if not add free text Comment)", - "rdfs:label": "PassedQC", + "rdfs:comment": "Width of the scan for GeoMx Analysis", + "rdfs:label": "ScanWidth", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No-ChannelsQC" - } - ], - "sms:displayName": "Passed QC", + "sms:displayName": "Scan Width", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:FOVnumber", + "@id": "bts:ScanOffsetX", "@type": "rdfs:Class", - "rdfs:comment": "Index of FOV (as it pertains to its sequence order). Integer >= 1", - "rdfs:label": "FOVnumber", + "rdfs:comment": "Offset X of the scan for GeoMx Analysis", + "rdfs:label": "ScanOffsetX", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "FOV number", - "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] + "sms:displayName": "Scan Offset X", + "sms:required": "sms:true", + "sms:validationRules": [] }, { - "@id": "bts:FOVX", + "@id": "bts:ScanOffsetY", "@type": "rdfs:Class", - "rdfs:comment": "Field of view X dimension. Floating point", - "rdfs:label": "FOVX", + "rdfs:comment": "Offset Y of the scan for GeoMx Analysis", + "rdfs:label": "ScanOffsetY", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "FOVX", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:FOVXUnit" - } - ], - "sms:validationRules": [ - "num" - ] + "sms:displayName": "Scan Offset Y", + "sms:required": "sms:true", + "sms:validationRules": [] }, { - "@id": "bts:FOVXUnit", + "@id": "bts:BindingDensity", "@type": "rdfs:Class", - "rdfs:comment": "Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "FOVXUnit", + "rdfs:comment": "The binding density as reported by the application", + "rdfs:label": "BindingDensity", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Cm" - }, - { - "@id": "bts:Mm" - }, - { - "@id": "bts:Μm" - }, - { - "@id": "bts:Nm" - }, - { - "@id": "bts:Å" - } - ], - "sms:displayName": "FOVXUnit", + "sms:displayName": "Binding Density", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FOVY", + "@id": "bts:Positivenormfactor", "@type": "rdfs:Class", - "rdfs:comment": "Field of view Y dimension. Floating point value", - "rdfs:label": "FOVY", + "rdfs:comment": "The Positive Control Normalization factor calculated using pos-hyb controls", + "rdfs:label": "Positivenormfactor", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "FOVY", + "sms:displayName": "Positive norm factor", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:FOVYUnit" - } - ], - "sms:validationRules": [ - "num" - ] + "sms:validationRules": [] }, { - "@id": "bts:FOVYUnit", + "@id": "bts:Surfacearea", "@type": "rdfs:Class", - "rdfs:comment": "Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "FOVYUnit", + "rdfs:comment": "Surface area of the ROI in square microns (µm^2). In CosMx, this is referred to as the Scan Area. In Xenium, this is referred to as the Region Area", + "rdfs:label": "Surfacearea", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + }, + { + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Cm" - }, - { - "@id": "bts:Mm" - }, - { - "@id": "bts:Μm" - }, + "sms:displayName": "Surface area", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Nucleicount", + "@type": "rdfs:Class", + "rdfs:comment": "Number of nuclei detected in the segment (if applicable)", + "rdfs:label": "Nucleicount", + "rdfs:subClassOf": [ { - "@id": "bts:Nm" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" }, { - "@id": "bts:Å" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], - "sms:displayName": "FOVYUnit", - "sms:required": "sms:false", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Nuclei count", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:FrameAveraging", + "@id": "bts:TissueStain", "@type": "rdfs:Class", - "rdfs:comment": "Number of frames averaged together (if no averaging, set to 1). Integer >= 1", - "rdfs:label": "FrameAveraging", + "rdfs:comment": "e.g. CD45 or PanCK (if masking was performed)", + "rdfs:label": "TissueStain", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Frame Averaging", + "sms:displayName": "Tissue Stain", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ImageID", + "@id": "bts:Slidename", "@type": "rdfs:Class", - "rdfs:comment": "Unique internal image identifier. eg \"Image:0\". (To be extracted from OME-XML)", - "rdfs:label": "ImageID", + "rdfs:comment": "Similar to a Run ID, the slide name indicates the slide a given ROI is linked to (as reported in Segment Summary).", + "rdfs:label": "Slidename", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Image ID", - "sms:required": "sms:true", + "sms:displayName": "Slide name", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DimensionOrder", + "@id": "bts:Rawreads", "@type": "rdfs:Class", - "rdfs:comment": "The order in which the individual planes of data are interleaved.", - "rdfs:label": "DimensionOrder", + "rdfs:comment": "Reads not yet analyzed in any way to be used for data analysis. The number of reads that pass filter from the flow cell represented in the FASTQ file.", + "rdfs:label": "Rawreads", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:XYZCT" - }, - { - "@id": "bts:XYZTC" - }, - { - "@id": "bts:XYCTZ" - }, - { - "@id": "bts:XYCZT" - }, - { - "@id": "bts:XYTZC" - }, - { - "@id": "bts:ZYX" - } - ], - "sms:displayName": "DimensionOrder", - "sms:required": "sms:true", + "sms:displayName": "Raw reads", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PhysicalSizeX", + "@id": "bts:Stitchedreads", "@type": "rdfs:Class", - "rdfs:comment": "Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.", - "rdfs:label": "PhysicalSizeX", + "rdfs:comment": "Represents consensus from the overlapping sequence of read 1 and 2. This is a % of the aligned reads that were overlapped and consensus confirmed, usually upward of 80% but less in terms of number of reads than aligned reads", + "rdfs:label": "Stitchedreads", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "PhysicalSizeX", - "sms:required": "sms:true", - "sms:requiresDependency": [ - { - "@id": "bts:PhysicalSizeXUnit" - } - ], + "sms:displayName": "Stitched reads", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PhysicalSizeXUnit", + "@id": "bts:Alignedreads", "@type": "rdfs:Class", - "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "PhysicalSizeXUnit", + "rdfs:comment": "Is a sequence that has been aligned to a gene/probe. Typically these reads can number from the hundreds of thousands to tens of millions. In GeoMx alignment is via mapping the RTS ID to a white list of sequences that represent targets.", + "rdfs:label": "Alignedreads", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Cm" - }, - { - "@id": "bts:Mm" - }, - { - "@id": "bts:Μm" - }, - { - "@id": "bts:Nm" - }, - { - "@id": "bts:Å" - } - ], - "sms:displayName": "PhysicalSizeXUnit", - "sms:required": "sms:true", + "sms:displayName": "Aligned reads", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PhysicalSizeY", + "@id": "bts:Deduplicatedreads", "@type": "rdfs:Class", - "rdfs:comment": "Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.", - "rdfs:label": "PhysicalSizeY", + "rdfs:comment": "Is the replacement of blocks of duplicate data with a Virtual Index Pointer linking the new sub-block to the existing block of data in a duplicate repository. This is used to reduce the amount of space need to store the data.", + "rdfs:label": "Deduplicatedreads", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "PhysicalSizeY", - "sms:required": "sms:true", - "sms:requiresDependency": [ - { - "@id": "bts:PhysicalSizeYUnit" - } - ], + "sms:displayName": "Deduplicated reads", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PhysicalSizeYUnit", + "@id": "bts:InSituNegativemedian", "@type": "rdfs:Class", - "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "PhysicalSizeYUnit", + "rdfs:comment": "Is the median of all negative control probes for a given segment. A measure of signal to background for each segment.", + "rdfs:label": "InSituNegativemedian", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Cm" - }, - { - "@id": "bts:Mm" - }, - { - "@id": "bts:Μm" - }, - { - "@id": "bts:Nm" - }, - { - "@id": "bts:Å" - } - ], - "sms:displayName": "PhysicalSizeYUnit", - "sms:required": "sms:true", + "sms:displayName": "In Situ Negative median", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PhysicalSizeZ", + "@id": "bts:Biologicalprobemedian", "@type": "rdfs:Class", - "rdfs:comment": "Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.", - "rdfs:label": "PhysicalSizeZ", + "rdfs:comment": "Is the median count from all probes except the negative control probes. A measure of signal to background for each segment", + "rdfs:label": "Biologicalprobemedian", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "PhysicalSizeZ", - "sms:required": "sms:true", - "sms:requiresDependency": [ - { - "@id": "bts:PhysicalSizeZUnit" - } - ], + "sms:displayName": "Biological probe median", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PhysicalSizeZUnit", + "@id": "bts:HI-C-seqLevel1", "@type": "rdfs:Class", - "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "PhysicalSizeZUnit", + "rdfs:comment": "Unaligned sequence data", + "rdfs:label": "HI-C-seqLevel1", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "HI-C-seq Level 1", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:Cm" + "@id": "bts:Biospecimen" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:Mm" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:Μm" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:Nm" + "@id": "bts:Filename" }, { - "@id": "bts:Å" - } - ], - "sms:displayName": "PhysicalSizeZUnit", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:PixelsBigEndian", - "@type": "rdfs:Class", - "rdfs:comment": "Boolean (True/False)", - "rdfs:label": "PixelsBigEndian", - "rdfs:subClassOf": [ + "@id": "bts:FileFormat" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:GenomicReference" + }, { - "@id": "bts:True" + "@id": "bts:SequencingPlatform" }, { - "@id": "bts:False" + "@id": "bts:NucleicAcidSource" + }, + { + "@id": "bts:TechnicalReplicateGroup" + }, + { + "@id": "bts:TranspositionReaction" + }, + { + "@id": "bts:CrosslinkingCondtion" + }, + { + "@id": "bts:DNADigestionCondition" + }, + { + "@id": "bts:NucleiPermeabilizationMethod" + }, + { + "@id": "bts:LigationCondition" + }, + { + "@id": "bts:BiotinEnrichment" + }, + { + "@id": "bts:DNAInputAmount" + }, + { + "@id": "bts:TotalReads" + }, + { + "@id": "bts:ProtocolLink" } ], - "sms:displayName": "Pixels BigEndian", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PlaneCount", + "@id": "bts:CrosslinkingCondtion", "@type": "rdfs:Class", - "rdfs:comment": "Number of Z-planes (not to be confused with downsampled \"pyramid\"). Integer >=1", - "rdfs:label": "PlaneCount", + "rdfs:comment": "Detailed condition for DNA crosslinking", + "rdfs:label": "CrosslinkingCondtion", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "PlaneCount", + "sms:displayName": "Crosslinking Condtion", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SizeC", + "@id": "bts:DNADigestionCondition", "@type": "rdfs:Class", - "rdfs:comment": "Number of channels. Integer >= 1", - "rdfs:label": "SizeC", + "rdfs:comment": "Enzymes and treatment length/temperature for genome digestion", + "rdfs:label": "DNADigestionCondition", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SizeC", + "sms:displayName": "DNA Digestion Condition", "sms:required": "sms:true", - "sms:validationRules": [ - "int" - ] + "sms:validationRules": [] }, { - "@id": "bts:SizeT", + "@id": "bts:NucleiPermeabilizationMethod", "@type": "rdfs:Class", - "rdfs:comment": "Number of time points. Integer >= 1", - "rdfs:label": "SizeT", + "rdfs:comment": "Detergent and treatment condition for nuclei permeabilization and crosslinking softening", + "rdfs:label": "NucleiPermeabilizationMethod", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SizeT", + "sms:displayName": "Nuclei Permeabilization Method", "sms:required": "sms:true", - "sms:validationRules": [ - "int" - ] + "sms:validationRules": [] }, { - "@id": "bts:SizeX", + "@id": "bts:LigationCondition", "@type": "rdfs:Class", - "rdfs:comment": "Size of image: X dimension (in pixels). Integer >= 1", - "rdfs:label": "SizeX", + "rdfs:comment": "Name of ligase and condition for proximity ligation", + "rdfs:label": "LigationCondition", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SizeX", + "sms:displayName": "Ligation Condition", "sms:required": "sms:true", - "sms:validationRules": [ - "int" - ] + "sms:validationRules": [] }, { - "@id": "bts:SizeY", + "@id": "bts:BiotinEnrichment", "@type": "rdfs:Class", - "rdfs:comment": "Size of image: Y dimension (in pixels). Integer >= 1", - "rdfs:label": "SizeY", + "rdfs:comment": "Whether biotin is used for enriching ligation product", + "rdfs:label": "BiotinEnrichment", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SizeY", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + } + ], + "sms:displayName": "Biotin Enrichment", "sms:required": "sms:true", - "sms:validationRules": [ - "int" - ] + "sms:validationRules": [] }, { - "@id": "bts:SizeZ", + "@id": "bts:DNAInputAmount", "@type": "rdfs:Class", - "rdfs:comment": "Size of image: Z dimension (in pixels). Integer >= 1", - "rdfs:label": "SizeZ", + "rdfs:comment": "Amount of DNA for library construction, in nanograms.", + "rdfs:label": "DNAInputAmount", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "SizeZ", + "sms:displayName": "DNA Input Amount", "sms:required": "sms:true", "sms:validationRules": [ "int" ] }, { - "@id": "bts:PixelType", + "@id": "bts:HI-C-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Data type for each pixel value. E.g. \"uint16\"", - "rdfs:label": "PixelType", + "rdfs:comment": "Aligned read pairs, contact matrix", + "rdfs:label": "HI-C-seqLevel2", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "HI-C-seq Level 2", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:Int8" + "@id": "bts:HI-C-seqLevel1" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:Int16" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:Int32" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:Uint8" + "@id": "bts:Filename" }, { - "@id": "bts:Uint16" + "@id": "bts:FileFormat" }, { - "@id": "bts:Uint32" + "@id": "bts:GenomicReference" }, { - "@id": "bts:Float" + "@id": "bts:AlignedReadLength" + }, + { + "@id": "bts:Tool" }, { - "@id": "bts:Double" + "@id": "bts:Resolution" }, { - "@id": "bts:Bit" + "@id": "bts:NormalizationMethod" } ], - "sms:displayName": "PixelType", + "sms:validationRules": [] + }, + { + "@id": "bts:AlignedReadLength", + "@type": "rdfs:Class", + "rdfs:comment": "Read length used for alignment if hard trimming was applied", + "rdfs:label": "AlignedReadLength", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Aligned Read Length", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MERFISHPositionsFile", + "@id": "bts:Tool", "@type": "rdfs:Class", - "rdfs:comment": "The positions file is an auxiliary MERFISH file that describes the location of bead positions in the assay.", - "rdfs:label": "MERFISHPositionsFile", + "rdfs:comment": "Were any software or computational tools generated for this content", + "rdfs:label": "Tool", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Publication" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MERFISH Positions File", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + } + ], + "sms:displayName": "Tool", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MERFISHCodebookFile", + "@id": "bts:Resolution", "@type": "rdfs:Class", - "rdfs:comment": "The codebook is an auxiliary MERFISH file that describes how each grouping of bits is converted to a gene name.", - "rdfs:label": "MERFISHCodebookFile", + "rdfs:comment": "Binning size used for generating contact matrix, in basepair.", + "rdfs:label": "Resolution", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MERFISH Codebook File", - "sms:required": "sms:false", + "sms:displayName": "Resolution", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ImagingLevel3Segmentation", + "@id": "bts:HI-C-seqLevel3", "@type": "rdfs:Class", - "rdfs:comment": "Object segmentations", - "rdfs:label": "ImagingLevel3Segmentation", + "rdfs:comment": "Summary data for the HI-C-seq assay.", + "rdfs:label": "HI-C-seqLevel3", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Imaging Level 3 Segmentation", + "sms:displayName": "HI-C-seq Level 3", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:ImagingLevel2" + "@id": "bts:HI-C-seqLevel2" } ], "sms:requiresDependency": [ { "@id": "bts:Component" }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, { "@id": "bts:HTANParentDataFileID" }, @@ -42227,34 +46080,37 @@ "@id": "bts:HTANDataFileID" }, { - "@id": "bts:ImagingSegmentationDataType" + "@id": "bts:Filename" }, { - "@id": "bts:Parameterfile" + "@id": "bts:FileFormat" }, { - "@id": "bts:SoftwareandVersion" + "@id": "bts:GenomicReference" }, { - "@id": "bts:CommitSHA" + "@id": "bts:StripeCalling" }, { - "@id": "bts:ImagingObjectClass" + "@id": "bts:LoopWindow" }, { - "@id": "bts:NumberofObjects" + "@id": "bts:StripeWindow" + }, + { + "@id": "bts:LoopCalling" } ], "sms:validationRules": [] }, { - "@id": "bts:ImagingSegmentationDataType", + "@id": "bts:StripeCalling", "@type": "rdfs:Class", - "rdfs:comment": "Specifies how the segmentation is stored", - "rdfs:label": "ImagingSegmentationDataType", + "rdfs:comment": "Tool used for identifying architectural stripe-forming, interaction hotspots.", + "rdfs:label": "StripeCalling", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -42262,557 +46118,526 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Mask" - }, - { - "@id": "bts:Outline" - }, - { - "@id": "bts:Polygon" - }, - { - "@id": "bts:ProbabilityMap" + "@id": "bts:MACS2" }, { - "@id": "bts:Point" + "@id": "bts:Other" } ], - "sms:displayName": "Imaging Segmentation Data Type", + "sms:displayName": "Stripe Calling", "sms:required": "sms:true", - "sms:validationRules": [] + "sms:validationRules": [ + "list", + "-?\\d+" + ] }, { - "@id": "bts:Parameterfile", + "@id": "bts:LoopWindow", "@type": "rdfs:Class", - "rdfs:comment": "Path in Syanpse to a text file listing algorithm version numbers and relevant parameters needed to reproduce the analysis", - "rdfs:label": "Parameterfile", + "rdfs:comment": "Binning size used for calling significant dot interactions (loops)", + "rdfs:label": "LoopWindow", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Parameter file", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "Loop Window", + "sms:required": "sms:true", + "sms:validationRules": [ + "list like ", + " regex search -?\\d+" + ] }, { - "@id": "bts:ImagingObjectClass", + "@id": "bts:StripeWindow", "@type": "rdfs:Class", - "rdfs:comment": "Defines the structure that the mask delineates", - "rdfs:label": "ImagingObjectClass", + "rdfs:comment": "Binning size used for calling significant architectural stripes. Can be an integer or comma-separated list of integers indicating bin size and sliding window size if different.", + "rdfs:label": "StripeWindow", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Nucleus" - }, - { - "@id": "bts:Cytoplasm" - }, - { - "@id": "bts:Plasmamembrane" - }, - { - "@id": "bts:Wholecell" - }, - { - "@id": "bts:Spot" - }, - { - "@id": "bts:ImagingObjectClassOther" - } - ], - "sms:displayName": "Imaging Object Class", + "sms:displayName": "Stripe Window", "sms:required": "sms:true", "sms:validationRules": [ - "list like" + "list like ", + " regex search -?\\d+" ] }, { - "@id": "bts:NumberofObjects", + "@id": "bts:LoopCalling", "@type": "rdfs:Class", - "rdfs:comment": "The number of objects (eg cells) described", - "rdfs:label": "NumberofObjects", + "rdfs:comment": "Tool used for identifying loop interactions", + "rdfs:label": "LoopCalling", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Number of Objects", + "schema:rangeIncludes": [ + { + "@id": "bts:HiCCUPS" + }, + { + "@id": "bts:Cooltools" + }, + { + "@id": "bts:Other" + } + ], + "sms:displayName": "Loop Calling", "sms:required": "sms:true", - "sms:validationRules": [ - "int" - ] + "sms:validationRules": [] }, { - "@id": "bts:ImagingLevel3Image", + "@id": "bts:Yes", "@type": "rdfs:Class", - "rdfs:comment": "Quality controlled imaging data", - "rdfs:label": "ImagingLevel3Image", + "rdfs:comment": "TBD", + "rdfs:label": "Yes", "rdfs:subClassOf": [ { - "@id": "bts:Assay" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Imaging Level 3 Image", - "sms:required": "sms:false", - "sms:requiresComponent": [ + "@id": "bts:BiotinEnrichment" + }, { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:ChannelPassedQC" }, { - "@id": "bts:ImagingLevel2" - } - ], - "sms:requiresDependency": [ + "@id": "bts:Pyramid" + }, { - "@id": "bts:Component" + "@id": "bts:Zstack" }, { - "@id": "bts:Filename" + "@id": "bts:Tseries" }, { - "@id": "bts:FileFormat" + "@id": "bts:PassedQC" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:WellIndex" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:CryopreservedCellsinSample" }, { - "@id": "bts:HTANParentChannelMetadataID" + "@id": "bts:PrematureAtBirth" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:AlcoholHistory" }, { - "@id": "bts:ImagingAssayType" + "@id": "bts:AsbestosExposure" }, { - "@id": "bts:ProtocolLink" + "@id": "bts:CoalDustExposure" }, { - "@id": "bts:SoftwareandVersion" + "@id": "bts:EnvironmentalTobaccoSmokeExposure" }, { - "@id": "bts:Microscope" + "@id": "bts:RadonExposure" }, { - "@id": "bts:Objective" + "@id": "bts:RespirableCrystallineSilicaExposure" }, { - "@id": "bts:NominalMagnification" + "@id": "bts:SecondhandSmokeasChild" }, { - "@id": "bts:LensNA" + "@id": "bts:HepatitisSustainedVirologicalResponse" }, { - "@id": "bts:WorkingDistance" + "@id": "bts:HAARTTreatmentIndicator" }, { - "@id": "bts:Immersion" + "@id": "bts:RiskFactorTreatment" }, { - "@id": "bts:Pyramid" + "@id": "bts:ChemoConcurrenttoRadiation" }, { - "@id": "bts:Zstack" + "@id": "bts:TreatmentEffectIndicator" }, { - "@id": "bts:Tseries" + "@id": "bts:SatelliteMetastasisPresentIndicator" }, { - "@id": "bts:PassedQC" + "@id": "bts:Immunosuppression" }, { - "@id": "bts:Comment" + "@id": "bts:COVID19OccurrenceIndicator" }, { - "@id": "bts:FOVnumber" + "@id": "bts:COVID19PositiveLabTestIndicator" }, { - "@id": "bts:FOVX" + "@id": "bts:COVID19CancerTreatmentFollowup" }, { - "@id": "bts:FOVY" + "@id": "bts:KnownGeneticPredispositionMutation" }, { - "@id": "bts:FrameAveraging" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:HTANParentChannelMetadataID", - "@type": "rdfs:Class", - "rdfs:comment": "HTAN ID for a level 3 channels table.", - "rdfs:label": "HTANParentChannelMetadataID", - "rdfs:subClassOf": [ + "@id": "bts:MismatchRepairMutation" + }, { - "@id": "bts:ImagingLevel4" + "@id": "bts:NonNodalTumorDeposits" + }, + { + "@id": "bts:PregnantatDiagnosis" + }, + { + "@id": "bts:PriorMalignancy" + }, + { + "@id": "bts:PriorTreatment" + }, + { + "@id": "bts:LymphaticInvasionPresent" + }, + { + "@id": "bts:PerineuralInvasionPresent" + }, + { + "@id": "bts:SynchronousMalignancy" + }, + { + "@id": "bts:TumorConfinedtoOrganofOrigin" + }, + { + "@id": "bts:HistoryofPriorColonPolyps" + }, + { + "@id": "bts:FamilyColonCancerHistoryIndicator" + }, + { + "@id": "bts:FamilyMedicalHistoryColorectalPolypDiagnosis" + }, + { + "@id": "bts:PatientColonoscopyPerformedIndicator" + }, + { + "@id": "bts:ColorectalCancerKRASIndicator" + }, + { + "@id": "bts:ColonPolypOccurenceIndicator" + }, + { + "@id": "bts:FamilyHistoryColorectalPolyp" + }, + { + "@id": "bts:ColorectalPolypNewIndicator" + }, + { + "@id": "bts:HormoneTherapyBreastCancerPreventionIndicator" + }, + { + "@id": "bts:MultifocalBreastCarcinomaPresentIndicator" + }, + { + "@id": "bts:MulticentricBreastCarcinomaPresentIndicator" + }, + { + "@id": "bts:HistoryofBlisteringSunburn" + }, + { + "@id": "bts:Tool" + }, + { + "@id": "bts:PublicationcontainsHTANID" + }, + { + "@id": "bts:BarrettsEsophagusGobletCellsPresent" + }, + { + "@id": "bts:TreatmentorTherapy" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HTAN Parent Channel Metadata ID", - "sms:required": "sms:true", + "sms:displayName": "yes", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ImagingLevel3Channels", + "@id": "bts:No", "@type": "rdfs:Class", - "rdfs:comment": "Channel-level Metadata Attributes", - "rdfs:label": "ImagingLevel3Channels", + "rdfs:comment": "TBD", + "rdfs:label": "No", "rdfs:subClassOf": [ { - "@id": "bts:Assay" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Imaging Level 3 Channels", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:HTANChannelMetadataID" + "@id": "bts:BiotinEnrichment" }, { - "@id": "bts:ChannelID" + "@id": "bts:Pyramid" }, { - "@id": "bts:ChannelName" + "@id": "bts:Zstack" }, { - "@id": "bts:ChannelPassedQC" + "@id": "bts:Tseries" }, { - "@id": "bts:CycleNumber" + "@id": "bts:WellIndex" }, { - "@id": "bts:SubCycleNumber" + "@id": "bts:CryopreservedCellsinSample" }, { - "@id": "bts:AntibodyRole" + "@id": "bts:ToTrimAdapterSequence" }, { - "@id": "bts:TargetName" + "@id": "bts:AppliedHardTrimming" }, { - "@id": "bts:AntibodyName" + "@id": "bts:PseudoAlignmentUsed" }, { - "@id": "bts:RRIDidentifier" + "@id": "bts:FusionGeneDetected" }, { - "@id": "bts:Fluorophore" + "@id": "bts:PrematureAtBirth" }, { - "@id": "bts:Clone" + "@id": "bts:AlcoholHistory" }, { - "@id": "bts:Lot" + "@id": "bts:AsbestosExposure" }, { - "@id": "bts:Vendor" + "@id": "bts:CoalDustExposure" }, { - "@id": "bts:CatalogNumber" + "@id": "bts:EnvironmentalTobaccoSmokeExposure" }, { - "@id": "bts:ExcitationWavelength" + "@id": "bts:RadonExposure" }, { - "@id": "bts:EmissionWavelength" + "@id": "bts:RespirableCrystallineSilicaExposure" }, { - "@id": "bts:ExcitationBandwidth" + "@id": "bts:SecondhandSmokeasChild" }, { - "@id": "bts:EmissionBandwidth" + "@id": "bts:HepatitisSustainedVirologicalResponse" }, { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:HAARTTreatmentIndicator" }, { - "@id": "bts:MetalIsotopeMass" + "@id": "bts:ProgressionorRecurrence" }, { - "@id": "bts:OligoBarcodeUpperStrand" + "@id": "bts:RiskFactorTreatment" }, { - "@id": "bts:OligoBarcodeLowerStrand" + "@id": "bts:ChemoConcurrenttoRadiation" }, { - "@id": "bts:Dilution" + "@id": "bts:TreatmentEffectIndicator" }, { - "@id": "bts:Concentration" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel1", - "@type": "rdfs:Class", - "rdfs:comment": "Files contain raw RNA-seq data associated with spot/slide data.", - "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel1", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 1", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Biospecimen" - } - ], - "sms:requiresDependency": [ + "@id": "bts:SatelliteMetastasisPresentIndicator" + }, { - "@id": "bts:Component" + "@id": "bts:Immunosuppression" }, { - "@id": "bts:Filename" + "@id": "bts:COVID19OccurrenceIndicator" }, { - "@id": "bts:RunID" + "@id": "bts:COVID19PositiveLabTestIndicator" }, { - "@id": "bts:FileFormat" + "@id": "bts:COVID19CancerTreatmentFollowup" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:KnownGeneticPredispositionMutation" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:MismatchRepairMutation" }, { - "@id": "bts:ReadIndicator" + "@id": "bts:NonNodalTumorDeposits" }, { - "@id": "bts:SpatialRead1" + "@id": "bts:PregnantatDiagnosis" }, { - "@id": "bts:SpatialRead2" + "@id": "bts:PriorMalignancy" }, { - "@id": "bts:SpatialLibraryConstructionMethod" + "@id": "bts:PriorTreatment" }, { - "@id": "bts:LibraryPreparationDaysfromIndex" + "@id": "bts:AnaplasiaPresent" }, { - "@id": "bts:SequencingLibraryConstructionDaysfromIndex" + "@id": "bts:LymphaticInvasionPresent" }, { - "@id": "bts:EndBias" + "@id": "bts:PerineuralInvasionPresent" }, { - "@id": "bts:ReverseTranscriptionPrimer" + "@id": "bts:SynchronousMalignancy" }, { - "@id": "bts:SequencingPlatform" + "@id": "bts:TumorConfinedtoOrganofOrigin" }, { - "@id": "bts:CaptureArea" + "@id": "bts:VascularInvasionPresent" }, { - "@id": "bts:ProtocolLink" + "@id": "bts:HistoryofPriorColonPolyps" }, { - "@id": "bts:SlideVersion" + "@id": "bts:FamilyColonCancerHistoryIndicator" }, { - "@id": "bts:SlideID" + "@id": "bts:FamilyMedicalHistoryColorectalPolypDiagnosis" }, { - "@id": "bts:ImageRe-orientation" + "@id": "bts:PatientColonoscopyPerformedIndicator" }, { - "@id": "bts:PermeabilizationTime" + "@id": "bts:ColorectalCancerKRASIndicator" }, { - "@id": "bts:RIN" + "@id": "bts:ColonPolypOccurenceIndicator" }, { - "@id": "bts:DV200" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:CaptureArea", - "@type": "rdfs:Class", - "rdfs:comment": "Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.", - "rdfs:label": "CaptureArea", - "rdfs:subClassOf": [ + "@id": "bts:FamilyHistoryColorectalPolyp" + }, { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:ColorectalPolypNewIndicator" + }, { - "@id": "bts:A" + "@id": "bts:HormoneTherapyBreastCancerPreventionIndicator" }, { - "@id": "bts:B" + "@id": "bts:MultifocalBreastCarcinomaPresentIndicator" }, { - "@id": "bts:C" + "@id": "bts:MulticentricBreastCarcinomaPresentIndicator" }, { - "@id": "bts:D" + "@id": "bts:HistoryofBlisteringSunburn" }, { - "@id": "bts:A1" + "@id": "bts:Tool" }, { - "@id": "bts:B1" + "@id": "bts:Islowestlevel" }, { - "@id": "bts:C1" + "@id": "bts:PublicationcontainsHTANID" }, { - "@id": "bts:D1" - } - ], - "sms:displayName": "Capture Area", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SlideVersion", - "@type": "rdfs:Class", - "rdfs:comment": "Version of imaging slide used. Slide version is critical for the analysis of the sequencing data as different slides have different capture area layouts.", - "rdfs:label": "SlideVersion", - "rdfs:subClassOf": [ + "@id": "bts:BarrettsEsophagusGobletCellsPresent" + }, { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:PrecancerCase" + }, { - "@id": "bts:V1" + "@id": "bts:TreatmentorTherapy" }, { - "@id": "bts:V2" + "@id": "bts:PatientInflammatoryBowelDiseasePersonalMedicaHistory" }, { - "@id": "bts:V3" + "@id": "bts:HistoryofAtypicalNevi" }, { - "@id": "bts:V4" + "@id": "bts:MetalIsotopeElement" } ], - "sms:displayName": "Slide Version", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "no", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SlideID", + "@id": "bts:MACS2", "@type": "rdfs:Class", - "rdfs:comment": "For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide.", - "rdfs:label": "SlideID", + "rdfs:comment": "TBD", + "rdfs:label": "MACS2", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:StripeCalling" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Slide ID", + "sms:displayName": "MACS2", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ImageRe-orientation", + "@id": "bts:HiCCUPS", "@type": "rdfs:Class", - "rdfs:comment": "To ensure good fiducial alignment and tissue spots detection, it is important to correct for this shift in orientation.", - "rdfs:label": "ImageRe-orientation", + "rdfs:comment": "TBD", + "rdfs:label": "HiCCUPS", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:LoopCalling" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:TRUE" - }, - { - "@id": "bts:FALSE" - } - ], - "sms:displayName": "Image Re-orientation", + "sms:displayName": "HiCCUPS", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PermeabilizationTime", + "@id": "bts:Cooltools", "@type": "rdfs:Class", - "rdfs:comment": "Fixed and stained tissue sections are permeabilized for different times. Each Capture Area captures polyadenylated mRNA from the attached tissue section. Measure is provided in minutes.", - "rdfs:label": "PermeabilizationTime", + "rdfs:comment": "TBD", + "rdfs:label": "Cooltools", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:LoopCalling" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Permeabilization Time", + "sms:displayName": "Cooltools", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel2", + "@id": "bts:ImagingLevel4", "@type": "rdfs:Class", - "rdfs:comment": "Alignment workflows downstream of Spatial Transcriptomics RNA-seq Level 1.", - "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel2", + "rdfs:comment": "Derived imaging data: Object-by-feature array", + "rdfs:label": "ImagingLevel4", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 2", + "sms:displayName": "Imaging Level 4", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel1" + "@id": "bts:ImagingLevel3Channels" } ], "sms:requiresDependency": [ @@ -42825,359 +46650,211 @@ { "@id": "bts:FileFormat" }, - { - "@id": "bts:Checksum" - }, { "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:UMITag" - }, - { - "@id": "bts:WhitelistSpatialBarcodeFileLink" - }, - { - "@id": "bts:SpatialBarcodeTag" - }, - { - "@id": "bts:AppliedHardTrimming" + "@id": "bts:HTANParentChannelMetadataID" }, { - "@id": "bts:WorkflowVersion" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:WorkflowLink" + "@id": "bts:Parameterfile" }, { - "@id": "bts:GenomicReference" + "@id": "bts:SoftwareandVersion" }, { - "@id": "bts:GenomicReferenceURL" + "@id": "bts:CommitSHA" }, { - "@id": "bts:GenomeAnnotationURL" + "@id": "bts:NumberofObjects" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:NumberofFeatures" }, { - "@id": "bts:RunID" + "@id": "bts:ImagingObjectClass" }, { - "@id": "bts:CaptureArea" + "@id": "bts:ImagingSummaryStatistic" } ], "sms:validationRules": [] }, { - "@id": "bts:WhitelistSpatialBarcodeFileLink", + "@id": "bts:NumberofFeatures", "@type": "rdfs:Class", - "rdfs:comment": "Link to file listing all possible spatial barcodes. URL", - "rdfs:label": "WhitelistSpatialBarcodeFileLink", + "rdfs:comment": "The number of features (eg channels) described", + "rdfs:label": "NumberofFeatures", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Whitelist Spatial Barcode File Link", + "sms:displayName": "Number of Features", "sms:required": "sms:true", - "sms:validationRules": [] + "sms:validationRules": [ + "int" + ] }, { - "@id": "bts:10xVisiumSpatialTranscriptomics-AuxiliaryFiles", + "@id": "bts:ImagingSummaryStatistic", "@type": "rdfs:Class", - "rdfs:comment": "Auxiliary data associated with spot/slide analysis (aligned Images, quality control files, etc) from Spatial Transcriptomics.", - "rdfs:label": "10xVisiumSpatialTranscriptomics-AuxiliaryFiles", + "rdfs:comment": "Function used to summarize object/feature intensity", + "rdfs:label": "ImagingSummaryStatistic", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "10x Visium Spatial Transcriptomics - Auxiliary Files", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel1" - }, - { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel2" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:RunID" - }, - { - "@id": "bts:VisiumFileType" - }, - { - "@id": "bts:SlideID" - }, + "schema:rangeIncludes": [ { - "@id": "bts:CaptureArea" + "@id": "bts:Mean" }, { - "@id": "bts:WorkflowVersion" + "@id": "bts:Median" }, { - "@id": "bts:WorkflowLink" + "@id": "bts:NotSpecified" } ], + "sms:displayName": "Imaging Summary Statistic", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:VisiumFileType", + "@id": "bts:SRRSImagingLevel2", "@type": "rdfs:Class", - "rdfs:comment": "The file type generated for the visium experiment.", - "rdfs:label": "VisiumFileType", + "rdfs:comment": "SRRS-specific HTAN raw and pre-processed image data", + "rdfs:label": "SRRSImagingLevel2", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Referencepng" - }, + "sms:displayName": "SRRS Imaging Level 2", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:Referencejpg" - }, + "@id": "bts:Biospecimen" + } + ], + "sms:requiresDependency": [ { - "@id": "bts:Jsonscalefactors" + "@id": "bts:Component" }, { - "@id": "bts:Probedatasetcsv" + "@id": "bts:Filename" }, { - "@id": "bts:Qcresulthtml" + "@id": "bts:FileFormat" }, { - "@id": "bts:Filteredmex" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:Unfilteredmex" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:TissuePositions" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:Barcodes" + "@id": "bts:ChannelMetadataFilename" }, { - "@id": "bts:Features" + "@id": "bts:ImagingAssayType" }, { - "@id": "bts:Fiducialimagepng" + "@id": "bts:ProtocolLink" }, { - "@id": "bts:Fiducialimagejpg" + "@id": "bts:SoftwareandVersion" }, { - "@id": "bts:Detectedimagepng" + "@id": "bts:Microscope" }, { - "@id": "bts:Detectedjpg" + "@id": "bts:Objective" }, { - "@id": "bts:Highresimage" + "@id": "bts:NominalMagnification" }, { - "@id": "bts:Lowresimage" - } - ], - "sms:displayName": "Visium File Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel3", - "@type": "rdfs:Class", - "rdfs:comment": "Processed data files based on Spatial Transcriptomics RNA-seq Level 2 and Spatial Transcriptomics Auxiliary files.", - "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel3", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 3", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel2" + "@id": "bts:Pyramid" }, { - "@id": "bts:10xVisiumSpatialTranscriptomics-AuxiliaryFiles" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" + "@id": "bts:Zstack" }, { - "@id": "bts:Filename" + "@id": "bts:Tseries" }, { - "@id": "bts:FileFormat" + "@id": "bts:PassedQC" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:FrameAveraging" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:ImageID" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:DimensionOrder" }, { - "@id": "bts:RunID" + "@id": "bts:PhysicalSizeX" }, { - "@id": "bts:VisiumFileType" + "@id": "bts:PhysicalSizeXUnit" }, { - "@id": "bts:WorkflowVersion" + "@id": "bts:PhysicalSizeY" }, { - "@id": "bts:WorkflowLink" + "@id": "bts:PhysicalSizeYUnit" }, { - "@id": "bts:CaptureArea" + "@id": "bts:PixelsBigEndian" }, { - "@id": "bts:Spotsundertissue" + "@id": "bts:PlaneCount" }, { - "@id": "bts:MeanReadsperSpatialSpot" + "@id": "bts:SizeC" }, { - "@id": "bts:MedianNumberGenesperSpatialSpot" + "@id": "bts:SizeT" }, { - "@id": "bts:SequencingSaturation" + "@id": "bts:SizeX" }, { - "@id": "bts:ProportionReadsMapped" + "@id": "bts:SizeY" }, { - "@id": "bts:ProportionReadsMappedtoTranscriptome" + "@id": "bts:SizeZ" }, { - "@id": "bts:MedianUMICountsperSpot" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:Spotsundertissue", - "@type": "rdfs:Class", - "rdfs:comment": "The number of barcodes associated with a spot under tissue.", - "rdfs:label": "Spotsundertissue", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Spots under tissue", - "sms:required": "sms:true", - "sms:validationRules": [ - "num" - ] - }, - { - "@id": "bts:MeanReadsperSpatialSpot", - "@type": "rdfs:Class", - "rdfs:comment": "The number of reads, both under and outside of tissue, divided by the number of barcodes associated with a spot under tissue.", - "rdfs:label": "MeanReadsperSpatialSpot", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Mean Reads per Spatial Spot", - "sms:required": "sms:true", - "sms:validationRules": [ - "num" - ] - }, - { - "@id": "bts:SequencingSaturation", - "@type": "rdfs:Class", - "rdfs:comment": "The fraction of reads originating from an already-observed UMI. This is a function of library complexity and sequencing depth. More specifically, this is the fraction of confidently mapped, valid spot-barcode, valid UMI reads that had a non-unique (spot-barcode, UMI, gene).", - "rdfs:label": "SequencingSaturation", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Sequencing Saturation", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ProportionReadsMappedtoTranscriptome", - "@type": "rdfs:Class", - "rdfs:comment": "Fraction of reads that mapped to a unique gene in the transcriptome. The read must be consistent with annotated splice junctions. These reads are considered for UMI counting.", - "rdfs:label": "ProportionReadsMappedtoTranscriptome", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:PixelType" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Proportion Reads Mapped to Transcriptome", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel4", + "@id": "bts:10XGenomicsXeniumISSExperiment", "@type": "rdfs:Class", - "rdfs:comment": "Processed data files based on Spatial Transcriptomics RNA-seq Level 3.", - "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel4", + "rdfs:comment": "All data pertaining to the 10X Genomics Xenium In-Situ Hybridization experiment", + "rdfs:label": "10XGenomicsXeniumISSExperiment", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -43186,11 +46863,11 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 4", + "sms:displayName": "10X Genomics Xenium ISS Experiment", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel3" + "@id": "bts:Biospecimen" } ], "sms:requiresDependency": [ @@ -43207,921 +46884,756 @@ "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:XeniumBundleContents" }, { - "@id": "bts:RunID" + "@id": "bts:SlideID" }, { - "@id": "bts:WorkflowVersion" + "@id": "bts:ROIname" }, { - "@id": "bts:WorkflowLink" + "@id": "bts:PanelName" }, { - "@id": "bts:VisiumWorkflowType" + "@id": "bts:ProtocolLink" }, { - "@id": "bts:VisiumWorkflowParametersDescription" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:VisiumWorkflowType", - "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze the visium data set.", - "rdfs:label": "VisiumWorkflowType", - "rdfs:subClassOf": [ + "@id": "bts:SoftwareandVersion" + }, { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Visium Workflow Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:VisiumWorkflowParametersDescription", - "@type": "rdfs:Class", - "rdfs:comment": "Parameters used to run the workflow..", - "rdfs:label": "VisiumWorkflowParametersDescription", - "rdfs:subClassOf": [ + "@id": "bts:TotalNumberofCells" + }, { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Visium Workflow Parameters Description", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Referencepng", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Referencepng", - "rdfs:subClassOf": [ + "@id": "bts:TotalNumberofTargets" + }, { - "@id": "bts:VisiumFileType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "reference png", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Referencejpg", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Referencejpg", - "rdfs:subClassOf": [ + "@id": "bts:Surfacearea" + }, { - "@id": "bts:VisiumFileType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "reference jpg", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Jsonscalefactors", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Jsonscalefactors", - "rdfs:subClassOf": [ + "@id": "bts:ExperimentIFChannels" + }, { - "@id": "bts:VisiumFileType" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "json scale factors", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Probedatasetcsv", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Probedatasetcsv", - "rdfs:subClassOf": [ + "@id": "bts:TranscriptsperCell" + }, + { + "@id": "bts:PercentofTranscriptswithinCells" + }, { - "@id": "bts:VisiumFileType" + "@id": "bts:DecodedTranscripts" + }, + { + "@id": "bts:XeniumIFimageHTANFileID" + }, + { + "@id": "bts:XeniumHEimageHTANFileID" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "probe dataset csv", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Qcresulthtml", + "@id": "bts:XeniumBundleContents", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Qcresulthtml", + "rdfs:comment": "A comma separated list of filenames within the Xenium bundle zip file", + "rdfs:label": "XeniumBundleContents", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "qc result html", - "sms:required": "sms:false", + "sms:displayName": "Xenium Bundle Contents", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Filteredmex", + "@id": "bts:PanelName", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Filteredmex", + "rdfs:comment": "The human-readable panel name. This could be the Gene Panel name or Protein Panel name. In Xenium, this refers to the string entered as the name in panel specification (e.g. Xenium Human Immuno-Oncology Add-on B Gene Expression). In CosMx, this refers to the panel name as it appears in the CosMx catalog (e.g. CosMx Human Universal Cell Characterization Panel (1000-plex))", + "rdfs:label": "PanelName", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "filtered mex", - "sms:required": "sms:false", + "sms:displayName": "Panel Name", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Unfilteredmex", + "@id": "bts:TotalNumberofCells", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Unfilteredmex", + "rdfs:comment": "The total number of cells analyzed on the flow cell", + "rdfs:label": "TotalNumberofCells", "rdfs:subClassOf": [ { - "@id": "bts:VisiumFileType" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "unfiltered mex", - "sms:required": "sms:false", + "sms:displayName": "Total Number of Cells", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TissuePositions", + "@id": "bts:TotalNumberofTargets", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "TissuePositions", + "rdfs:comment": "Refers to the target of an assay. 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"@id": "bts:D1", + "@id": "bts:PhosphoproteinFlag", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "D1", + "rdfs:comment": "A flag the denotes if an antibody targets a phosphoprotein.", + "rdfs:label": "PhosphoproteinFlag", "rdfs:subClassOf": [ { - "@id": "bts:CaptureArea" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "D1", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:True" + }, + { + "@id": "bts:False" + } + ], + "sms:displayName": "Phosphoprotein Flag", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:V1", + "@id": "bts:Vendor", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "V1", + "rdfs:comment": "Vendor", + "rdfs:label": "Vendor", "rdfs:subClassOf": [ { - "@id": "bts:SlideVersion" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "V1", + "sms:displayName": "Vendor", "sms:required": "sms:false", "sms:validationRules": [] }, { - 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"@id": "bts:FALSE", + "@id": "bts:PhosphoSite", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "FALSE", + "rdfs:comment": "The protein site for a phosphoprotein targeting antibody. Report AA and site (i.e. S442)", + "rdfs:label": "PhosphoSite", "rdfs:subClassOf": [ { - "@id": "bts:ImageRe-orientation" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "FALSE", + "sms:displayName": "Phospho Site", "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:PhosphoproteinFlag" + } + ], "sms:validationRules": [] }, { - "@id": "bts:SpatialBarcodeLength", + "@id": "bts:RPPAValidationStatus", "@type": "rdfs:Class", - "rdfs:comment": "Length of spot barcode read (in bp): number", - "rdfs:label": "SpatialBarcodeLength", + "rdfs:comment": "Valid = RPPA and WB correlation > 0.7; Use with Caution = RPPA and WB correlation < 0.7; Under Evaluation = Antibody has given mixed results and/or evaluated by another lab; We are in the process of (re)validating; Used for QC = These antibodies are used for tissue sample quality control (QC)", + "rdfs:label": "RPPAValidationStatus", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Spatial Barcode Length", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:CDNA", - "@type": "rdfs:Class", - "rdfs:comment": "Complementary DNA. 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"rdfs:comment": "TBD", - "rdfs:label": "10xV1.0", + "rdfs:comment": "Level 3 Reverse Phase Protein Array (RPPA) data contains intra-batch normalized intensities.", + "rdfs:label": "RPPALevel3", "rdfs:subClassOf": [ { - "@id": "bts:SpatialLibraryConstructionMethod" - }, - { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "10xV1.0", + "sms:displayName": "RPPA Level 3", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:10xV1.1", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "10xV1.1", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialLibraryConstructionMethod" - }, + "sms:requiresComponent": [ { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:Biospecimen" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "10xV1.1", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:10xV2", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "10xV2", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:SpatialLibraryConstructionMethod" + "@id": "bts:Component" }, { - "@id": "bts:LibraryConstructionMethod" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "10xV2", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:10xV3", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "10xV3", - "rdfs:subClassOf": [ + "@id": "bts:Filename" + }, { - "@id": "bts:SpatialLibraryConstructionMethod" + "@id": "bts:FileFormat" }, { - "@id": "bts:LibraryConstructionMethod" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "10xV3", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:10xV3.1", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "10xV3.1", - "rdfs:subClassOf": [ + "@id": "bts:HTANParticipantID" + }, { - "@id": "bts:SpatialLibraryConstructionMethod" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:LibraryConstructionMethod" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "10xV3.1", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Drop-seq", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Drop-seq", - "rdfs:subClassOf": [ + "@id": "bts:HTANParentDataFileID" + }, { - "@id": "bts:SpatialLibraryConstructionMethod" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:LibraryConstructionMethod" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Drop-seq", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:InDropsV2", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "InDropsV2", - "rdfs:subClassOf": [ + "@id": "bts:AssayType" + }, { - "@id": "bts:SpatialLibraryConstructionMethod" + "@id": "bts:SoftwareandVersion" }, { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:NormalizationMethod" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "inDropsV2", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:InDropsV3", + "@id": "bts:RPPALevel4", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "InDropsV3", + "rdfs:comment": "Level 4 Reverse Phase Protein Array (RPPA) data contains intra-batch corrected intensities.", + "rdfs:label": "RPPALevel4", "rdfs:subClassOf": [ { - "@id": "bts:SpatialLibraryConstructionMethod" - }, - { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "inDropsV3", + "sms:displayName": "RPPA Level 4", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TruDrop", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "TruDrop", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialLibraryConstructionMethod" - }, + "sms:requiresComponent": [ { - "@id": "bts:LibraryConstructionMethod" + "@id": "bts:RPPALevel2" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "TruDrop", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:NexteraXT", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "NexteraXT", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:SpatialLibraryConstructionMethod" + "@id": "bts:Component" }, { - "@id": "bts:LibraryConstructionMethod" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Nextera XT", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:UMIBarcodeOffset", - "@type": "rdfs:Class", - "rdfs:comment": "Start position of UMI barcode in the sequence. Values: number, 0 for start of read", - "rdfs:label": "UMIBarcodeOffset", - "rdfs:subClassOf": [ + "@id": "bts:Filename" + }, { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParticipantID" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:AssayType" + }, + { + "@id": "bts:BatchCorrectionMethod" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "UMI Barcode Offset", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:UMIBarcodeLength", + "@id": "bts:BatchCorrectionMethod", "@type": "rdfs:Class", - "rdfs:comment": "Length of UMI barcode read (in bp): number", - "rdfs:label": "UMIBarcodeLength", + "rdfs:comment": "Method that was used to batch correct Level 3 data", + "rdfs:label": "BatchCorrectionMethod", "rdfs:subClassOf": [ { - "@id": "bts:ScRNA-seqLevel1" + "@id": "bts:RPPALevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "UMI Barcode Length", - "sms:required": "sms:true", + "sms:displayName": "Batch Correction Method", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NanoStringGeoMxDSPSpatialTranscriptomicsLevel1", + "@id": "bts:NanostringCosMxSMIExperiment", "@type": "rdfs:Class", - "rdfs:comment": "Files contain raw data output from the NanoString GeoMx DSP Pipeline. These can include RCC or DCC Files.", - "rdfs:label": "NanoStringGeoMxDSPSpatialTranscriptomicsLevel1", + "rdfs:comment": "RNA and Protein Panel assays applied as part of Nanostring CosMx Spatial Molecular Imager (SMI)", + "rdfs:label": "NanostringCosMxSMIExperiment", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -44130,17 +47642,11 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "NanoString GeoMx DSP Spatial Transcriptomics Level 1", + "sms:displayName": "Nanostring CosMx SMI Experiment", "sms:required": "sms:false", "sms:requiresComponent": [ { "@id": "bts:Biospecimen" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "sms:requiresDependency": [ @@ -44160,37 +47666,61 @@ "@id": "bts:HTANDataFileID" }, { - "@id": "bts:SynapseIDofGeoMxDSPPKCFile" + "@id": "bts:CosMxBundleContents" }, { - "@id": "bts:GeoMxDSPNGSSequencingPlatform" + "@id": "bts:SlideID" }, { - "@id": "bts:GeoMxDSPNGSLibrarySelectionMethod" + "@id": "bts:CosMxAssayType" }, { - "@id": "bts:GeoMxDSPNGSLibraryPreparationKitName" + "@id": "bts:PanelName" }, { - "@id": "bts:GeoMxDSPLibraryPreparationKitVendor" + "@id": "bts:ProtocolLink" }, { - "@id": "bts:GeoMxDSPLibraryPreparationKitVersion" + "@id": "bts:SoftwareandVersion" }, { - "@id": "bts:SynapseIDofGeoMxLabWorksheetFile" + "@id": "bts:TotalNumberofCells" }, { - "@id": "bts:SoftwareandVersion" + "@id": "bts:TotalNumberofTargets" + }, + { + "@id": "bts:NumberofFOVs" + }, + { + "@id": "bts:Surfacearea" + }, + { + "@id": "bts:ExperimentIFChannels" + }, + { + "@id": "bts:TranscriptsperCell" + }, + { + "@id": "bts:PercentofTranscriptswithinCells" + }, + { + "@id": "bts:MeanTotalTranscriptsperArea" + }, + { + "@id": "bts:UniqueGenes" + }, + { + "@id": "bts:TotalNegativeProbeCounts" } ], "sms:validationRules": [] }, { - "@id": "bts:SynapseIDofGeoMxDSPPKCFile", + "@id": "bts:CosMxBundleContents", "@type": "rdfs:Class", - "rdfs:comment": "The Synapse ID(s) associated with the PKC mapping file for the assay. Multiple files are listed as comma separated values.", - "rdfs:label": "SynapseIDofGeoMxDSPPKCFile", + "rdfs:comment": "A comma separated list of filenames within the CosMx bundle zip file", + "rdfs:label": "CosMxBundleContents", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -44199,18 +47729,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Synapse ID of GeoMx DSP PKC File", + "sms:displayName": "CosMx Bundle Contents", "sms:required": "sms:true", - "sms:validationRules": [ - "list", - "regex match syn\\d+" - ] + "sms:validationRules": [] }, { - "@id": "bts:GeoMxDSPNGSSequencingPlatform", + "@id": "bts:CosMxAssayType", "@type": "rdfs:Class", - "rdfs:comment": "A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.", - "rdfs:label": "GeoMxDSPNGSSequencingPlatform", + "rdfs:comment": "The specification for barcodes on each image. Either RNA probe or protein antibody according to the assay", + "rdfs:label": "CosMxAssayType", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -44219,15 +47746,23 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP NGS Sequencing Platform", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:RNA" + }, + { + "@id": "bts:Protein" + } + ], + "sms:displayName": "CosMx Assay Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:GeoMxDSPNGSLibrarySelectionMethod", + "@id": "bts:NumberofFOVs", "@type": "rdfs:Class", - "rdfs:comment": "How RNA molecules are isolated.", - "rdfs:label": "GeoMxDSPNGSLibrarySelectionMethod", + "rdfs:comment": "The total number of FOVs recorded for the sample on a single flow cell", + "rdfs:label": "NumberofFOVs", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -44236,15 +47771,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP NGS Library Selection Method", - "sms:required": "sms:false", + "sms:displayName": "Number of FOVs", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:GeoMxDSPNGSLibraryPreparationKitName", + "@id": "bts:MeanTotalTranscriptsperArea", "@type": "rdfs:Class", - "rdfs:comment": "Name of Library Preparation Kit. String", - "rdfs:label": "GeoMxDSPNGSLibraryPreparationKitName", + "rdfs:comment": "The mean total transcripts per um3", + "rdfs:label": "MeanTotalTranscriptsperArea", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -44253,15 +47788,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP NGS Library Preparation Kit Name", - "sms:required": "sms:false", + "sms:displayName": "Mean Total Transcripts per Area", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:GeoMxDSPLibraryPreparationKitVendor", + "@id": "bts:UniqueGenes", "@type": "rdfs:Class", - "rdfs:comment": "Vendor of Library Preparation Kit. String", - "rdfs:label": "GeoMxDSPLibraryPreparationKitVendor", + "rdfs:comment": "The total unique genes detected above background", + "rdfs:label": "UniqueGenes", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -44270,15 +47805,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP Library Preparation Kit Vendor", + "sms:displayName": "Unique Genes", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GeoMxDSPLibraryPreparationKitVersion", + "@id": "bts:TotalNegativeProbeCounts", "@type": "rdfs:Class", - "rdfs:comment": "Version of Library Preparation Kit. String", - "rdfs:label": "GeoMxDSPLibraryPreparationKitVersion", + "rdfs:comment": "Mean Total Negative probe counts/cell", + "rdfs:label": "TotalNegativeProbeCounts", "rdfs:subClassOf": [ { "@id": "bts:SpatialTranscriptomics" @@ -44287,105 +47822,55 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP Library Preparation Kit Version", - "sms:required": "sms:false", + "sms:displayName": "Total Negative Probe Counts", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SynapseIDofGeoMxLabWorksheetFile", + "@id": "bts:RNA", "@type": "rdfs:Class", - "rdfs:comment": "Synapse ID(s) of Lab Worksheet Files output from the GeoMx DSP workflow. Multiple files are listed as comma separated values.", - "rdfs:label": "SynapseIDofGeoMxLabWorksheetFile", + "rdfs:comment": "TBD", + "rdfs:label": "RNA", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:CosMxAssayType" + }, + { + "@id": "bts:MicroarrayMolecule" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Synapse ID of GeoMx Lab Worksheet File", + "sms:displayName": "RNA", "sms:required": "sms:false", - "sms:validationRules": [ - "list", - "regex match syn\\d+" - ] + "sms:validationRules": [] }, { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata", + "@id": "bts:Protein", "@type": "rdfs:Class", - "rdfs:comment": "GeoMx ROI and Segment Metadata Attributes. The assayed biospecimen should be reported one per row with the associated ROI coordinates.", - "rdfs:label": "NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata", + "rdfs:comment": "TBD", + "rdfs:label": "Protein", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:CosMxAssayType" + }, + { + "@id": "bts:AnalyteType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "NanoString GeoMx DSP ROI RCC Segment Annotation Metadata", + "sms:displayName": "protein", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:Scanname" - }, - { - "@id": "bts:ROIname" - }, - { - "@id": "bts:Segmentname" - }, - { - "@id": "bts:ROIXCoordinate" - }, - { - "@id": "bts:ROIYCoordinate" - }, - { - "@id": "bts:Tags" - }, - { - "@id": "bts:QCstatus" - }, - { - "@id": "bts:ScanHeight" - }, - { - "@id": "bts:ScanWidth" - }, - { - "@id": "bts:ScanOffsetX" - }, - { - "@id": "bts:ScanOffsetY" - }, - { - "@id": "bts:BindingDensity" - }, - { - "@id": "bts:Positivenormfactor" - }, - { - "@id": "bts:Surfacearea" - }, - { - "@id": "bts:Nucleicount" - }, - { - "@id": "bts:TissueStain" - } - ], "sms:validationRules": [] }, { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata", + "@id": "bts:MassSpectrometryLevel1", "@type": "rdfs:Class", - "rdfs:comment": "GeoMx ROI and Segment Metadata Attributes. The assayed biospecimen should be reported one per row with the associated ROI coordinates.", - "rdfs:label": "NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata", + "rdfs:comment": "Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 1", + "rdfs:label": "MassSpectrometryLevel1", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -44394,825 +47879,743 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "NanoString GeoMx DSP ROI DCC Segment Annotation Metadata", + "sms:displayName": "Mass Spectrometry Level 1", "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:Biospecimen" + } + ], "sms:requiresDependency": [ { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:Component" }, { - "@id": "bts:Scanname" + "@id": "bts:Filename" }, { - "@id": "bts:Slidename" + "@id": "bts:FileFormat" }, { - "@id": "bts:ROIname" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:Segmentname" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:ROIXCoordinate" + "@id": "bts:MSBatchID" }, { - "@id": "bts:ROIYCoordinate" + "@id": "bts:MS-basedAssayType" }, { - "@id": "bts:Tags" + "@id": "bts:AnalyteType" }, { - "@id": "bts:ScanHeight" + "@id": "bts:MS-basedTargeted" }, { - "@id": "bts:ScanWidth" + "@id": "bts:MSInstrumentVendorandModel" }, { - "@id": "bts:ScanOffsetX" + "@id": "bts:MSSource" }, { - "@id": "bts:ScanOffsetY" + "@id": "bts:Polarity" }, { - "@id": "bts:Surfacearea" + "@id": "bts:MassRangeLowValue" }, { - "@id": "bts:Nucleicount" + "@id": "bts:MassRangeHighValue" }, { - "@id": "bts:SequencingSaturation" + "@id": "bts:DataCollectionMode" }, { - "@id": "bts:MapQ30" + "@id": "bts:MSScanMode" }, { - "@id": "bts:Rawreads" + "@id": "bts:MSLabeling" }, { - "@id": "bts:Stitchedreads" + "@id": "bts:ProtocolLink" }, { - "@id": "bts:Alignedreads" + "@id": "bts:LCInstrumentVendorandModel" }, { - "@id": "bts:Deduplicatedreads" + "@id": "bts:LCColumnVendorandModel" }, { - "@id": "bts:InSituNegativemedian" + "@id": "bts:LCResin" }, { - "@id": "bts:Biologicalprobemedian" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:GeoMxDSPAssayType", - "@type": "rdfs:Class", - "rdfs:comment": "The assay type which was used for the GeoMx DSP pipeline.", - "rdfs:label": "GeoMxDSPAssayType", - "rdfs:subClassOf": [ + "@id": "bts:LCLengthValue" + }, { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:LCTempValue" + }, + { + "@id": "bts:LCIDValue" + }, + { + "@id": "bts:LCFlowRate" + }, { - "@id": "bts:RNAnCounter" + "@id": "bts:LCGradient" }, { - "@id": "bts:ProteinnCounter" + "@id": "bts:LCMobilePhaseA" }, { - "@id": "bts:ProteinNGS" + "@id": "bts:LCMobilePhaseB" }, { - "@id": "bts:RNANGS" - } - ], - "sms:displayName": "GeoMx DSP Assay Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:RNAnCounter", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "RNAnCounter", - "rdfs:subClassOf": [ + "@id": "bts:SoftwareandVersion" + }, { - "@id": "bts:GeoMxDSPAssayType" + "@id": "bts:MSInstrumentMetadataFile" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "RNA nCounter", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ProteinnCounter", + "@id": "bts:MSBatchID", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "ProteinnCounter", + "rdfs:comment": "Batch ID indicating a set of samples that were run together.", + "rdfs:label": "MSBatchID", "rdfs:subClassOf": [ { - "@id": "bts:GeoMxDSPAssayType" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Protein nCounter", - "sms:required": "sms:false", + "sms:displayName": "MS Batch ID", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ProteinNGS", + "@id": "bts:MS-basedAssayType", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "ProteinNGS", + "rdfs:comment": "Analytes are the target molecules being measured with the assay.", + "rdfs:label": "MS-basedAssayType", "rdfs:subClassOf": [ { - "@id": "bts:GeoMxDSPAssayType" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Protein NGS", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:RNANGS", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "RNANGS", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:GeoMxDSPAssayType" + "@id": "bts:LC-MS" + }, + { + "@id": "bts:MS" + }, + { + "@id": "bts:TMT" + }, + { + "@id": "bts:LC-MS/MS" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "RNA NGS", - "sms:required": "sms:false", + "sms:displayName": "MS-based Assay Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:NanoStringGeoMxDSPSpatialTranscriptomicsLevel3", + "@id": "bts:AnalyteType", "@type": "rdfs:Class", - "rdfs:comment": "Files contain processed data from the NanoString GeoMx DSP Pipeline. This level depends on GeoMx Level 1 and Imaging Level 2.", - "rdfs:label": "NanoStringGeoMxDSPSpatialTranscriptomicsLevel3", + "rdfs:comment": "The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen", + "rdfs:label": "AnalyteType", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "NanoString GeoMx DSP Spatial Transcriptomics Level 3", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:NanoStringGeoMxDSPSpatialTranscriptomicsLevel1" - }, - { - "@id": "bts:ImagingLevel2" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" - } - ], - "sms:requiresDependency": [ + "schema:rangeIncludes": [ { - "@id": "bts:Component" + "@id": "bts:CfDNAAnalyte" }, { - "@id": "bts:Filename" + "@id": "bts:DNAAnalyte" }, { - "@id": "bts:FileFormat" + "@id": "bts:RNAAnalyte" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:TotalRNAAnalyte" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:TissueBlockAnalyte" }, { - "@id": "bts:GeoMxDSPAssayType" + "@id": "bts:TissueSectionAnalyte" }, { - "@id": "bts:SynapseIDofGeoMxDSPROISegmentAnnotationFile" + "@id": "bts:PBMCsorPlasmaorSerumAnalyte" }, { - "@id": "bts:GeoMxDSPUniqueProbeCount" + "@id": "bts:CDNALibrariesAnalyte" }, { - "@id": "bts:GeoMxDSPUniqueTargetCount" + "@id": "bts:PBMCs" }, { - "@id": "bts:GeoMxDSPGenomicReference" + "@id": "bts:Plasma" }, { - "@id": "bts:MatrixType" + "@id": "bts:SerumAnalyte" }, { - "@id": "bts:GeoMxDSPWorkflowType" + "@id": "bts:Lipid" }, { - "@id": "bts:GeoMxDSPWorkflowParameterDescription" + "@id": "bts:Protein" }, { - "@id": "bts:GeoMxDSPWorkflowLink" + "@id": "bts:Metabolite" } ], + "sms:displayName": "Analyte Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SynapseIDofGeoMxDSPROISegmentAnnotationFile", + "@id": "bts:MS-basedTargeted", "@type": "rdfs:Class", - "rdfs:comment": "Synapse ID(s) for ROI/Segmentation annotations in the GeoMx DSP experiment.", - "rdfs:label": "SynapseIDofGeoMxDSPROISegmentAnnotationFile", + "rdfs:comment": "Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. Example: The MALDI Imaging analyte is lipids.", + "rdfs:label": "MS-basedTargeted", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Synapse ID of GeoMx DSP ROI Segment Annotation File", - "sms:required": "sms:true", - "sms:validationRules": [ - "list", - "regex match syn\\d+" - ] - }, - { - "@id": "bts:GeoMxDSPUniqueProbeCount", - "@type": "rdfs:Class", - "rdfs:comment": "Total number of unique probes reported.", - "rdfs:label": "GeoMxDSPUniqueProbeCount", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Targeted" + }, + { + "@id": "bts:Untargeted" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "GeoMx DSP Unique Probe Count", - "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] + "sms:displayName": "MS-based Targeted", + "sms:required": "sms:true", + "sms:validationRules": [] }, { - "@id": "bts:GeoMxDSPUniqueTargetCount", + "@id": "bts:MSInstrumentVendorandModel", "@type": "rdfs:Class", - "rdfs:comment": "Total number of unique genes reported.", - "rdfs:label": "GeoMxDSPUniqueTargetCount", + "rdfs:comment": "An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass.", + "rdfs:label": "MSInstrumentVendorandModel", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP Unique Target Count", - "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] + "sms:displayName": "MS Instrument Vendor and Model", + "sms:required": "sms:true", + "sms:validationRules": [] }, { - "@id": "bts:GeoMxDSPGenomicReference", + "@id": "bts:MSSource", "@type": "rdfs:Class", - "rdfs:comment": "Exact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/). Only applicable to some applications in GeoMx", - "rdfs:label": "GeoMxDSPGenomicReference", + "rdfs:comment": "The ion source type used for surface sampling (MALDI, MALDI-2, DESI, or SIMS) or LC-MS/MS data acquisition (nESI)", + "rdfs:label": "MSSource", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP Genomic Reference", - "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] - }, - { - "@id": "bts:GeoMxDSPWorkflowType", - "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze the GeoMx DSP data set.", - "rdfs:label": "GeoMxDSPWorkflowType", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:MALDI" + }, + { + "@id": "bts:MALDI-2" + }, + { + "@id": "bts:DESI" + }, + { + "@id": "bts:SIMS" + }, + { + "@id": "bts:NESI" + }, + { + "@id": "bts:Other" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "GeoMx DSP Workflow Type", - "sms:required": "sms:false", + "sms:displayName": "MS Source", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:GeoMxDSPWorkflowParameterDescription", + "@id": "bts:Polarity", "@type": "rdfs:Class", - "rdfs:comment": "Parameters used to run the GeoMx DSP workflow.", - "rdfs:label": "GeoMxDSPWorkflowParameterDescription", + "rdfs:comment": "The polarity of the mass analysis (positive or negative ion modes)", + "rdfs:label": "Polarity", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP Workflow Parameter Description", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:GeoMxDSPWorkflowLink", - "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow or command. DockStore.org recommended. URL", - "rdfs:label": "GeoMxDSPWorkflowLink", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Positive" + }, + { + "@id": "bts:Negative" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "GeoMx DSP Workflow Link", - "sms:required": "sms:false", + "sms:displayName": "Polarity", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Scanname", + "@id": "bts:MassRangeLowValue", "@type": "rdfs:Class", - "rdfs:comment": "GeoMx Scan name (as appears in Segment Summary)", - "rdfs:label": "Scanname", + "rdfs:comment": "The low value of the scanned mass range for MS1 in m/z.", + "rdfs:label": "MassRangeLowValue", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Scan name", + "sms:displayName": "Mass Range Low Value", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ROIname", + "@id": "bts:MassRangeHighValue", "@type": "rdfs:Class", - "rdfs:comment": "ROI name (application generated). For Xenium this is referred to as the “region name”", - "rdfs:label": "ROIname", + "rdfs:comment": "The high value of the scanned mass range for MS1 in m/z.", + "rdfs:label": "MassRangeHighValue", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "ROI name", + "sms:displayName": "Mass Range High Value", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Segmentname", + "@id": "bts:DataCollectionMode", "@type": "rdfs:Class", - "rdfs:comment": "Name given to segment at time of generation", - "rdfs:label": "Segmentname", + "rdfs:comment": "Mode of data collection in tandem MS assays. Either DDA (Data-dependent acquisition) or DIA (Data-indemendent acquisition.", + "rdfs:label": "DataCollectionMode", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Segment name", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ROIXCoordinate", - "@type": "rdfs:Class", - "rdfs:comment": "X location within the image", - "rdfs:label": "ROIXCoordinate", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:DDA" }, { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:DIA" + }, + { + "@id": "bts:Other" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "ROI X Coordinate", + "sms:displayName": "Data Collection Mode", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ROIYCoordinate", + "@id": "bts:MSScanMode", "@type": "rdfs:Class", - "rdfs:comment": "Y location within the image", - "rdfs:label": "ROIYCoordinate", + "rdfs:comment": "Indicates whether experiment is MS, MS/MS, or other (possibly MS3 for TMT)", + "rdfs:label": "MSScanMode", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "ROI Y Coordinate", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Tags", - "@type": "rdfs:Class", - "rdfs:comment": "Unique descriptor of a variable group (ie. MAPK+)", - "rdfs:label": "Tags", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:MS" }, { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:MS/MS" + }, + { + "@id": "bts:MS3" + }, + { + "@id": "bts:Other" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Tags", + "sms:displayName": "MS Scan Mode", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:QCstatus", + "@id": "bts:MSLabeling", "@type": "rdfs:Class", - "rdfs:comment": "ROI quality control flag as reported by the application", - "rdfs:label": "QCstatus", + "rdfs:comment": "Indicates whether samples were labeled prior to MS analysis (e.g., TMT)", + "rdfs:label": "MSLabeling", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "QC status", - "sms:required": "sms:false", + "sms:displayName": "MS Labeling", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ScanHeight", + "@id": "bts:LCInstrumentVendorandModel", "@type": "rdfs:Class", - "rdfs:comment": "Height of the scan for GeoMx Analysis", - "rdfs:label": "ScanHeight", + "rdfs:comment": "The manufacturer of the instrument used for LC.", + "rdfs:label": "LCInstrumentVendorandModel", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Scan Height", + "sms:displayName": "LC Instrument Vendor and Model", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ScanWidth", + "@id": "bts:LCColumnVendorandModel", "@type": "rdfs:Class", - "rdfs:comment": "Width of the scan for GeoMx Analysis", - "rdfs:label": "ScanWidth", + "rdfs:comment": "The manufacturer of the LC Column unless self-packed, pulled tip capilary is used and the model number/name of the LC Column - IF custom self-packed, pulled tip calillary is used enter 'Pulled tip capilary'", + "rdfs:label": "LCColumnVendorandModel", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Scan Width", + "sms:displayName": "LC Column Vendor and Model", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ScanOffsetX", + "@id": "bts:LCResin", "@type": "rdfs:Class", - "rdfs:comment": "Offset X of the scan for GeoMx Analysis", - "rdfs:label": "ScanOffsetX", + "rdfs:comment": "Details of the resin used for lc, including vendor, particle size, pore size", + "rdfs:label": "LCResin", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Scan Offset X", + "sms:displayName": "LC Resin", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ScanOffsetY", + "@id": "bts:LCLengthValue", "@type": "rdfs:Class", - "rdfs:comment": "Offset Y of the scan for GeoMx Analysis", - "rdfs:label": "ScanOffsetY", + "rdfs:comment": "LC column length in cm.", + "rdfs:label": "LCLengthValue", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Scan Offset Y", + "sms:displayName": "LC Length Value", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BindingDensity", + "@id": "bts:LCTempValue", "@type": "rdfs:Class", - "rdfs:comment": "The binding density as reported by the application", - "rdfs:label": "BindingDensity", + "rdfs:comment": "LC temperature in C.", + "rdfs:label": "LCTempValue", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Binding Density", - "sms:required": "sms:false", + "sms:displayName": "LC Temp Value", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Positivenormfactor", + "@id": "bts:LCIDValue", "@type": "rdfs:Class", - "rdfs:comment": "The Positive Control Normalization factor calculated using pos-hyb controls", - "rdfs:label": "Positivenormfactor", + "rdfs:comment": "LC column inner diameter in microns.", + "rdfs:label": "LCIDValue", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Positive norm factor", - "sms:required": "sms:false", + "sms:displayName": "LC ID Value", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Surfacearea", + "@id": "bts:LCFlowRate", "@type": "rdfs:Class", - "rdfs:comment": "Surface area of the ROI in square microns (µm^2). In CosMx, this is referred to as the Scan Area. In Xenium, this is referred to as the Region Area", - "rdfs:label": "Surfacearea", + "rdfs:comment": "LC flow rate in nL/min.", + "rdfs:label": "LCFlowRate", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Surface area", + "sms:displayName": "LC Flow Rate", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Nucleicount", + "@id": "bts:LCGradient", "@type": "rdfs:Class", - "rdfs:comment": "Number of nuclei detected in the segment (if applicable)", - "rdfs:label": "Nucleicount", + "rdfs:comment": "The program dictates the mobile phase solvent composition over the course of the chromatographic run.", + "rdfs:label": "LCGradient", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Nuclei count", + "sms:displayName": "LC Gradient", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TissueStain", + "@id": "bts:LCMobilePhaseA", "@type": "rdfs:Class", - "rdfs:comment": "e.g. CD45 or PanCK (if masking was performed)", - "rdfs:label": "TissueStain", + "rdfs:comment": "Composition of mobile phase A", + "rdfs:label": "LCMobilePhaseA", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Tissue Stain", - "sms:required": "sms:false", + "sms:displayName": "LC Mobile Phase A", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Slidename", + "@id": "bts:LCMobilePhaseB", "@type": "rdfs:Class", - "rdfs:comment": "Similar to a Run ID, the slide name indicates the slide a given ROI is linked to (as reported in Segment Summary).", - "rdfs:label": "Slidename", + "rdfs:comment": "Composition of mobile phase B", + "rdfs:label": "LCMobilePhaseB", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Slide name", - "sms:required": "sms:false", + "sms:displayName": "LC Mobile Phase B", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Rawreads", + "@id": "bts:MSInstrumentMetadataFile", "@type": "rdfs:Class", - "rdfs:comment": "Reads not yet analyzed in any way to be used for data analysis. The number of reads that pass filter from the flow cell represented in the FASTQ file.", - "rdfs:label": "Rawreads", + "rdfs:comment": "Additional file containing instrument metadata details. Use either synapse_path or entity_Id", + "rdfs:label": "MSInstrumentMetadataFile", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Raw reads", + "sms:displayName": "MS Instrument Metadata File", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Stitchedreads", + "@id": "bts:MassSpectrometryLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Represents consensus from the overlapping sequence of read 1 and 2. This is a % of the aligned reads that were overlapped and consensus confirmed, usually upward of 80% but less in terms of number of reads than aligned reads", - "rdfs:label": "Stitchedreads", + "rdfs:comment": "Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 2", + "rdfs:label": "MassSpectrometryLevel2", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Stitched reads", + "sms:displayName": "Mass Spectrometry Level 2", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Alignedreads", - "@type": "rdfs:Class", - "rdfs:comment": "Is a sequence that has been aligned to a gene/probe. Typically these reads can number from the hundreds of thousands to tens of millions. In GeoMx alignment is via mapping the RTS ID to a white list of sequences that represent targets.", - "rdfs:label": "Alignedreads", - "rdfs:subClassOf": [ + "sms:requiresComponent": [ { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:MassSpectrometryLevel1" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Aligned reads", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Deduplicatedreads", - "@type": "rdfs:Class", - "rdfs:comment": "Is the replacement of blocks of duplicate data with a Virtual Index Pointer linking the new sub-block to the existing block of data in a duplicate repository. This is used to reduce the amount of space need to store the data.", - "rdfs:label": "Deduplicatedreads", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:MSAssayCategory" + }, + { + "@id": "bts:SoftwareandVersion" + }, + { + "@id": "bts:MassSpectrometryAuxiliaryFile" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Deduplicated reads", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:InSituNegativemedian", + "@id": "bts:MSAssayCategory", "@type": "rdfs:Class", - "rdfs:comment": "Is the median of all negative control probes for a given segment. A measure of signal to background for each segment.", - "rdfs:label": "InSituNegativemedian", + "rdfs:comment": "Type of Mass Spectrometry performed.", + "rdfs:label": "MSAssayCategory", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:MassSpectrometryLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "In Situ Negative median", - "sms:required": "sms:false", + "sms:displayName": "MS Assay Category", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Biologicalprobemedian", + "@id": "bts:MassSpectrometryAuxiliaryFile", "@type": "rdfs:Class", - "rdfs:comment": "Is the median count from all probes except the negative control probes. A measure of signal to background for each segment", - "rdfs:label": "Biologicalprobemedian", + "rdfs:comment": "Auxiliary software parameter file used in mass spectrometry data processing, recorded as synapse ID (syn12345).", + "rdfs:label": "MassSpectrometryAuxiliaryFile", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Biological probe median", + "sms:displayName": "Mass Spectrometry Auxiliary File", "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" + } + ], "sms:validationRules": [] }, { - "@id": "bts:HI-C-seqLevel1", + "@id": "bts:MassSpectrometryLevel3", "@type": "rdfs:Class", - "rdfs:comment": "Unaligned sequence data", - "rdfs:label": "HI-C-seqLevel1", + "rdfs:comment": "Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 3", + "rdfs:label": "MassSpectrometryLevel3", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HI-C-seq Level 1", + "sms:displayName": "Mass Spectrometry Level 3", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:Biospecimen" + "@id": "bts:MassSpectrometryLevel2" } ], "sms:requiresDependency": [ { "@id": "bts:Component" }, - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:HTANDataFileID" - }, { "@id": "bts:Filename" }, @@ -45220,123 +48623,136 @@ "@id": "bts:FileFormat" }, { - "@id": "bts:GenomicReference" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:SequencingPlatform" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:NucleicAcidSource" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:TechnicalReplicateGroup" + "@id": "bts:MSAssayCategory" }, { - "@id": "bts:TranspositionReaction" + "@id": "bts:SoftwareandVersion" }, { - "@id": "bts:CrosslinkingCondtion" + "@id": "bts:MassSpectrometryAuxiliaryFile" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:MassSpectrometryLevel4", + "@type": "rdfs:Class", + "rdfs:comment": "Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 4", + "rdfs:label": "MassSpectrometryLevel4", + "rdfs:subClassOf": [ + { + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Mass Spectrometry Level 4", + "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:MassSpectrometryLevel3" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:DNADigestionCondition" + "@id": "bts:Filename" }, { - "@id": "bts:NucleiPermeabilizationMethod" + "@id": "bts:FileFormat" }, { - "@id": "bts:LigationCondition" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:BiotinEnrichment" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:DNAInputAmount" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:TotalReads" + "@id": "bts:MSAssayCategory" }, { - "@id": "bts:ProtocolLink" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:CrosslinkingCondtion", - "@type": "rdfs:Class", - "rdfs:comment": "Detailed condition for DNA crosslinking", - "rdfs:label": "CrosslinkingCondtion", - "rdfs:subClassOf": [ + "@id": "bts:SoftwareandVersion" + }, { - "@id": "bts:Sequencing" + "@id": "bts:MassSpectrometryAuxiliaryFile" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Crosslinking Condtion", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:DNADigestionCondition", + "@id": "bts:HTANChannelMetadataID", "@type": "rdfs:Class", - "rdfs:comment": "Enzymes and treatment length/temperature for genome digestion", - "rdfs:label": "DNADigestionCondition", + "rdfs:comment": "HTAN ID for this channel metadata table (same for all rows)", + "rdfs:label": "HTANChannelMetadataID", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "DNA Digestion Condition", + "sms:displayName": "HTAN Channel Metadata ID", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:NucleiPermeabilizationMethod", + "@id": "bts:ChannelID", "@type": "rdfs:Class", - "rdfs:comment": "Detergent and treatment condition for nuclei permeabilization and crosslinking softening", - "rdfs:label": "NucleiPermeabilizationMethod", + "rdfs:comment": "This must match the corresponding field in the OME-XML / TIFF header. (eg 'Channel:0:1')", + "rdfs:label": "ChannelID", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Nuclei Permeabilization Method", + "sms:displayName": "Channel ID", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LigationCondition", + "@id": "bts:ChannelName", "@type": "rdfs:Class", - "rdfs:comment": "Name of ligase and condition for proximity ligation", - "rdfs:label": "LigationCondition", + "rdfs:comment": "This must match the corresponding field in the OME-XML / TIFF header. (eg 'Blue' or 'CD45' or 'E-cadherin')", + "rdfs:label": "ChannelName", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ligation Condition", + "sms:displayName": "Channel Name", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BiotinEnrichment", + "@id": "bts:ChannelPassedQC", "@type": "rdfs:Class", - "rdfs:comment": "Whether biotin is used for enriching ligation product", - "rdfs:label": "BiotinEnrichment", + "rdfs:comment": "Identify stains that did not pass QC but are included in the dataset.", + "rdfs:label": "ChannelPassedQC", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { @@ -45347,275 +48763,247 @@ "@id": "bts:Yes" }, { - "@id": "bts:No" + "@id": "bts:No-ChannelFailedQC" } ], - "sms:displayName": "Biotin Enrichment", + "sms:displayName": "Channel Passed QC", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:DNAInputAmount", + "@id": "bts:CycleNumber", "@type": "rdfs:Class", - "rdfs:comment": "Amount of DNA for library construction, in nanograms.", - "rdfs:label": "DNAInputAmount", + "rdfs:comment": "The cycle # in which the co-listed reagent(s) was(were) used. Integer >= 1 (up to number of cycles)", + "rdfs:label": "CycleNumber", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "DNA Input Amount", - "sms:required": "sms:true", + "sms:displayName": "Cycle Number", + "sms:required": "sms:false", "sms:validationRules": [ "int" ] }, { - "@id": "bts:HI-C-seqLevel2", + "@id": "bts:SubCycleNumber", "@type": "rdfs:Class", - "rdfs:comment": "Aligned read pairs, contact matrix", - "rdfs:label": "HI-C-seqLevel2", + "rdfs:comment": "Sub cycle number", + "rdfs:label": "SubCycleNumber", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HI-C-seq Level 2", + "sms:displayName": "Sub Cycle Number", "sms:required": "sms:false", - "sms:requiresComponent": [ + "sms:validationRules": [ + "int" + ] + }, + { + "@id": "bts:AntibodyRole", + "@type": "rdfs:Class", + "rdfs:comment": "\"Is this antibody acting as a primary or secondary antibody\"", + "rdfs:label": "AntibodyRole", + "rdfs:subClassOf": [ { - "@id": "bts:HI-C-seqLevel1" + "@id": "bts:ImagingLevel3Channels" } ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:GenomicReference" - }, - { - "@id": "bts:AlignedReadLength" - }, - { - "@id": "bts:Tool" - }, + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Resolution" + "@id": "bts:Primary" }, { - "@id": "bts:NormalizationMethod" + "@id": "bts:Secondary" } ], + "sms:displayName": "Antibody Role", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AlignedReadLength", + "@id": "bts:TargetName", "@type": "rdfs:Class", - "rdfs:comment": "Read length used for alignment if hard trimming was applied", - "rdfs:label": "AlignedReadLength", + "rdfs:comment": "Short descriptive name (abbreviation) for this target (antigen)", + "rdfs:label": "TargetName", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Aligned Read Length", + "sms:displayName": "Target Name", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Tool", + "@id": "bts:AntibodyName", "@type": "rdfs:Class", - "rdfs:comment": "Were any software or computational tools generated for this content", - "rdfs:label": "Tool", + "rdfs:comment": "Antibody Name (free text (eg “Keratin”, “CD163”, “DNA”))", + "rdfs:label": "AntibodyName", "rdfs:subClassOf": [ { - "@id": "bts:Publication" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" - } - ], - "sms:displayName": "Tool", + "sms:displayName": "Antibody Name", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Resolution", + "@id": "bts:RRIDidentifier", "@type": "rdfs:Class", - "rdfs:comment": "Binning size used for generating contact matrix, in basepair.", - "rdfs:label": "Resolution", + "rdfs:comment": "Research Resource Identifier (eg “RRID: AB_394606”)", + "rdfs:label": "RRIDidentifier", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Resolution", + "sms:displayName": "RRID identifier", "sms:required": "sms:true", - "sms:validationRules": [] + "sms:validationRules": [ + "regex match AB_\\d+" + ] }, { - "@id": "bts:HI-C-seqLevel3", + "@id": "bts:Fluorophore", "@type": "rdfs:Class", - "rdfs:comment": "Summary data for the HI-C-seq assay.", - "rdfs:label": "HI-C-seqLevel3", + "rdfs:comment": "Fluorescent dye label (eg Alexa Fluor 488)", + "rdfs:label": "Fluorophore", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HI-C-seq Level 3", + "sms:displayName": "Fluorophore", "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:HI-C-seqLevel2" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:GenomicReference" - }, - { - "@id": "bts:StripeCalling" - }, - { - "@id": "bts:LoopWindow" - }, - { - "@id": "bts:StripeWindow" - }, + "sms:validationRules": [] + }, + { + "@id": "bts:Lot", + "@type": "rdfs:Class", + "rdfs:comment": "Lot number from vendor", + "rdfs:label": "Lot", + "rdfs:subClassOf": [ { - "@id": "bts:LoopCalling" + "@id": "bts:ImagingLevel3Channels" } ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Lot", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:StripeCalling", + "@id": "bts:ExcitationWavelength", "@type": "rdfs:Class", - "rdfs:comment": "Tool used for identifying architectural stripe-forming, interaction hotspots.", - "rdfs:label": "StripeCalling", + "rdfs:comment": "Center/peak of the excitation spectrum (nm)", + "rdfs:label": "ExcitationWavelength", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:MACS2" - }, + "sms:displayName": "Excitation Wavelength", + "sms:required": "sms:false", + "sms:validationRules": [ + "num" + ] + }, + { + "@id": "bts:EmissionWavelength", + "@type": "rdfs:Class", + "rdfs:comment": "Center/peak of the emission spectrum (nm)", + "rdfs:label": "EmissionWavelength", + "rdfs:subClassOf": [ { - "@id": "bts:Other" + "@id": "bts:ImagingLevel3Channels" } ], - "sms:displayName": "Stripe Calling", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Emission Wavelength", + "sms:required": "sms:false", "sms:validationRules": [ - "list", - "-?\\d+" + "num" ] }, { - "@id": "bts:LoopWindow", + "@id": "bts:ExcitationBandwidth", "@type": "rdfs:Class", - "rdfs:comment": "Binning size used for calling significant dot interactions (loops)", - "rdfs:label": "LoopWindow", + "rdfs:comment": "Nominal width of excitation spectrum (nm)", + "rdfs:label": "ExcitationBandwidth", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Loop Window", - "sms:required": "sms:true", + "sms:displayName": "Excitation Bandwidth", + "sms:required": "sms:false", "sms:validationRules": [ - "list like ", - " regex search -?\\d+" + "num" ] }, { - "@id": "bts:StripeWindow", + "@id": "bts:EmissionBandwidth", "@type": "rdfs:Class", - "rdfs:comment": "Binning size used for calling significant architectural stripes. Can be an integer or comma-separated list of integers indicating bin size and sliding window size if different.", - "rdfs:label": "StripeWindow", + "rdfs:comment": "Nominal width of emission spectrum (nm)", + "rdfs:label": "EmissionBandwidth", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Stripe Window", - "sms:required": "sms:true", + "sms:displayName": "Emission Bandwidth", + "sms:required": "sms:false", "sms:validationRules": [ - "list like ", - " regex search -?\\d+" + "num" ] }, { - "@id": "bts:LoopCalling", + "@id": "bts:MetalIsotopeElement", "@type": "rdfs:Class", - "rdfs:comment": "Tool used for identifying loop interactions", - "rdfs:label": "LoopCalling", + "rdfs:comment": "Element abbreviation. eg “La” or “Nd”", + "rdfs:label": "MetalIsotopeElement", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { @@ -45623,7528 +49011,6372 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:HiCCUPS" + "@id": "bts:H" }, { - "@id": "bts:Cooltools" + "@id": "bts:He" }, { - "@id": "bts:Other" - } - ], - "sms:displayName": "Loop Calling", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Yes", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Yes", - "rdfs:subClassOf": [ + "@id": "bts:Li" + }, { - "@id": "bts:BiotinEnrichment" + "@id": "bts:Be" }, { - "@id": "bts:ChannelPassedQC" + "@id": "bts:B" }, { - "@id": "bts:Pyramid" + "@id": "bts:C" }, { - "@id": "bts:Zstack" + "@id": "bts:N" }, { - "@id": "bts:Tseries" + "@id": "bts:O" }, { - "@id": "bts:PassedQC" + "@id": "bts:F" }, { - "@id": "bts:WellIndex" + "@id": "bts:Ne" }, { - "@id": "bts:CryopreservedCellsinSample" + "@id": "bts:Na" }, { - "@id": "bts:PrematureAtBirth" + "@id": "bts:Mg" }, { - "@id": "bts:AlcoholHistory" + "@id": "bts:Al" }, { - "@id": "bts:AsbestosExposure" + "@id": "bts:Si" }, { - "@id": "bts:CoalDustExposure" + "@id": "bts:P" }, { - "@id": "bts:EnvironmentalTobaccoSmokeExposure" + "@id": "bts:S" + }, + { + "@id": "bts:Cl" }, { - "@id": "bts:RadonExposure" + "@id": "bts:Ar" }, { - "@id": "bts:RespirableCrystallineSilicaExposure" + "@id": "bts:K" }, { - "@id": "bts:SecondhandSmokeasChild" + "@id": "bts:Ca" }, { - "@id": "bts:HepatitisSustainedVirologicalResponse" + "@id": "bts:Sc" }, { - "@id": "bts:HAARTTreatmentIndicator" + "@id": "bts:Ti" }, { - "@id": "bts:RiskFactorTreatment" + "@id": "bts:V" }, { - "@id": "bts:ChemoConcurrenttoRadiation" + "@id": "bts:Cr" }, { - "@id": "bts:TreatmentEffectIndicator" + "@id": "bts:Mn" }, { - "@id": "bts:SatelliteMetastasisPresentIndicator" + "@id": "bts:Fe" }, { - "@id": "bts:Immunosuppression" + "@id": "bts:Co" }, { - "@id": "bts:COVID19OccurrenceIndicator" + "@id": "bts:Ni" }, { - "@id": "bts:COVID19PositiveLabTestIndicator" + "@id": "bts:Cu" }, { - "@id": "bts:COVID19CancerTreatmentFollowup" + "@id": "bts:Zn" }, { - "@id": "bts:KnownGeneticPredispositionMutation" + "@id": "bts:Ga" }, { - "@id": "bts:MismatchRepairMutation" + "@id": "bts:Ge" }, { - "@id": "bts:NonNodalTumorDeposits" + "@id": "bts:As" }, { - "@id": "bts:PregnantatDiagnosis" + "@id": "bts:Se" }, { - "@id": "bts:PriorMalignancy" + "@id": "bts:Br" }, { - "@id": "bts:PriorTreatment" + "@id": "bts:Kr" }, { - "@id": "bts:LymphaticInvasionPresent" + "@id": "bts:Rb" }, { - "@id": "bts:PerineuralInvasionPresent" + "@id": "bts:Sr" }, { - "@id": "bts:SynchronousMalignancy" + "@id": "bts:Y" }, { - "@id": "bts:TumorConfinedtoOrganofOrigin" + "@id": "bts:Zr" }, { - "@id": "bts:HistoryofPriorColonPolyps" + "@id": "bts:Nb" }, { - "@id": "bts:FamilyColonCancerHistoryIndicator" + "@id": "bts:Mo" }, { - "@id": "bts:FamilyMedicalHistoryColorectalPolypDiagnosis" + "@id": "bts:Tc" }, { - "@id": "bts:PatientColonoscopyPerformedIndicator" + "@id": "bts:Ru" }, { - "@id": "bts:ColorectalCancerKRASIndicator" + "@id": "bts:Rh" }, { - "@id": "bts:ColonPolypOccurenceIndicator" + "@id": "bts:Pd" }, { - "@id": "bts:FamilyHistoryColorectalPolyp" + "@id": "bts:Ag" }, { - "@id": "bts:ColorectalPolypNewIndicator" + "@id": "bts:Cd" }, { - "@id": "bts:HormoneTherapyBreastCancerPreventionIndicator" + "@id": "bts:In" }, { - 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Can be genes/transcripts or probes", - "rdfs:label": "TotalNumberofTargets", + "rdfs:comment": "TBD", + "rdfs:label": "O", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Total Number of Targets", - "sms:required": "sms:true", + "sms:displayName": "O", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ExperimentIFChannels", + "@id": "bts:F", "@type": "rdfs:Class", - "rdfs:comment": "A comma-separated list with any number of channels the user deems appropriate(Example: PanCK, CD45, CD3, DAPI)", - "rdfs:label": "ExperimentIFChannels", + "rdfs:comment": "TBD", + "rdfs:label": "F", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Experiment IF Channels", - "sms:required": "sms:true", + "sms:displayName": "F", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TranscriptsperCell", + "@id": "bts:Ne", "@type": "rdfs:Class", - "rdfs:comment": "Mean or Median transcript count per cell analyzed on the flow cell or slide", - "rdfs:label": "TranscriptsperCell", + "rdfs:comment": "TBD", + "rdfs:label": "Ne", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Transcripts per Cell", - "sms:required": "sms:true", + "sms:displayName": "Ne", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentofTranscriptswithinCells", + "@id": "bts:Na", "@type": "rdfs:Class", - "rdfs:comment": "The percentage of transcripts assigned to assayed cells", - "rdfs:label": "PercentofTranscriptswithinCells", + "rdfs:comment": "TBD", + "rdfs:label": "Na", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent of Transcripts within Cells", - "sms:required": "sms:true", + "sms:displayName": "Na", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DecodedTranscripts", + "@id": "bts:Mg", "@type": "rdfs:Class", - "rdfs:comment": "In Xenium, this is the number of high-quality, decoded-to-gene nuclear transcripts divided by the total segmented nuclear area to get a transcript density (units are reported in 100um^2).", - "rdfs:label": "DecodedTranscripts", + "rdfs:comment": "TBD", + "rdfs:label": "Mg", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Decoded Transcripts", - "sms:required": "sms:true", + "sms:displayName": "Mg", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:XeniumIFimageHTANFileID", + "@id": "bts:Al", "@type": "rdfs:Class", - "rdfs:comment": "The HTAN Data File ID of a Imaging Level 2 file", - "rdfs:label": "XeniumIFimageHTANFileID", + "rdfs:comment": "TBD", + "rdfs:label": "Al", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Xenium IF image HTAN File ID", + "sms:displayName": "Al", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:XeniumHEimageHTANFileID", + "@id": "bts:Si", "@type": "rdfs:Class", - "rdfs:comment": "The HTAN Data File ID of a Imaging Level 2 file", - "rdfs:label": "XeniumHEimageHTANFileID", + "rdfs:comment": "TBD", + "rdfs:label": "Si", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Xenium HE image HTAN File ID", + "sms:displayName": "Si", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RPPALevel2", + "@id": "bts:P", "@type": "rdfs:Class", - "rdfs:comment": "Array based protemics. Each dilution curve of spot intensities is fitted using the monotone increasing B-spline model in the SuperCurve R package. This fits a single curve using all the samples on a slide with the signal intensity as the response variable and the dilution steps as independent variables. 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(eg 'Channel:0:1')", - "rdfs:label": "ChannelID", + "rdfs:comment": "TBD", + "rdfs:label": "Pa", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Channel ID", - "sms:required": "sms:true", + "sms:displayName": "Pa", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ChannelName", + "@id": "bts:U", "@type": "rdfs:Class", - "rdfs:comment": "This must match the corresponding field in the OME-XML / TIFF header. (eg 'Blue' or 'CD45' or 'E-cadherin')", - "rdfs:label": "ChannelName", + "rdfs:comment": "TBD", + "rdfs:label": "U", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Channel Name", - "sms:required": "sms:true", + "sms:displayName": "U", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ChannelPassedQC", + "@id": "bts:Np", "@type": "rdfs:Class", - "rdfs:comment": "Identify stains that did not pass QC but are included in the dataset.", - "rdfs:label": "ChannelPassedQC", + "rdfs:comment": "TBD", + "rdfs:label": "Np", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" - }, - { - "@id": "bts:No-ChannelFailedQC" - } - ], - "sms:displayName": "Channel Passed QC", - "sms:required": "sms:true", + "sms:displayName": "Np", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CycleNumber", + "@id": "bts:Pu", "@type": "rdfs:Class", - "rdfs:comment": "The cycle # in which the co-listed reagent(s) was(were) used. Integer >= 1 (up to number of cycles)", - "rdfs:label": "CycleNumber", + "rdfs:comment": "TBD", + "rdfs:label": "Pu", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cycle Number", + "sms:displayName": "Pu", "sms:required": "sms:false", - "sms:validationRules": [ - "int" - ] + "sms:validationRules": [] }, { - "@id": "bts:SubCycleNumber", + "@id": "bts:Bk", "@type": "rdfs:Class", - "rdfs:comment": "Sub cycle number", - "rdfs:label": "SubCycleNumber", + "rdfs:comment": "TBD", + "rdfs:label": "Bk", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Sub Cycle Number", + "sms:displayName": "Bk", "sms:required": "sms:false", - "sms:validationRules": [ - "int" - ] + "sms:validationRules": [] }, { - "@id": "bts:AntibodyRole", + "@id": "bts:Cf", "@type": "rdfs:Class", - "rdfs:comment": "\"Is this antibody acting as a primary or secondary antibody\"", - "rdfs:label": "AntibodyRole", + "rdfs:comment": "TBD", + "rdfs:label": "Cf", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Primary" - }, - { - "@id": "bts:Secondary" - } - ], - "sms:displayName": "Antibody Role", - "sms:required": "sms:true", + "sms:displayName": "Cf", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TargetName", + "@id": "bts:Es", "@type": "rdfs:Class", - "rdfs:comment": "Short descriptive name (abbreviation) for this target (antigen)", - "rdfs:label": "TargetName", + "rdfs:comment": "TBD", + "rdfs:label": "Es", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Target Name", - "sms:required": "sms:true", + "sms:displayName": "Es", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AntibodyName", + "@id": "bts:Fm", "@type": "rdfs:Class", - "rdfs:comment": "Antibody Name (free text (eg “Keratin”, “CD163”, “DNA”))", - "rdfs:label": "AntibodyName", + "rdfs:comment": "TBD", + "rdfs:label": "Fm", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Antibody Name", - "sms:required": "sms:true", + "sms:displayName": "Fm", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RRIDidentifier", + "@id": "bts:Lr", "@type": "rdfs:Class", - "rdfs:comment": "Research Resource Identifier (eg “RRID: AB_394606”)", - "rdfs:label": "RRIDidentifier", + "rdfs:comment": "TBD", + "rdfs:label": "Lr", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "RRID identifier", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match AB_\\d+" - ] + "sms:displayName": "Lr", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:Fluorophore", + "@id": "bts:Rf", "@type": "rdfs:Class", - "rdfs:comment": "Fluorescent dye label (eg Alexa Fluor 488)", - "rdfs:label": "Fluorophore", + "rdfs:comment": "TBD", + "rdfs:label": "Rf", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Fluorophore", + "sms:displayName": "Rf", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Lot", + "@id": "bts:Db", "@type": "rdfs:Class", - "rdfs:comment": "Lot number from vendor", - "rdfs:label": "Lot", + "rdfs:comment": "TBD", + "rdfs:label": "Db", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Lot", + "sms:displayName": "Db", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ExcitationWavelength", + "@id": "bts:Sg", "@type": "rdfs:Class", - "rdfs:comment": "Center/peak of the excitation spectrum (nm)", - "rdfs:label": "ExcitationWavelength", + "rdfs:comment": "TBD", + "rdfs:label": "Sg", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Excitation Wavelength", + "sms:displayName": "Sg", "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] + "sms:validationRules": [] }, { - "@id": "bts:EmissionWavelength", + "@id": "bts:Bh", "@type": "rdfs:Class", - "rdfs:comment": "Center/peak of the emission spectrum (nm)", - "rdfs:label": "EmissionWavelength", + "rdfs:comment": "TBD", + "rdfs:label": "Bh", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Emission Wavelength", + "sms:displayName": "Bh", "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] + "sms:validationRules": [] }, { - "@id": "bts:ExcitationBandwidth", + "@id": "bts:Hs", "@type": "rdfs:Class", - "rdfs:comment": "Nominal width of excitation spectrum (nm)", - "rdfs:label": "ExcitationBandwidth", + "rdfs:comment": "TBD", + "rdfs:label": "Hs", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Excitation Bandwidth", + "sms:displayName": "Hs", "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] + "sms:validationRules": [] }, { - "@id": "bts:EmissionBandwidth", + "@id": "bts:Mt", "@type": "rdfs:Class", - "rdfs:comment": "Nominal width of emission spectrum (nm)", - "rdfs:label": "EmissionBandwidth", + "rdfs:comment": "TBD", + "rdfs:label": "Mt", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Emission Bandwidth", + "sms:displayName": "Mt", "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] + "sms:validationRules": [] }, { - "@id": "bts:MetalIsotopeElement", + "@id": "bts:Ds", "@type": "rdfs:Class", - "rdfs:comment": "Element abbreviation. eg “La” or “Nd”", - "rdfs:label": "MetalIsotopeElement", + "rdfs:comment": "TBD", + "rdfs:label": "Ds", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:H" - }, - { - "@id": "bts:He" - }, - { - "@id": "bts:Li" - }, - { - "@id": "bts:Be" - }, - { - "@id": "bts:B" - }, - { - "@id": "bts:C" - }, - { - "@id": "bts:N" - }, - { - "@id": "bts:O" - }, - { - "@id": "bts:F" - }, - { - "@id": "bts:Ne" - }, - { - "@id": "bts:Na" - }, - { - "@id": "bts:Mg" - }, - { - "@id": "bts:Al" - }, - { - "@id": "bts:Si" - }, - { - "@id": "bts:P" - }, - { - "@id": "bts:S" - }, - { - "@id": "bts:Cl" - }, - { - "@id": "bts:Ar" - }, - { - "@id": "bts:K" - }, - { - "@id": "bts:Ca" - }, - { - "@id": "bts:Sc" - }, - { - "@id": "bts:Ti" - }, - { - "@id": "bts:V" - }, - { - "@id": "bts:Cr" - }, - { - "@id": "bts:Mn" - }, - { - "@id": "bts:Fe" - }, - { - "@id": "bts:Co" - }, - { - "@id": "bts:Ni" - }, - { - "@id": "bts:Cu" - }, - { - "@id": "bts:Zn" - }, - { - "@id": "bts:Ga" - }, - { - "@id": "bts:Ge" - }, - { - "@id": "bts:As" - }, - { - "@id": "bts:Se" - }, - { - "@id": "bts:Br" - }, - { - "@id": "bts:Kr" - }, - { - "@id": "bts:Rb" - }, - { - "@id": "bts:Sr" - }, - { - "@id": "bts:Y" - }, - { - "@id": "bts:Zr" - }, - { - "@id": "bts:Nb" - }, - { - "@id": "bts:Mo" - }, - { - "@id": "bts:Tc" - }, - { - "@id": "bts:Ru" - }, - { - "@id": "bts:Rh" - }, - { - "@id": "bts:Pd" - }, - { - "@id": "bts:Ag" - }, - { - "@id": "bts:Cd" - }, - { - "@id": "bts:In" - }, - { - "@id": "bts:Sn" - }, - { - "@id": "bts:Sb" - }, - { - "@id": "bts:Te" - }, - { - "@id": "bts:I" - }, - { - "@id": "bts:Xe" - }, - { - "@id": "bts:Cs" - }, - { - "@id": "bts:Ba" - }, - { - "@id": "bts:La" - }, - { - "@id": "bts:Ce" - }, - { - "@id": "bts:Pr" - }, - { - "@id": "bts:Nd" - }, - { - "@id": "bts:Pm" - }, - { - "@id": "bts:Sm" - }, - { - "@id": "bts:Eu" - }, - { - "@id": "bts:Gd" - }, - { - "@id": "bts:Tb" - }, - { - "@id": "bts:Dy" - }, - { - "@id": "bts:Ho" - }, - { - "@id": "bts:Er" - }, - { - "@id": "bts:Tm" - }, - { - "@id": "bts:Yb" - }, - { - "@id": "bts:Lu" - }, - { - "@id": "bts:Hf" - }, - { - "@id": "bts:Ta" - }, - { - "@id": "bts:W" - }, - { - "@id": "bts:Re" - }, - { - "@id": "bts:Os" - }, - { - "@id": "bts:Ir" - }, - { - "@id": "bts:Pt" - }, - { - "@id": "bts:Au" - }, - { - "@id": "bts:Hg" - }, - { - "@id": "bts:Tl" - }, - { - "@id": "bts:Pb" - }, - { - "@id": "bts:Bi" - }, - { - "@id": "bts:Po" - }, - { - "@id": "bts:At" - }, - { - "@id": "bts:Rn" - }, - { - "@id": "bts:Fr" - }, - { - "@id": "bts:Ra" - }, - { - "@id": "bts:Ac" - }, - { - "@id": "bts:Th" - }, - { - "@id": "bts:Pa" - }, - { - "@id": "bts:U" - }, - { - "@id": "bts:Np" - }, - { - "@id": "bts:Pu" - }, - { - "@id": "bts:Am" - }, - { - "@id": "bts:Bk" - }, - { - "@id": "bts:Cf" - }, - { - "@id": "bts:Es" - }, - { - "@id": "bts:Fm" - }, - { - "@id": "bts:Md" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Lr" - }, - { - "@id": "bts:Rf" - }, - { - "@id": "bts:Db" - }, - { - "@id": "bts:Sg" - }, - { - "@id": "bts:Bh" - }, - { - "@id": "bts:Hs" - }, - { - "@id": "bts:Mt" - }, - { - "@id": "bts:Ds" - }, - { - "@id": "bts:Rg" - }, - { - "@id": "bts:Cn" - }, - { - "@id": "bts:Nh" - }, - { - "@id": "bts:Fl" - }, - { - "@id": "bts:Mc" - }, - { - "@id": "bts:Lv" - }, - { - "@id": "bts:Ts" - }, - { - "@id": "bts:Og" - } - ], - "sms:displayName": "Metal Isotope Element", + "sms:displayName": "Ds", "sms:required": "sms:false", - "sms:validationRules": [ - "str" - ] + "sms:validationRules": [] }, { - "@id": "bts:MetalIsotopeMass", + "@id": "bts:Rg", "@type": "rdfs:Class", - "rdfs:comment": "Element mass number", - "rdfs:label": "MetalIsotopeMass", + "rdfs:comment": "TBD", + "rdfs:label": "Rg", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Metal Isotope Mass", + "sms:displayName": "Rg", "sms:required": "sms:false", - "sms:validationRules": [ - "int" - ] + "sms:validationRules": [] }, { - "@id": "bts:OligoBarcodeUpperStrand", + "@id": "bts:Cn", "@type": "rdfs:Class", - "rdfs:comment": "Oligo Barcode - Upper Strand", - "rdfs:label": "OligoBarcodeUpperStrand", + "rdfs:comment": "TBD", + "rdfs:label": "Cn", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Oligo Barcode Upper Strand", + "sms:displayName": "Cn", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:OligoBarcodeLowerStrand", + "@id": "bts:Nh", "@type": "rdfs:Class", - "rdfs:comment": "Oligo Barcode - Lower Strand", - "rdfs:label": "OligoBarcodeLowerStrand", + "rdfs:comment": "TBD", + "rdfs:label": "Nh", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Oligo Barcode Lower Strand", + "sms:displayName": "Nh", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Dilution", + "@id": "bts:Fl", "@type": "rdfs:Class", - "rdfs:comment": "Dilution (eg 1:1000)", - "rdfs:label": "Dilution", + "rdfs:comment": "TBD", + "rdfs:label": "Fl", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Dilution", + "sms:displayName": "Fl", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Concentration", + "@id": "bts:Mc", "@type": "rdfs:Class", - "rdfs:comment": "Concentration (eg 10ug/mL)", - "rdfs:label": "Concentration", + "rdfs:comment": "TBD", + "rdfs:label": "Mc", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Concentration", + "sms:displayName": "Mc", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:No-ChannelFailedQC", + "@id": "bts:Lv", "@type": "rdfs:Class", - "rdfs:comment": "Channel failed QC", - "rdfs:label": "No-ChannelFailedQC", + "rdfs:comment": "TBD", + "rdfs:label": "Lv", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" - }, - { - "@id": "bts:ChannelPassedQC" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "No - Channel Failed QC", + "sms:displayName": "Lv", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:ChannelQCFailureType" - } - ], "sms:validationRules": [] }, { - "@id": "bts:ChannelQCFailureType", + "@id": "bts:Ts", "@type": "rdfs:Class", - "rdfs:comment": "Reason the channel failed QC", - "rdfs:label": "ChannelQCFailureType", + "rdfs:comment": "TBD", + "rdfs:label": "Ts", "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Off-targetstaining" - }, - { - "@id": "bts:Auto-fluoresence" - }, - { - "@id": "bts:Stainingartefacet" - }, - { - "@id": "bts:Imagingartefact" - }, - { - "@id": "bts:Other/multiplechannelQCfaliuretypes" - } - ], - "sms:displayName": "Channel QC Failure Type", + "sms:displayName": "Ts", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Off-targetstaining", + "@id": "bts:Og", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Off-targetstaining", + "rdfs:label": "Og", "rdfs:subClassOf": [ { - "@id": "bts:ChannelQCFailureType" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Off-target staining", + "sms:displayName": "Og", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Auto-fluoresence", + "@id": "bts:H&E", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Auto-fluoresence", + "rdfs:label": "H&E", "rdfs:subClassOf": [ { - "@id": "bts:ChannelQCFailureType" + "@id": "bts:ImagingAssayType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Auto-fluoresence", + "sms:displayName": "H&E", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Stainingartefacet", + "@id": "bts:CyCIF", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Stainingartefacet", + "rdfs:label": "CyCIF", "rdfs:subClassOf": [ { - "@id": "bts:ChannelQCFailureType" + "@id": "bts:ImagingAssayType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Staining artefacet", + "sms:displayName": "CyCIF", "sms:required": "sms:false", "sms:validationRules": [] }, { - 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Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]", - "rdfs:label": "FeatureReferenceId", - "rdfs:subClassOf": [ + "@id": "bts:PriorSitesofRadiation" + }, { - "@id": "bts:ScRNA-seqLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Feature Reference Id", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ERCC", - "@type": "rdfs:Class", - "rdfs:comment": "The External RNA Controls Consortium (ERCC) spike in set is commonly used in single-cell experiments for normalization", - "rdfs:label": "ERCC", - "rdfs:subClassOf": [ + "@id": "bts:TopographyCode" + }, { - "@id": "bts:SpikeIn" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "ERCC", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "@id": "bts:ProgressionorRecurrenceAnatomicSite" + }, { - "@id": "bts:SpikeInConcentration" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:OtherSpikeIn", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "OtherSpikeIn", - "rdfs:subClassOf": [ + "@id": "bts:TreatmentAnatomicSite" + }, { - "@id": "bts:SpikeIn" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Other Spike In", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:NoSpikeIn", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "NoSpikeIn", - "rdfs:subClassOf": [ + "@id": "bts:SiteofResectionorBiopsy" + }, { - "@id": "bts:SpikeIn" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "No Spike In", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PhiX", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "PhiX", - "rdfs:subClassOf": [ + "@id": "bts:TissueorOrganofOrigin" + }, { - "@id": "bts:SpikeIn" + "@id": "bts:PrimaryDiagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "PhiX", + "sms:displayName": "Not Reported", "sms:required": "sms:false", "sms:validationRules": [] }, - { - "@id": "bts:SpikeInConcentration", - "@type": "rdfs:Class", - "rdfs:comment": "The final concentration or dilution (for commercial sets) of the spike in mix [PMID:21816910]", - "rdfs:label": "SpikeInConcentration", - "rdfs:subClassOf": [ - { - "@id": "bts:ERCC" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Spike In Concentration", - "sms:required": "sms:true", - "sms:validationRules": [] - }, { "@id": "bts:NIB", "@type": "rdfs:Class", @@ -54132,27 +56364,10 @@ "sms:validationRules": [] }, { - "@id": "bts:HybridSelection", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "HybridSelection", - "rdfs:subClassOf": [ - { - "@id": "bts:LibrarySelectionMethod" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Hybrid Selection", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PCR", + "@id": "bts:AffinityEnrichment", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "PCR", + "rdfs:label": "AffinityEnrichment", "rdfs:subClassOf": [ { "@id": "bts:LibrarySelectionMethod" @@ -54161,15 +56376,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "PCR", + "sms:displayName": "Affinity Enrichment", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AffinityEnrichment", + "@id": "bts:Poly-TEnrichment", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "AffinityEnrichment", + "rdfs:label": "Poly-TEnrichment", "rdfs:subClassOf": [ { "@id": "bts:LibrarySelectionMethod" @@ -54178,15 +56393,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Affinity Enrichment", + "sms:displayName": "Poly-T Enrichment", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Poly-TEnrichment", + "@id": "bts:RRNADepletion", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Poly-TEnrichment", + "rdfs:label": "RRNADepletion", "rdfs:subClassOf": [ { "@id": "bts:LibrarySelectionMethod" @@ -54195,7 +56410,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Poly-T Enrichment", + "sms:displayName": "rRNA Depletion", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -60257,29 +62472,6 @@ "sms:required": "sms:false", "sms:validationRules": [] }, - { - "@id": "bts:Unspecified", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Unspecified", - "rdfs:subClassOf": [ - { - "@id": "bts:Gender" - }, - { - "@id": "bts:RelationshipGender" - }, - { - "@id": "bts:TumorExtranodalExtensionIndicator" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Unspecified", - "sms:required": "sms:false", - "sms:validationRules": [] - }, { "@id": "bts:White", "@type": "rdfs:Class", @@ -111617,23 +113809,6 @@ "sms:required": "sms:false", "sms:validationRules": [] }, - { - "@id": "bts:RT-PCR", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "RT-PCR", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularAnalysisMethod" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "RT-PCR", - "sms:required": "sms:false", - "sms:validationRules": [] - }, { "@id": "bts:SequencingNOS", "@type": "rdfs:Class", @@ -111685,40 +113860,6 @@ "sms:required": "sms:false", "sms:validationRules": [] }, - { - "@id": "bts:WGS", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "WGS", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularAnalysisMethod" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "WGS", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:WXS", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "WXS", - "rdfs:subClassOf": [ - { - "@id": "bts:MolecularAnalysisMethod" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "WXS", - "sms:required": "sms:false", - "sms:validationRules": [] - }, { "@id": "bts:AbnormalNOS", "@type": "rdfs:Class", @@ -142441,6 +144582,23 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:Publication", + "@type": "rdfs:Class", + "rdfs:comment": "An empty parent attribute for publications", + "rdfs:label": "Publication", + "rdfs:subClassOf": [ + { + "@id": "bts:Thing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Publication", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:PublicationManifest", "@type": "rdfs:Class", @@ -149800,6 +151958,329 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:10xVisiumSpatialTranscriptomics", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "10xVisiumSpatialTranscriptomics", + "rdfs:subClassOf": [ + { + "@id": "bts:DataType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "10x Visium Spatial Transcriptomics", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BulkMethylation-seq", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "BulkMethylation-seq", + "rdfs:subClassOf": [ + { + "@id": "bts:DataType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Bulk Methylation-seq", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BulkRNA-seq", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "BulkRNA-seq", + "rdfs:subClassOf": [ + { + "@id": "bts:DataType" + } + ], + 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