From 182c37c7c5c7cc4083bc0fe344d4921e7e0c40bf Mon Sep 17 00:00:00 2001 From: A N V <32753274+anngvu@users.noreply.github.com> Date: Fri, 19 May 2023 10:30:43 -0600 Subject: [PATCH] Patch/new terms with linter (#292) * changes to metadata * deleted assays added previously * Update annotationProperty.csv * Update annotationProperty.csv * Update File_Format.csv * Update annotationProperty.csv * Update annotationProperty.csv * Update annotationProperty.csv * Update Assay.csv * Update Assay.csv * Update annotationProperty.csv * Update File_Format.csv * Reorganize utils and add linter * Update ci workflow * Challenge linter with incorrect update * Fix, resolve #209 * Build jsonld --------- Co-authored-by: cconrad8 Co-authored-by: Christina Conrad <114612268+cconrad8@users.noreply.github.com> Co-authored-by: nf-osi[bot] --- .github/workflows/schematic-ci.yml | 19 +- NF.csv | 23 +- NF.jsonld | 1764 ++++++++++++++------------ modules/Assay/Assay.csv | 5 +- modules/Assay/Assay_Parameter.csv | 1 + modules/Assay/Platform.csv | 1 - modules/Assay/annotationProperty.csv | 10 +- modules/Data/File_Format.csv | 2 + modules/Data/annotationProperty.csv | 6 +- utils/lint.clj | 41 + {scripts => utils}/toolsdb_sync.R | 0 11 files changed, 1003 insertions(+), 869 deletions(-) create mode 100644 utils/lint.clj rename {scripts => utils}/toolsdb_sync.R (100%) diff --git a/.github/workflows/schematic-ci.yml b/.github/workflows/schematic-ci.yml index 43a236ca..c038dcf3 100644 --- a/.github/workflows/schematic-ci.yml +++ b/.github/workflows/schematic-ci.yml @@ -17,17 +17,24 @@ jobs: runs-on: ubuntu-20.04 steps: - - name: Install System Dependencies - run: | - sudo apt-get update - sudo apt-get install -y pip python3.8-venv libcurl4-openssl-dev - - uses: actions/checkout@v3 with: ref: ${{ github.event.pull_request.head.ref }} persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal access token. fetch-depth: 0 # otherwise, there would be errors pushing refs to the destination repository - + + - name: Lint source in modules + shell: bash + run: | + bash < <(curl -s https://raw.githubusercontent.com/babashka/babashka/master/install) + FILES=$(git diff --name-only ${{ github.event.pull_request.head.ref }} origin/main -- modules/) + bb utils/lint.clj --files ${FILES} + + - name: Install other deps for schematic + run: | + sudo apt-get update + sudo apt-get install -y pip python3.8-venv libcurl4-openssl-dev + - name: Install schematic and convert schema shell: bash run: | diff --git a/NF.csv b/NF.csv index 2e72c99c..c89e74d1 100644 --- a/NF.csv +++ b/NF.csv @@ -40,7 +40,7 @@ western blot,A multistep process in which a mixture of proteins is separated by whole genome sequencing,Laboratory technique to sequence the complete DNA sequence of an organism's genome at a single time,,,FALSE,http://edamontology.org/topic_3673,assay,,,,Whole_Genome_Seq,Class,Assay,Assay,DNA_Assay,,, polymerase chain reaction,"A rapid technique for in vitro amplification of specific DNA or RNA sequences, allowing small quantities of short sequences to be analyzed without cloning",,,FALSE,http://purl.obolibrary.org/obo/MMO_0000459,assay,,,,Polymerase_Chain_Reaction,Class,Assay,Assay,RNA_Assay,,, cell viability assay,This assay type measures the cellular state of living or dying by measuring an indicator of life or death,,,FALSE,http://www.bioassayontology.org/bao#BAO_0003009,assay,,,,Cell_Viability_Assay,Class,Assay,Assay,Cell_Assay,,, -2D Incucyte,Cell viability assay on a 2D monolayer model.,,,FALSE,,assay,,,,2D_Incucyte_Assay,Class,Assay,Assay,Cell_Viability_Assay,,, +2D Incucyte,Cell viability assay on a 2D monolayer model.,,,FALSE,https://www.essenbioscience.com/en/resources/documents/,assay,,,,2D_Incucyte_Assay,Class,Assay,Assay,Cell_Viability_Assay,,, 2D CellTiter-Glo,Cell viability assay based on detection of ATP.,,,FALSE,https://www.promega.com/products/cell-health-assays/cell-viability-and-cytotoxicity-assays/celltiter_glo-2_0-assay/?catNum=G9241,assay,,,,2D_Cell_Titer_Glo_Assay,Class,Assay,Assay,Cell_Viability_Assay,,, 3D microtissue viability,Cell viability assay on a 3D microtissue model.,,,FALSE,https://www.ncbi.nlm.nih.gov/books/NBK343426/,assay,,,,3D_Microtissue_Viability_Assay,Class,Assay,Assay,Cell_Viability_Assay,,, 2D AlamarBlue fluorescence,"Cell viability assay based on detection of AlamarBlue (resazurin). Living cells reduce blue, non-fluorescent resazurin to the red, fluorescent molecule resorufin. The amount of fluorescence or absorbance is proportional to the number of living cells and corresponds to the cell’s metabolic activity. For the fluorescence-based assay, color change and fluorescence can be detected using 560/590 nm (excitation/emission).",,,FALSE,https://www.thermofisher.com/us/en/home/life-science/cell-analysis/fluorescence-microplate-assays/microplate-assays-cell-viability/alamarblue-assay-cell-viability.html,assay,,,,2D_AlamarBlue_Fluorescence,Class,Assay,Assay,Cell_Viability_Assay,,, @@ -124,8 +124,9 @@ in vitro tumorigenesis,"An in vitro assay devised to measure tumor formation",,, Matrigel-based tumorigenesis assay,"An assay in which tumor cells are loaded into a Matrigel matrix and measured for tumor formation characteristics",,,FALSE,,assay,,,,Matrigel-based_Tumorigenesis_Assay,Class,Assay,Assay,Tumorigenesis_Assay,,,See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3230200/ calcium retention capacity assay,"The CRC assay assesses Ca2+-related mitochondrial functions",,,FALSE,,assay,,,,Calcium_Retention_Capacity_Assay,Class,Assay,Assay,Cell_Assay,,,See https://pubmed.ncbi.nlm.nih.gov/29781984/ quantitative PCR,"Quantitative PCR (Q-PCR) is used to measure the quantity of a PCR product (commonly in real-time). It quantitatively measures starting amounts of DNA, cDNA, or RNA.",,,FALSE,http://purl.obolibrary.org/obo/MI_1195,assay,,,,Quantitative_PCR,Class,Assay,Assay,RNA_Assay,,, -clinical data, "Data pertaining to the medical well-being or status of a patient. Category also includes clinical reports and individual patient data.",,, FALSE,http://purl.obolibrary.org/obo/NCIT_C15783,assay,,,,Clinical_Data_Assay,Class,Assay,Assay,Assay,,, +clinical data,"Data pertaining to the medical well-being or status of a patient. Category also includes clinical reports and individual patient data.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C15783,assay,,,,Clinical_Data_Assay,Class,Assay,Assay,Assay,,, photograph,An image recorded by a camera.,"","",FALSE,http://purl.obolibrary.org/obo/NCIT_C86035,assay,,"","",Photograph,"",Assay,Assay,"","","","" +cAMP-Glo Max Assay,"The cAMP-Glo Max Assay from Promega is a bioluminescent assay used for the quantification of cyclic AMP (cAMP) in cell-based assays. It utilizes a luminescent luciferase-based detection system to detect the levels of cAMP in cell lysates, which can be used to study G protein-coupled receptor (GPCR) signaling and other intracellular signaling pathways.",,,FALSE,https://www.promega.com/products/cell-signaling/gpcr-signaling/camp_glo-max-assay/?catNum=V1681,assay,,,,cAMP_Glo_Max,Class,Assay,Assay,Assay,,, channel,Fluorescent color labeling for an array,"Cy5, Cy3","",TRUE,"",array,,"","",Channel,"",Assay,Assay_Parameter,"","","","" MRISequence,The scanning sequence/modality that is used for a conventional MRI scan.,"T1-weighted,T2-weighted,PD-weighted,Short Tau Inversion Recovery","",FALSE,Sage Bionetworks,experimentalData,,"","",MRI_Sequence,Class,Assay,Assay_Parameter,"","","","" T1-weighted,"","","",FALSE,Sage Bionetworks,MRISequence,,"","",T1-weighted,Class,Assay,Assay_Parameter,MRI_Sequence,"","","" @@ -171,6 +172,7 @@ forward,Read 1 (or unpaired read) comes from the forward strand and read 2 (if a reverse,read 1 (or unpaired read) comes from the reverse strand and read 2 (if applicable) comes from the forward strand; equivalent to Tophat 'fr-firststrand' type,"","",FALSE,Sage Bionetworks,readStrandOrigin,,"","",Reverse_Read,Class,Assay,Assay_Parameter,Read_Strand_Origin,"","","" singleEnd,A library preparation that results in the creation of a library of 5' ends of DNA.,"","",FALSE,Sage Bionetworks,runType,,"","",Single_End,Class,Assay,Assay_Parameter,Run_Type,"","","" pairedEnd,A library preparation that results in the creation of a library of the 5' and 3' ends of DNA or cDNA fragments using adaptors and endonucleases. The preparation may or may not include cloning process.,"","",FALSE,http://purl.obolibrary.org/obo/OBI_0001852,runType,,"","",Paired_End,Class,Assay,Assay_Parameter,Run_Type,"","","" +KAPA mRNA HyperPrep Kit,The KAPA mRNA HyperPrep Kit is a highly efficient library preparation kit designed for generating stranded RNA-seq libraries with low input amounts and reduced bias.,,,FALSE,https://sequencing.roche.com/global/en/products/group/kapa-rna-hyperprep-kits.html,libraryPreparationMethod,,,,KAPA_mRNA_HyperPrep,Class,Assay,Assay_Parameter,Library_Prep,,, jumpingLibrary,"","","",FALSE,"",assay,,"","",Jumping_Library,Class,Assay,Method,"","","","" RNAi,High throughput sample analysis of RNAi molecules for potential application in gene knockdown or gene silencing of target genes,"","",FALSE,http://purl.obolibrary.org/obo/ERO_0001688,genePerturbationTechnology,,"","",RNAi,Class,Assay,Method,Gene_Perturbation_Technology,"","","" CRISPR,"","","",FALSE,"",genePerturbationTechnology,,"","",CRISPR,Class,Assay,Method,Gene_Perturbation_Technology,"","","" @@ -235,10 +237,9 @@ LifeViz Micro System,"(From vendor) Portable 3D imaging system for skin microstr LifeViz Infinity System,"(From vendor) All-in-one 3D imaging system for face, body and breast.",,,FALSE,https://www.quantificare.com/3d-photography-systems_old/lifeviz-infinity/,platform,,,,LifeViz_Infinity_System,Class,Assay,Platform,Platform,,, Promega GloMax Discover,"(From vendor) Microplate reader with high-performance luminescence, fluorescence, UV-Visible absorbance, BRET and FRET, two-color filtered luminescence and kinetic measurement capabilities.",,,FALSE,https://www.promega.com/products/microplate-readers-fluorometers-luminometers/microplate-readers/glomax-discover-system/?catNum=GM3000,platform,,,,Promega_GloMax_Discover,Class,Assay,Platform,Platform,,, BGISEQ-500,"(From vendor) BGISEQ-500 is an industry leading high-throughput sequencing solution, powered by combinatorial Probe-Anchor Synthesis (cPAS) and improved DNA Nanoballs (DNB™) technology.",,,FALSE,https://www.bgi.com/wp-content/uploads/sites/4/2017/05/GLOBAL_BGISEQ-500_WholeGenomeSeq_ServiceOverview_04-17.pdf,platform,,,,BGISEQ_500,Class,Assay,Platform,Platform,,, - drugScreenType,String describing general class of drug screen,"singleMolecule, smallMoleculeLibraryScreen, combinationLibraryScreen, combinationScreen",,FALSE,,compoundScreen,,,,drugScreenType,Property,Assay,annotationProperty,,,, -assay,The technology used to generate the data in this file,"HPLC,elevated plus maze test,open field test,rotarod performance test,mRNA counts,high content screen,immunocytochemistry,immunofluorescence,autoradiography,reporter gene assay,electrochemiluminescence,in vivo tumor growth,blood chemistry measurement,in vivo bioluminescence,immunohistochemistry,NOMe-seq,FIA-MSMS,ultra high-performance liquid chromatography/tandem mass spectrometry,high-performance liquid chromatography/tandem mass spectrometry,liquid chromatography-electrochemical detection,RNA-seq,miRNA-seq,liquid chromatography/tandem mass spectrometry,liquid chromatography/mass spectrometry,lncRNA-seq,whole exome sequencing,Sanger sequencing,ChIP-seq,RNA array,SNP array,methylation array,miRNA array,bisulfite sequencing,ATAC-seq,HI-C,ERR bisulfite sequencing,ISO-seq,western blot,whole genome sequencing,polymerase chain reaction,cell viability assay,2D Incucyte,2D CellTiter-Glo,3D microtissue viability,2D AlamarBlue fluorescence,2D AlamarBlue absorbance,in vivo PDX viability,atomic force microscopy,brightfield microscopy,traction force microscopy,phase-contrast microscopy,next generation targeted sequencing,MIB/MS,scCGI-seq,MudPIT,questionnaire,DNA optical mapping,oxBS-seq,ribo-seq,positron emission tomography,RPPA,ELISA,long term potentiation assay,local field potential recording,whole-cell patch clamp,sandwich ELISA,laser speckle imaging,genotyping,TMT quantitation,mass spectrometry,label free mass spectrometry,cell count,immunoassay,conventional MRI,functional MRI,magnetic resonance spectroscopy,FTIR spectroscopy,rheometry,gel filtration chromatography,differential scanning calorimetry,single molecule drug screen assay,small molecule library screen,combination library screen,combination screen,compound screen,array,single-cell RNA-seq,spatial transcriptomics,massively parallel reporter assay,Riccardi and Ablon scales,spatial frequency domain imaging,optical coherence tomography,CUT&RUN,3D imaging,high frequency ultrasound,dynamic light scattering,static light scattering,light scattering assay,flow cytometry,pattern electroretinogram,optokinetic reflex assay,SUSHI,3D confocal imaging,3D electron microscopy,cell competition,body size trait measurement,twin spot assay,perineurial cell thickness,survival,gait measurement,sorbitol dehydrogenase activity level assay,T cell receptor repertoire sequencing,cell proliferation,oxygen consumption assay,reactive oxygen species assay,ATPase activity assay,novelty response behavior assay,contextual conditioning behavior assay,active avoidance learning behavior assay,focus forming assayblue native PAGE,in vitro tumorigenesis,Matrigel-based tumorigenesis assay,calcium retention capacity assay,quantitative PCR,photograph",,TRUE,,experimentalData,,,,assayType,Property,Assay,annotationProperty,,Assay,one, -platform,"A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","Illumina HiSeq 3000, Illumina HiSeq 2500, Illumina HiSeq 4000, Illumina NextSeq 500, Illumina HiSeq 2000, Illumina MiSeq, Zeiss LSM 980, Affymetrix Genome-Wide Human SNP 5.0 Array, Affymetrix Genome-Wide Human SNP 6.0 Array, PacBio RS II, Illumina Genome Analyzer IIx, Illumina HumanOmni1-Quadv1.0, Illumina 1M, Illumina h650, Illumina Omni2pt5M, Illumina Omni5M, Illumina MouseWG-6 v2.0 expression beadchip, Perlegen 300Karray, Agilent 44Karray, Illumina WholeGenome DASL, Illumina HumanHap300, Nanostring Counter, LTQ Orbitrap XL, Illumina HumanMethylation450, Illumina Infinium MethylationEPIC BeadChip v1.0 (850k),Illumina Infinium MethylationEPIC BeadChip v2.0 (935k), Affymetrix U133AB, Affymetrix Human Gene 1.0 ST Array, Affymetrix Human Genome U133 Plus 2.0 Array, Illumina HiSeq X, Bionano Irys, Infinium HumanOmniExpressExome, Illumina NextSeq 550, Illumina NextSeq 1000, Illumina NextSeq 2000, PacBio Sequel IIe System, PacBio Sequel II System, Nanostring GeoMx, LI-COR Odyssey CLx, Spectramax M Series, Olympus DP80, Orbitrap Fusion Lumos Tribrid, Illumina NovaSeq 6000, Chromium X,EnVision 2103 Multiplate Reader,Vectra H1 3D Imaging System,Vevo 3100 Imaging System,10x Visium Spatial Gene Expression,Cherry Imaging TRACE Platform,Cherry Imaging FACE Platform,LifeViz Micro System,LifeViz Infinity System,BGISEQ-500",,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group&anchor=platform,experimentalData,,,,platform,Property,Assay,annotationProperty,,Platform,, +assay,The technology used to generate the data in this file,"HPLC,elevated plus maze test,open field test,rotarod performance test,mRNA counts,high content screen,immunocytochemistry,immunofluorescence,autoradiography,reporter gene assay,electrochemiluminescence,in vivo tumor growth,blood chemistry measurement,in vivo bioluminescence,immunohistochemistry,NOMe-seq,FIA-MSMS,ultra high-performance liquid chromatography/tandem mass spectrometry,high-performance liquid chromatography/tandem mass spectrometry,liquid chromatography-electrochemical detection,RNA-seq,miRNA-seq,liquid chromatography/tandem mass spectrometry,liquid chromatography/mass spectrometry,lncRNA-seq,whole exome sequencing,Sanger sequencing,ChIP-seq,RNA array,SNP array,methylation array,miRNA array,bisulfite sequencing,ATAC-seq,HI-C,ERR bisulfite sequencing,ISO-seq,western blot,whole genome sequencing,polymerase chain reaction,cell viability assay,2D Incucyte,2D CellTiter-Glo,3D microtissue viability,2D AlamarBlue fluorescence,2D AlamarBlue absorbance,in vivo PDX viability,atomic force microscopy,brightfield microscopy,traction force microscopy,phase-contrast microscopy,next generation targeted sequencing,MIB/MS,scCGI-seq,MudPIT,questionnaire,DNA optical mapping,oxBS-seq,ribo-seq,positron emission tomography,RPPA,ELISA,long term potentiation assay,local field potential recording,whole-cell patch clamp,sandwich ELISA,laser speckle imaging,genotyping,TMT quantitation,mass spectrometry,label free mass spectrometry,cell count,immunoassay,conventional MRI,functional MRI,magnetic resonance spectroscopy,FTIR spectroscopy,rheometry,gel filtration chromatography,differential scanning calorimetry,single molecule drug screen assay,small molecule library screen,combination library screen,combination screen,compound screen,array,single-cell RNA-seq,spatial transcriptomics,massively parallel reporter assay,Riccardi and Ablon scales,spatial frequency domain imaging,optical coherence tomography,CUT&RUN,3D imaging,high frequency ultrasound,dynamic light scattering,static light scattering,light scattering assay,flow cytometry,pattern electroretinogram,optokinetic reflex assay,SUSHI,3D confocal imaging,3D electron microscopy,cell competition,body size trait measurement,twin spot assay,perineurial cell thickness,survival,gait measurement,sorbitol dehydrogenase activity level assay,T cell receptor repertoire sequencing,cell proliferation,oxygen consumption assay,reactive oxygen species assay,ATPase activity assay,novelty response behavior assay,contextual conditioning behavior assay,active avoidance learning behavior assay,focus forming assayblue native PAGE,in vitro tumorigenesis,Matrigel-based tumorigenesis assay,calcium retention capacity assay,quantitative PCR,photograph,cAMP-Glo Max Assay",,TRUE,,experimentalData,,,,assayType,Property,Assay,annotationProperty,,Assay,one, +platform,"A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","Illumina HiSeq 3000, Illumina HiSeq 2500, Illumina HiSeq 4000, Illumina NextSeq 500, Illumina HiSeq 2000, Illumina MiSeq, Zeiss LSM 980, Affymetrix Genome-Wide Human SNP 5.0 Array, Affymetrix Genome-Wide Human SNP 6.0 Array, PacBio RS II, Illumina Genome Analyzer IIx, Illumina HumanOmni1-Quadv1.0, Illumina 1M, Illumina h650, Illumina Omni2pt5M, Illumina Omni5M, Illumina MouseWG-6 v2.0 expression beadchip, Perlegen 300Karray, Agilent 44Karray, Illumina WholeGenome DASL, Illumina HumanHap300, Nanostring Counter, LTQ Orbitrap XL, Illumina HumanMethylation450, Illumina Infinium MethylationEPIC BeadChip v1.0 (850k),Illumina Infinium MethylationEPIC BeadChip v2.0 (935k), Affymetrix U133AB, Affymetrix Human Gene 1.0 ST Array, Affymetrix Human Genome U133 Plus 2.0 Array, Illumina HiSeq X, Bionano Irys, Infinium HumanOmniExpressExome, Illumina NextSeq 550, Illumina NextSeq 1000, Illumina NextSeq 2000, PacBio Sequel IIe System, PacBio Sequel II System, Nanostring GeoMx, LI-COR Odyssey CLx, Spectramax M Series, Olympus DP80, Orbitrap Fusion Lumos Tribrid, Illumina NovaSeq 6000, Chromium X,EnVision 2103 Multiplate Reader,Vectra H1 3D Imaging System,Vevo 3100 Imaging System,10x Visium Spatial Gene Expression,Cherry Imaging TRACE Platform,Cherry Imaging FACE Platform,LifeViz Micro System,LifeViz Infinity System,BGISEQ-500",,TRUE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group&anchor=platform,experimentalData,,,,platform,Property,Assay,annotationProperty,,Platform,, targetCaptureKitID,"A unique identifier for the kit used to construct a genomic library using target capture-based techniques, which should be composed of the vendor name, kit name and kit version.",,,TRUE,http://purl.obolibrary.org/obo/NCIT_C177583,experimentalData,,,,targetCaptureKitID,Property,Assay,annotationProperty,,,,"For WES processing, the target BED used could be provided based on the target capture kit." libraryID,,,,TRUE,,experimentalData,,,,libraryID,Property,Assay,annotationProperty,,,, assayTarget,The HUGO gene symbol that represents the target analyte assayed.,,,FALSE,Sage Bionetworks,experimentalData,,,,assayTarget,Property,Assay,annotationProperty,,,, @@ -248,11 +249,11 @@ reporterSubstance,A gene which produces an easily assayed phenotype. Often used immunoAssayType,Type of immuno assay,"ChIP-seq, ATAC-seq",,TRUE,,immunoAssay,,,,immunoAssayType,Property,Assay,annotationProperty,,,, runType,Is the sequencing run single or paired end?,"singleEnd, pairedEnd","readPair,isStranded,readPairOrientation,readStrandOrigin,readLength,readDepth",FALSE,Sage Bionetworks,ngs,,,,runType,Property,Assay,annotationProperty,ngsParameter,Run_Type,, readPair,The read of origin,,,FALSE,,ngs,,,int,readPair,Property,Assay,annotationProperty,ngsParameter,Read_Pair,, -isStranded,Whether or not the library is stranded (Yes; No),"Yes, No",,FALSE,,ngs,,,,isStranded,Property,Assay,annotationProperty,ngsParameter,,, -readPairOrientation,The relative orientation of the reads in a paired-end protocol,"inward, outward, matching, fr-firststrand",,FALSE,,ngs,,,,readPairOrientation,Property,Assay,annotationProperty,ngsParameter,Read_Pair_Orientation,, +isStranded,Whether or not the library is stranded (Yes; No),"Yes, No",,TRUE,,ngs,,,,isStranded,Property,Assay,annotationProperty,ngsParameter,,, +readPairOrientation,The relative orientation of the reads in a paired-end protocol,"inward, outward, matching, fr-firststrand",,TRUE,,ngs,,,,readPairOrientation,Property,Assay,annotationProperty,ngsParameter,Read_Pair_Orientation,, readStrandOrigin,The strand from which the read originates in a strand-specific protocol,"forward, reverse",,FALSE,,ngs,,,,readStrandOrigin,Property,Assay,annotationProperty,ngsParameter,Read_Strand_Origin,, libraryPrep,The general strategy by which the library was prepared,"rRNAdepletion, polyAselection, lncRNAenrichment, miRNAenrichment","libraryPreparationMethod,nucleicAcidSource,dissociationMethod",FALSE,,ngs,,,,libraryPrep,Property,Assay,annotationProperty,ngsParameter,Library_Prep,, -libraryPreparationMethod,Method by which library was prepared,"10x, CEL-seq, Drop-Seq, Smart-seq2, TruSeq, Smart-seq4, Omni-ATAC, NEBNext mRNA Library Prep Reagent Set for Illumina, IDT xGen Exome Research Panel, TruSeq standard total RNA library kit, Illumina TruSeq DNA Nano, KAPA HyperPrep Kit PCR-free,KAPA RNA HyperPrep Kit with RiboErase (HMR),GTAC@WUSTL in-house prep",,FALSE,,ngs,,,,libraryPreparationMethod,Property,Assay,annotationProperty,ngsParameter,Library_Preparation_Method,, +libraryPreparationMethod,Method by which library was prepared,"10x, CEL-seq, Drop-Seq, Smart-seq2, TruSeq, Smart-seq4, Omni-ATAC, NEBNext mRNA Library Prep Reagent Set for Illumina, IDT xGen Exome Research Panel, TruSeq standard total RNA library kit, Illumina TruSeq DNA Nano, KAPA HyperPrep Kit PCR-free,KAPA RNA HyperPrep Kit with RiboErase (HMR),GTAC@WUSTL in-house prep, KAPA mRNA HyperPrep Kit",,TRUE,,ngs,,,,libraryPreparationMethod,Property,Assay,annotationProperty,ngsParameter,Library_Preparation_Method,, nucleicAcidSource,Source of the extracted nucleic acid used in the experiment,"bulk cell, single cell, bulk nuclei, single nucleus, mitochondria",,FALSE,Sage Bionetworks,ngs,,,,nucleicAcidSource,Property,Assay,annotationProperty,ngsParameter,Nucleic_Acid_Source,, dissociationMethod,Procedure by which a biological specimen is dissociated into individual cells or a cell suspension,"10x_v2, FACS, Fluidigm C1, drop-seq, inDrop, mouth pipette, bulk, enzymatic, mechanical, none",,FALSE,https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0009088,ngs,,,,dissociationMethod,Property,Assay,annotationProperty,ngsParameter,Dissociation_Method,, readLength,Number of base pairs (bp) sequenced for a read,,,TRUE,,ngs,,,,readLength,DataProperty,Assay,annotationProperty,ngsParameter,,, @@ -388,6 +389,8 @@ hdr,"MRI Header file, as in the NIFTI-1 Analyze 7.5 format","","",FALSE,https:// img,"MRI Data file, as in the NIFTI-1 Analyze 7.5 format","","",FALSE,https://nifti.nimh.nih.gov/pub/dist/src/niftilib/nifti1.h,fileFormat,,"","",img,Class,Data,File_Format,"","","","" sf,"Salmon’s main output is its quantification file. This file is a plain-text, tab-separated file with a single header line (which names all of the columns).","","",FALSE,https://salmon.readthedocs.io/en/latest/file_formats.html,fileFormat,,"","",sf,Class,Data,File_Format,"","","","" tom,"The .tom format is a specialized 3D image export format from the Vectra medical imaging systems that can optionally preserve trimmings and/or landmarks.","","",FALSE,http://canfieldupgrade.com/assets/media/VECTRA-M3-User-Guide.pdf,fileFormat,,"","",tom,Class,Data,File_Format,"","","","" +fcs,"Format standard of a digital entity that is conformant with the Flow Cytometry Data File Standard",,,FALSE,http://purl.obolibrary.org/obo/OBI_0000327,fileFormat,,"","",fcs,Class,Data,File_Format,"","","","" +NWB,"Neurodata Without Borders (NWB) is a data standard for neurophysiology data, designed to store data including from intracellular and extracellular electrophysiology experiments, data from optical physiology experiments, and tracking and stimulus data.","","",FALSE,https://www.nwb.org/,fileFormat,,"","",NWB,Class,Data,File_Format,"","","","" gene symbol,A unique gene name approved by an organism specific nomenclature committee.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C43568,curatedDataType,,,,Gene_Symbol,Class,Data,Metadata,,,, clinical data,Data obtained through patient examination or treatment.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C15783,curatedDataType,,,,Clinical_Curated_Data,Class,Data,Metadata,,,, gene function,A term that expresses the function of a gene product.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C48933,curatedDataType,,,,Gene_Function,Class,Data,Metadata,,,, @@ -423,7 +426,7 @@ programmingLanguage,A computer programming language,"Python, R, MATLAB, Java, C, runtimePlatform,"Runtime platform or script interpreter dependencies (e.g. Java v1, Python 2.3).",,,FALSE,Sage Bionetworks,,,,,runtimePlatform,Property,Data,annotationProperty,ngsParameter,,, documentation,URL to any documentation describing the resource and its use.,,,FALSE,Sage Bionetworks,,,,,documentation,Property,Data,annotationProperty,ngsParameter,,, resourceType,The type of resource being stored and annotated,"experimentalData, curatedData, result, tool, report, metadata, protocol, workflow report,weblink",,TRUE,,sageCommunity,,,,resourceType,Property,Data,annotationProperty,,Resource,, -fileFormat,"Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software","bash script,bedgraph,ai,idx,idat,bam,bai,excel,powerpoint,tif,png,doc,pdf,hdf,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,mzML,SPAR,SDAT,nii,PAR,REC,hdr,img,sf,MATLAB script, MATLAB data,tom",,TRUE,,sageCommunity,,,,fileFormat,Property,Data,annotationProperty,,File_Format,one, +fileFormat,"Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software","bash script,bedgraph,ai,idx,idat,bam,bai,excel,powerpoint,tif,png,doc,pdf,hdf,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,mzML,SPAR,SDAT,nii,PAR,REC,hdr,img,sf,MATLAB script, MATLAB data,tom,fcs,NWB",,TRUE,,sageCommunity,,,,fileFormat,Property,Data,annotationProperty,,File_Format,one, progressReportNumber,"Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",,FALSE,,template,,,,progressReportNumber,DataProperty,Data,annotationProperty,,,one, comments,Brief free-text comments that may also be important to understanding the resource.,,,FALSE,Sage Bionetworks,experimentalData,,,,comments,DataProperty,Data,annotationProperty,,,many, Resource_id,A UUID for a Resource from the NF Research Tools Database,,,FALSE,Sage Bionetworks,dccProperty,,,,Resource_id,Property,Data,annotationProperty,dccProperty,,, @@ -442,7 +445,7 @@ contentSize,(Files only) File size calculated by the platform.,,,FALSE,Sage Bion type,"Refers to the type of the resource on the platform, e.g. “file”.",,,FALSE,Sage Bionetworks,synapseProperty,,,,type,Property,Data,annotationProperty,synapseProperty,,, concreteType,Refers to the class model the data platform uses for representing the resource. This is a low-level field set by the platform and is not a user annotation.,,,FALSE,Sage Bionetworks,synapseProperty,,,,concreteType,Property,Data,annotationProperty,synapseProperty,,, author,"The author of the resource; preferably use an ORCID ID, GitHub profile link, etc., if available and a text name if not.",,,FALSE,Sage Bionetworks,,,,,,Property,Data,annotationProperty,,,, -license,Link to a license or name of license applicable for the resource.,,,,,,,,,,,,,,,, +license,Link to a license or name of license applicable for the resource.,,,FALSE,Sage Bionetworks,,,,,,Property,Data,annotationProperty,,,, allograft,"Tissues, cells, or organs transplanted between genetically different individuals of the same species","","",FALSE,https://www.ncbi.nlm.nih.gov/mesh/68064591,transplantationType,,"","",Allograft,Class,Experiment,Method,"","","","" xenograft,"Tissues, cells or organs transplanted between animals of different species","","transplantationRecipientSpecies,transplantationRecipientTissue",FALSE,https://www.ncbi.nlm.nih.gov/mesh/68064593,transplantationType,,"","",Xenograft,Class,Experiment,Method,"","","","" autograft,"Transplant comprised of an individual's own tissue, transferred from one part of the body to another.","","transplantationRecipientSpecies,transplantationRecipientTissue",FALSE,https://www.ncbi.nlm.nih.gov/mesh/68064592,transplantationType,,"","",Autograft,Class,Experiment,Method,"","","","" diff --git a/NF.jsonld b/NF.jsonld index a1948af9..50c98f65 100644 --- a/NF.jsonld +++ b/NF.jsonld @@ -1986,7 +1986,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "HPLC", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2003,7 +2003,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "elevated plus maze test", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2020,7 +2020,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "open field test", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2037,7 +2037,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "rotarod performance test", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2054,7 +2054,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "mRNA counts", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2071,7 +2071,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "high content screen", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2088,7 +2088,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "immunocytochemistry", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2105,7 +2105,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "immunofluorescence", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2122,7 +2122,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "autoradiography", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2139,7 +2139,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "reporter gene assay", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2156,7 +2156,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "electrochemiluminescence", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2173,7 +2173,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "in vivo tumor growth", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2190,7 +2190,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "blood chemistry measurement", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2207,7 +2207,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "in vivo bioluminescence", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2224,7 +2224,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "immunohistochemistry", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2241,7 +2241,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "NOMe-seq", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2258,7 +2258,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "FIA-MSMS", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2275,7 +2275,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "ultra high-performance liquid chromatography/tandem mass spectrometry", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2292,7 +2292,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "high-performance liquid chromatography/tandem mass spectrometry", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2309,7 +2309,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "liquid chromatography-electrochemical detection", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2326,7 +2326,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "RNA-seq", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2343,7 +2343,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "miRNA-seq", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2360,7 +2360,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "liquid chromatography/tandem mass spectrometry", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2377,7 +2377,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "liquid chromatography/mass spectrometry", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2394,7 +2394,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "lncRNA-seq", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2411,7 +2411,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "whole exome sequencing", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2428,7 +2428,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Sanger sequencing", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2445,7 +2445,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "ChIP-seq", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2462,7 +2462,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "RNA array", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2479,7 +2479,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "SNP array", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2496,7 +2496,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "methylation array", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2513,7 +2513,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "miRNA array", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2530,7 +2530,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "bisulfite sequencing", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2547,7 +2547,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "ATAC-seq", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2564,7 +2564,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "HI-C", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2581,7 +2581,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "ERR bisulfite sequencing", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2598,7 +2598,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "ISO-seq", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2615,7 +2615,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "western blot", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2632,7 +2632,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "whole genome sequencing", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2649,7 +2649,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "polymerase chain reaction", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2666,7 +2666,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "cell viability assay", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2683,7 +2683,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "2D Incucyte", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2700,7 +2700,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "2D CellTiter-Glo", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2717,7 +2717,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "3D microtissue viability", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2734,7 +2734,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "2D AlamarBlue fluorescence", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2751,7 +2751,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "2D AlamarBlue absorbance", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2768,7 +2768,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "in vivo PDX viability", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2785,7 +2785,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "atomic force microscopy", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2802,7 +2802,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "brightfield microscopy", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2819,7 +2819,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "traction force microscopy", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2836,7 +2836,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "phase-contrast microscopy", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2853,7 +2853,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "next generation targeted sequencing", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2870,7 +2870,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "MIB/MS", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2887,7 +2887,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "scCGI-seq", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2904,7 +2904,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "MudPIT", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2921,7 +2921,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "questionnaire", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2938,7 +2938,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "DNA optical mapping", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2955,7 +2955,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "oxBS-seq", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2972,7 +2972,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "ribo-seq", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -2989,7 +2989,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "positron emission tomography", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3006,7 +3006,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "RPPA", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3023,7 +3023,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "ELISA", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3040,7 +3040,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "long term potentiation assay", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3057,7 +3057,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "local field potential recording", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3074,7 +3074,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "whole-cell patch clamp", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3091,7 +3091,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "sandwich ELISA", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3108,7 +3108,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "laser speckle imaging", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3125,7 +3125,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "genotyping", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3142,7 +3142,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "TMT quantitation", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3159,7 +3159,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "mass spectrometry", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3176,7 +3176,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "label free mass spectrometry", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3193,7 +3193,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "cell count", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3210,7 +3210,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "immunoassay", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:ImmunoAssayType" @@ -3232,7 +3232,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "conventional MRI", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3249,7 +3249,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "functional MRI", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3266,7 +3266,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "magnetic resonance spectroscopy", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3283,7 +3283,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "FTIR spectroscopy", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3300,7 +3300,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "rheometry", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3317,7 +3317,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "gel filtration chromatography", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3334,7 +3334,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "differential scanning calorimetry", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3351,7 +3351,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "single molecule drug screen assay", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3368,7 +3368,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "small molecule library screen", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3385,7 +3385,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "combination library screen", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3402,7 +3402,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "combination screen", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3419,7 +3419,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "compound screen", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3436,7 +3436,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "array", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3453,7 +3453,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "single-cell RNA-seq", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3470,7 +3470,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "spatial transcriptomics", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3487,7 +3487,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "massively parallel reporter assay", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3504,7 +3504,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Riccardi and Ablon scales", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3521,7 +3521,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "spatial frequency domain imaging", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3538,7 +3538,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "optical coherence tomography", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3555,7 +3555,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "CUT&RUN", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3572,7 +3572,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "3D imaging", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Assay" @@ -3594,7 +3594,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "high frequency ultrasound", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Assay" @@ -3616,7 +3616,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "dynamic light scattering", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Assay" @@ -3638,7 +3638,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "static light scattering", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Assay" @@ -3660,7 +3660,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "light scattering assay", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Assay" @@ -3682,7 +3682,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "flow cytometry", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3699,7 +3699,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "pattern electroretinogram", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3716,7 +3716,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "optokinetic reflex assay", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3733,7 +3733,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "SUSHI", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3750,7 +3750,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "3D confocal imaging", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3767,7 +3767,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "3D electron microscopy", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3784,7 +3784,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "cell competition", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3801,7 +3801,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "body size trait measurement", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3818,7 +3818,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "twin spot assay", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3835,7 +3835,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "perineurial cell thickness", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3852,7 +3852,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "survival", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3869,7 +3869,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "gait measurement", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3886,7 +3886,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "sorbitol dehydrogenase activity level assay", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3903,7 +3903,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "T cell receptor repertoire sequencing", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3920,7 +3920,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "cell proliferation", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3937,7 +3937,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "oxygen consumption assay", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3954,7 +3954,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "reactive oxygen species assay", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3971,7 +3971,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "ATPase activity assay", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -3988,7 +3988,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "novelty response behavior assay", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4005,7 +4005,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "contextual conditioning behavior assay", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4022,7 +4022,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "active avoidance learning behavior assay", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4039,7 +4039,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "focus forming assay", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4056,7 +4056,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "blue native PAGE", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4073,7 +4073,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "in vitro tumorigenesis", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4090,7 +4090,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Matrigel-based tumorigenesis assay", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4107,7 +4107,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "calcium retention capacity assay", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4124,13 +4124,13 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "quantitative PCR", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Clinicaldata", "@type": "rdfs:Class", - "rdfs:comment": " \"Data pertaining to the medical well-being or status of a patient. Category also includes clinical reports and individual patient data.\"", + "rdfs:comment": "Data pertaining to the medical well-being or status of a patient. Category also includes clinical reports and individual patient data.", "rdfs:label": "Clinicaldata", "rdfs:subClassOf": [ { @@ -4141,7 +4141,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "clinical data", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4158,13 +4158,30 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "photograph", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Channel", + "@id": "bts:CAMP-GloMaxAssay", "@type": "rdfs:Class", - "rdfs:comment": "Fluorescent color labeling for an array", + "rdfs:comment": "The cAMP-Glo Max Assay from Promega is a bioluminescent assay used for the quantification of cyclic AMP (cAMP) in cell-based assays. It utilizes a luminescent luciferase-based detection system to detect the levels of cAMP in cell lysates, which can be used to study G protein-coupled receptor (GPCR) signaling and other intracellular signaling pathways.", + "rdfs:label": "CAMP-GloMaxAssay", + "rdfs:subClassOf": [ + { + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "cAMP-Glo Max Assay", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Channel", + "@type": "rdfs:Class", + "rdfs:comment": "Fluorescent color labeling for an array", "rdfs:label": "Channel", "rdfs:subClassOf": [ { @@ -4214,7 +4231,7 @@ } ], "sms:displayName": "MRISequence", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4231,7 +4248,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "T1-weighted", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4248,7 +4265,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "T2-weighted", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4265,7 +4282,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "PD-weighted", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4282,7 +4299,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Short Tau Inversion Recovery", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4299,7 +4316,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Cy5", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4316,7 +4333,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Cy3", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4333,7 +4350,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "overexpression", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4350,7 +4367,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "knockdown", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4367,7 +4384,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "knockout", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4384,7 +4401,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "non-targeting control", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4401,7 +4418,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "fr-firststrand", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4418,7 +4435,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "TruSeq standard total RNA library kit", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4435,7 +4452,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "10x", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4452,7 +4469,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "CEL-seq", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4469,7 +4486,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Drop-Seq", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4486,7 +4503,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Smart-seq2", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4503,7 +4520,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "TruSeq", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4520,7 +4537,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Smart-seq4", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4537,7 +4554,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Omni-ATAC", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4554,7 +4571,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "NEBNext mRNA Library Prep Reagent Set for Illumina", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4571,7 +4588,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "IDT xGen Exome Research Panel", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4588,7 +4605,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Illumina TruSeq DNA Nano", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4605,7 +4622,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "KAPA HyperPrep Kit PCR-free", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4622,7 +4639,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "KAPA RNA HyperPrep Kit with RiboErase (HMR)", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4639,7 +4656,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "GTAC@WUSTL in-house prep", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4656,7 +4673,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "bulk cell", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4673,7 +4690,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "single cell", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4690,7 +4707,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "bulk nuclei", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4707,7 +4724,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "single nucleus", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4724,7 +4741,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "mitochondria", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4741,7 +4758,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "cell lysate", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4758,7 +4775,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "nuclear extract", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4775,7 +4792,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "mitochondria", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4792,7 +4809,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "cytoplasm", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4809,7 +4826,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "1", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4826,7 +4843,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "2", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4843,7 +4860,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "inward", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4860,7 +4877,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "outward", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4877,7 +4894,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "matching", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4894,7 +4911,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "forward", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4911,7 +4928,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "reverse", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4928,7 +4945,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "singleEnd", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4945,7 +4962,24 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "pairedEnd", - "sms:required": "sms:true", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:KAPAmRNAHyperPrepKit", + "@type": "rdfs:Class", + "rdfs:comment": "The KAPA mRNA HyperPrep Kit is a highly efficient library preparation kit designed for generating stranded RNA-seq libraries with low input amounts and reduced bias.", + "rdfs:label": "KAPAmRNAHyperPrepKit", + "rdfs:subClassOf": [ + { + "@id": "bts:LibraryPreparationMethod" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "KAPA mRNA HyperPrep Kit", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4962,7 +4996,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "jumpingLibrary", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4979,7 +5013,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "RNAi", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -4996,7 +5030,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "CRISPR", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5013,7 +5047,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "CRE Recombinase", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5030,7 +5064,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "rRNAdepletion", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5047,7 +5081,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "polyAselection", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5064,7 +5098,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "lncRNAenrichment", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5081,7 +5115,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "miRNAenrichment", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5098,7 +5132,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "scale", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5115,7 +5149,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Olympus DP80", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5132,7 +5166,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Orbitrap Fusion Lumos Tribrid", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5149,7 +5183,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Spectramax M Series", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5166,7 +5200,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "LI-COR Odyssey CLx", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5183,7 +5217,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Q Exative HF", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5200,7 +5234,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Illumina HiSeq 3000", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5217,7 +5251,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Illumina HiSeq 2500", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5234,7 +5268,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Illumina HiSeq 4000", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5251,7 +5285,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Illumina NextSeq 500", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5268,7 +5302,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Illumina NextSeq 550", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5285,7 +5319,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Illumina NextSeq 1000", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5302,7 +5336,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Illumina NextSeq 2000", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5319,7 +5353,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Illumina HiSeq 2000", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5336,7 +5370,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Illumina MiSeq", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5353,7 +5387,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Zeiss LSM 980", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5370,7 +5404,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Affymetrix Genome-Wide Human SNP 5.0 Array", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5387,7 +5421,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Affymetrix Genome-Wide Human SNP 6.0 Array", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5404,7 +5438,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "PacBio RS II", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5421,7 +5455,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Illumina Genome Analyzer IIx", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5438,7 +5472,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Illumina HumanOmni1-Quadv1.0", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5455,7 +5489,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Illumina 1M", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5472,7 +5506,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Illumina h650", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5489,7 +5523,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Illumina Omni2pt5M", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5506,7 +5540,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Illumina Omni5M", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5523,7 +5557,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Illumina MouseWG-6 v2.0 expression beadchip", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5540,7 +5574,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Perlegen 300Karray", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5557,7 +5591,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Agilent 44Karray", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5574,7 +5608,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Illumina WholeGenome DASL", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5591,7 +5625,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Illumina HumanHap300", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5608,7 +5642,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Nanostring Counter", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5625,7 +5659,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "LTQ Orbitrap XL", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5642,7 +5676,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Illumina HumanMethylation450", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5659,7 +5693,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Illumina Infinium MethylationEPIC BeadChip v1.0 (850k)", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5676,7 +5710,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Illumina Infinium MethylationEPIC BeadChip v2.0 (935k)", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5693,7 +5727,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Affymetrix U133AB", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5710,7 +5744,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Affymetrix Human Gene 1.0 ST Array", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5727,7 +5761,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Affymetrix Human Genome U133 Plus 2.0 Array", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5744,7 +5778,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Illumina HiSeq X", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5761,7 +5795,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Bionano Irys", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5778,7 +5812,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Infinium HumanOmniExpressExome", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5795,7 +5829,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Illumina NovaSeq 6000", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5812,7 +5846,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "PacBio Sequel IIe System", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5829,7 +5863,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "PacBio Sequel II System", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5846,7 +5880,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Nanostring GeoMx", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5863,7 +5897,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Chromium X", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5880,7 +5914,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "10x Visium Spatial Gene Expression", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5897,7 +5931,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "EnVision 2103 Multiplate Reader", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5914,7 +5948,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Vectra H1 3D Imaging System", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5931,7 +5965,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Vevo 3100 Imaging System", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5948,7 +5982,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Cherry Imaging TRACE Platform", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5965,7 +5999,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Cherry Imaging FACE Platform", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5982,7 +6016,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "LifeViz Micro System", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -5999,7 +6033,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "LifeViz Infinity System", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -6016,7 +6050,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Promega GloMax Discover", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -6033,7 +6067,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "BGISEQ-500", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -6064,7 +6098,7 @@ } ], "sms:displayName": "drugScreenType", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -6455,10 +6489,13 @@ }, { "@id": "bts:Photograph" + }, + { + "@id": "bts:CAMP-GloMaxAssay" } ], "sms:displayName": "assay", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -6687,7 +6724,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "assayTarget", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -6735,7 +6772,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "reporterGene", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -6752,7 +6789,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "reporterSubstance", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -6802,7 +6839,7 @@ } ], "sms:displayName": "runType", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:ReadPair" @@ -6839,7 +6876,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "readPair", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [ "int" ] @@ -6922,7 +6959,7 @@ } ], "sms:displayName": "readStrandOrigin", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -6953,7 +6990,7 @@ } ], "sms:displayName": "libraryPrep", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:LibraryPreparationMethod" @@ -7022,6 +7059,9 @@ }, { "@id": "bts:GTAC@WUSTLin-houseprep" + }, + { + "@id": "bts:KAPAmRNAHyperPrepKit" } ], "sms:displayName": "libraryPreparationMethod", @@ -7059,7 +7099,7 @@ } ], "sms:displayName": "nucleicAcidSource", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -7108,7 +7148,7 @@ } ], "sms:displayName": "dissociationMethod", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -7142,7 +7182,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "readDepth", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -7167,7 +7207,7 @@ } ], "sms:displayName": "isPairedEnd", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -7184,7 +7224,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "totalReads", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -7201,7 +7241,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "targetDepth", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -7218,7 +7258,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "raw counts", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Assay" @@ -7240,7 +7280,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Volume", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Assay" @@ -7262,7 +7302,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Weight", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Assay" @@ -7284,7 +7324,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Pharmacokinetic Study", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Assay" @@ -7306,7 +7346,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "genomicVariants", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Assay" @@ -7328,7 +7368,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "AlignedReads", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Assay" @@ -7350,7 +7390,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "SomaticVariants", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Assay" @@ -7372,7 +7412,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "AnnotatedSomaticVariants", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Assay" @@ -7394,7 +7434,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "GermlineVariants", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Assay" @@ -7416,7 +7456,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "AnnotatedGermlineVariants", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Assay" @@ -7438,7 +7478,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "StructuralVariants", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Assay" @@ -7460,7 +7500,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "behavior process", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Assay" @@ -7482,7 +7522,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "metabolomics", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Assay" @@ -7504,7 +7544,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "image", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Assay" @@ -7526,7 +7566,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "geneExpression", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Assay" @@ -7548,7 +7588,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "isoformExpression", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Assay" @@ -7570,7 +7610,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "proteomics", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Assay" @@ -7592,7 +7632,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "particle characterization", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Assay" @@ -7614,7 +7654,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "kinomics", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Assay" @@ -7636,7 +7676,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "drugScreen", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Assay" @@ -7658,7 +7698,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "drugCombinationScreen", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -7675,7 +7715,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "cellularPhysiology", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Assay" @@ -7697,7 +7737,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "chromatinActivity", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -7714,7 +7754,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "surveyData", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Assay" @@ -7736,7 +7776,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "network", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -7753,7 +7793,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "clinical", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -7770,7 +7810,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "immunoassay", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -7787,7 +7827,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "electrophysiology", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -7804,7 +7844,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "mask image", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -7821,7 +7861,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "curatedData", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -7838,7 +7878,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "characteristic", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Assay" @@ -7860,7 +7900,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "normalized", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -7877,7 +7917,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "dataMatrix", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -7894,7 +7934,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "raw", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -7911,7 +7951,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "processed", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -7928,7 +7968,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "metadata", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -7945,7 +7985,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "representative", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -7962,7 +8002,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "bash script", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -7979,7 +8019,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "bedgraph", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -7996,7 +8036,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "ai", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8013,7 +8053,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "idx", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8030,7 +8070,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "idat", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8047,7 +8087,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "bam", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8064,7 +8104,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "bai", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8081,7 +8121,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "excel", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8098,7 +8138,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "powerpoint", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8115,7 +8155,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "tif", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8132,7 +8172,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "png", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8149,7 +8189,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "doc", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8166,7 +8206,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "pdf", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8183,7 +8223,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "hdf", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8200,7 +8240,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "fasta", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8217,7 +8257,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "fastq", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8234,7 +8274,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "sam", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8251,7 +8291,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "vcf", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8268,7 +8308,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "bcf", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8285,7 +8325,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "maf", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8302,7 +8342,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "bed", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8319,7 +8359,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "chp", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8336,7 +8376,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "cel", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8353,7 +8393,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "sif", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8370,7 +8410,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "tsv", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8387,7 +8427,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "csv", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8404,7 +8444,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "txt", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8421,7 +8461,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "plink", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8438,7 +8478,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "bigwig", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8455,7 +8495,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "wiggle", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8472,7 +8512,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "gct", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8489,7 +8529,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "bgzip", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8506,7 +8546,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "zip", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8523,7 +8563,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "seg", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8540,7 +8580,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "html", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8557,7 +8597,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "mov", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8574,7 +8614,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "hyperlink", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8591,7 +8631,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "svs", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8608,7 +8648,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "md", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8625,7 +8665,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "flagstat", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8642,7 +8682,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "gtf", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8659,7 +8699,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "raw", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8676,7 +8716,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "msf", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8693,7 +8733,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "rmd", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8710,7 +8750,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "bed narrowPeak", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8727,7 +8767,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "bed broadPeak", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8744,7 +8784,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "bed gappedPeak", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8761,7 +8801,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "avi", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8778,7 +8818,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "pzfx", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8795,7 +8835,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "fig", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8812,7 +8852,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "xml", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8829,7 +8869,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "tar", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8846,7 +8886,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "R script", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8863,7 +8903,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "abf", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8880,7 +8920,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "bpm", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8897,7 +8937,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "dat", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8914,7 +8954,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "jpg", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8931,7 +8971,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "locs", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8948,7 +8988,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Sentrix descriptor file", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8965,7 +9005,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Python script", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8982,7 +9022,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "MATLAB script", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -8999,7 +9039,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "MATLAB data", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9016,7 +9056,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "sav", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9033,7 +9073,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "gzip", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9050,7 +9090,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "sdf", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9067,7 +9107,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "RData", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9084,7 +9124,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "hic", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9101,7 +9141,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "ab1", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9118,7 +9158,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "7z", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9135,7 +9175,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "gff3", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9152,7 +9192,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "json", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9169,7 +9209,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "sqlite", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9186,7 +9226,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "svg", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9203,7 +9243,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "sra", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9220,7 +9260,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "recal", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9237,7 +9277,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "tranches", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9254,7 +9294,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "mtx", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9271,7 +9311,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "tagAlign", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9288,7 +9328,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "dup", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9305,7 +9345,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "DICOM", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9322,7 +9362,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "czi", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9339,7 +9379,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "mzML", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9356,7 +9396,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "SPAR", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9373,7 +9413,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "SDAT", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9390,7 +9430,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "nii", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9407,7 +9447,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "PAR", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9424,7 +9464,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "REC", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9441,7 +9481,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "hdr", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9458,7 +9498,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "img", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9475,7 +9515,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "sf", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9492,7 +9532,41 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "tom", - "sms:required": "sms:true", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Fcs", + "@type": "rdfs:Class", + "rdfs:comment": "Format standard of a digital entity that is conformant with the Flow Cytometry Data File Standard", + "rdfs:label": "Fcs", + "rdfs:subClassOf": [ + { + "@id": "bts:FileFormat" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "fcs", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:NWB", + "@type": "rdfs:Class", + "rdfs:comment": "Neurodata Without Borders (NWB) is a data standard for neurophysiology data, designed to store data including from intracellular and extracellular electrophysiology experiments, data from optical physiology experiments, and tracking and stimulus data.", + "rdfs:label": "NWB", + "rdfs:subClassOf": [ + { + "@id": "bts:FileFormat" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "NWB", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9509,7 +9583,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "gene symbol", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9526,7 +9600,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "clinical data", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9543,7 +9617,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "gene function", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9560,7 +9634,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "chemical descriptor", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9577,7 +9651,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "individual", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9594,7 +9668,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "biospecimen", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9611,7 +9685,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "assay", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9628,7 +9702,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "data dictionary", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9645,7 +9719,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "manifest", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9662,7 +9736,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "protocol", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9679,7 +9753,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "GRCh38", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9696,7 +9770,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "GRCh37", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9713,7 +9787,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "MMUL1.0", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9730,7 +9804,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "HRC", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9747,7 +9821,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "experimentalData", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9764,7 +9838,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "result", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9781,7 +9855,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "tool", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9798,7 +9872,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "workflow report", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9815,7 +9889,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "report", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9832,7 +9906,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "metadata", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9849,7 +9923,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "protocol", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9866,7 +9940,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "weblink", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -9948,7 +10022,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "reference sequence", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -10022,7 +10096,7 @@ } ], "sms:displayName": "metadataType", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -10266,7 +10340,7 @@ } ], "sms:displayName": "programmingLanguage", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -10283,7 +10357,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "runtimePlatform", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -10300,7 +10374,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "documentation", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -10635,6 +10709,12 @@ }, { "@id": "bts:Tom" + }, + { + "@id": "bts:Fcs" + }, + { + "@id": "bts:NWB" } ], "sms:displayName": "fileFormat", @@ -10690,7 +10770,7 @@ } ], "sms:displayName": "progressReportNumber", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -10707,7 +10787,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "comments", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -10724,7 +10804,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Resource_id", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -10741,7 +10821,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "initiative", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -10758,7 +10838,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "fundingAgency", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -10775,7 +10855,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "createdOn", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -10792,7 +10872,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "createdBy", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -10809,7 +10889,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "modifiedBy", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -10826,7 +10906,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "id", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -10843,7 +10923,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "etag", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -10860,7 +10940,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "parentId", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -10877,7 +10957,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "benefactorId", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -10894,7 +10974,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "currentVersion", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -10911,7 +10991,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "dataFileHandleId", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -10928,7 +11008,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "contentSize", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -10945,7 +11025,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "type", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -10962,7 +11042,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "concreteType", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -10979,7 +11059,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "author", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11013,7 +11093,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "allograft", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11030,7 +11110,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "xenograft", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:TransplantationRecipientSpecies" @@ -11055,7 +11135,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "autograft", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:TransplantationRecipientSpecies" @@ -11080,7 +11160,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "isograft", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11097,7 +11177,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "seconds", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11114,7 +11194,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "minutes", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11131,7 +11211,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "hours", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11148,7 +11228,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "days", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11165,7 +11245,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "weeks", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11182,7 +11262,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "months", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11199,7 +11279,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "quarters", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11230,7 +11310,7 @@ } ], "sms:displayName": "transplantationType", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:TransplantationRecipientSpecies" @@ -11263,7 +11343,7 @@ } ], "sms:displayName": "transplantationRecipientSpecies", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11303,7 +11383,7 @@ } ], "sms:displayName": "timePointUnit", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11320,7 +11400,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "experimentalCondition", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11337,7 +11417,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "experimentalTimepoint", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:TimePointUnit" @@ -11359,7 +11439,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "transplantationRecipientTissue", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11376,7 +11456,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "experimentId", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11393,7 +11473,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "compoundName", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:InChIKey" @@ -11415,7 +11495,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "compoundDose", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:CompoundDoseUnit" @@ -11437,7 +11517,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "compoundDoseUnit", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11454,7 +11534,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "InChIKey", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11488,7 +11568,7 @@ } ], "sms:displayName": "genePerturbationType", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11516,7 +11596,7 @@ } ], "sms:displayName": "genePerturbationTechnology", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11533,7 +11613,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "genePerturbed", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:GenePerturbationType" @@ -11558,7 +11638,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "JAX", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11575,7 +11655,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "sageCommunity", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11592,7 +11672,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "workflow", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:WorkflowLink" @@ -11614,7 +11694,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "workflowLink", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11631,7 +11711,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "genomicReference", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11648,7 +11728,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "averageInsertSize", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11665,7 +11745,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "averageReadLength", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11682,7 +11762,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "averageBaseQuality", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11699,7 +11779,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "pairsOnDifferentChr", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11716,7 +11796,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "readsDuplicatedPercent", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11733,7 +11813,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "readsMappedPercent", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11750,7 +11830,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "meanCoverage", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11767,7 +11847,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "proportionCoverage10x", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11784,7 +11864,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "proportionCoverage30x", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11801,7 +11881,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "isFilteredReads", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11818,7 +11898,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "head", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11835,7 +11915,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "lymph node", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11852,7 +11932,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "kidney", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11869,7 +11949,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "skin", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11886,7 +11966,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "mammary gland", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11903,7 +11983,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "nerves", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11920,7 +12000,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "brain", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11937,7 +12017,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "blood", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11954,7 +12034,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "breast", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11971,7 +12051,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "colon", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -11988,7 +12068,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "lung", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12005,7 +12085,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "prostate", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12022,7 +12102,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "pancreas", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12039,7 +12119,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "ovary", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12056,7 +12136,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "spleen", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12073,7 +12153,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "bone marrow", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12090,7 +12170,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Bursa Of Fabricius", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12107,7 +12187,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "nose", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12124,7 +12204,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Eye", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12141,7 +12221,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "mesentery", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12158,7 +12238,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "scalp", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12175,7 +12255,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "pelvis", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12192,7 +12272,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "neck", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12209,7 +12289,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "leg", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12226,7 +12306,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "liver", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12243,7 +12323,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "axilla", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12260,7 +12340,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "acetabulum", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12277,7 +12357,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "forearm", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12294,7 +12374,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "muscle", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12311,7 +12391,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "finger", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12328,7 +12408,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "thoracic spine", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12345,7 +12425,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "groin", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12362,7 +12442,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "back", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12379,7 +12459,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "iliac spine", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12396,7 +12476,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "spine", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12413,7 +12493,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "shoulder", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12430,7 +12510,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "scapula", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12447,7 +12527,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Schwann cell precursor", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12464,7 +12544,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "B-lymphocytes", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12481,7 +12561,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Embryonic stem cells", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12498,7 +12578,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "iPSC", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12515,7 +12595,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "iPSC-derived telencephalic organoids", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12532,7 +12612,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "GABAergic neurons", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12549,7 +12629,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "monocytes", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12566,7 +12646,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "microglia", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12583,7 +12663,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "macrophages", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12600,7 +12680,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "astrocytes", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12617,7 +12697,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "SH-SY5Y", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12634,7 +12714,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "GLUtamatergic neurons", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12651,7 +12731,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "NeuN+", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12668,7 +12748,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "NeuN-", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12685,7 +12765,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "epithelial", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12702,7 +12782,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "epithelial-like", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12719,7 +12799,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "fibroblast", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12736,7 +12816,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "round", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12753,7 +12833,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "lymphoblast", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12770,7 +12850,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "CD8+ T-Cells", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12787,7 +12867,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "arachnoid", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12804,7 +12884,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "meningioma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12821,7 +12901,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "schwannoma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12838,7 +12918,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "oligodendrocyte", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12855,7 +12935,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "schwann", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12872,7 +12952,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "iPSC-derived neuron", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12889,7 +12969,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "iPSC-derived glia", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12906,7 +12986,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "iPSC-derived astrocytes", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12923,7 +13003,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "monocyte-derived microglia", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12940,7 +13020,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "iPSC-derived neuronal progenitor cell", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12957,7 +13037,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "CD138+", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12974,7 +13054,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "CNON", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -12991,7 +13071,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "teratoma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13008,7 +13088,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "cultured Muller glia", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13025,7 +13105,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "DRG/nerve root neurosphere cell", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13042,7 +13122,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "28cNF", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13059,7 +13139,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "3PNF_FiPSsv_PM_2", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13076,7 +13156,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "3PNF_SiPSsv_MM_11", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13093,7 +13173,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "5PNF_TDiPSsv_MM_4", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13110,7 +13190,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "5PNF_TDiPSsv_PM_6", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13127,7 +13207,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "6PNF_SiPSrv_PM_2", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13144,7 +13224,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "7PNF_SiPSrv_PM_12", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13161,7 +13241,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "90-8", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13178,7 +13258,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "AC007-hTERT", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13195,7 +13275,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "BJFF.6", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13212,7 +13292,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Ben-Men-1", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13229,7 +13309,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Dh5 alpha", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13246,7 +13326,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Dhh-Cre; NF1Arg681*/flox Schwann Cells", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13263,7 +13343,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "ELK-TAD Luciferase Reporter HEK293 Stable", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13280,7 +13360,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "ELK-TAD Luciferase Reporter HEK293 Stable NF1 -/-", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13297,7 +13377,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Fb93.1", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13314,7 +13394,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "GM11601", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13331,7 +13411,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "GM11602", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13348,7 +13428,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "GM23338", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13365,7 +13445,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "HBE135-E6E7", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13382,7 +13462,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "HEK293", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13399,7 +13479,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "HEK293 NF1 -/- Exon 17 #A15 G629R cryptic splice", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13416,7 +13496,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "HEK293 NF1 -/- Exon 17 #B48 G629R cryptic splice", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13433,7 +13513,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "HEK293 NF1 -/- Exon 47 insT #14", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13450,7 +13530,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "HEK293 NF1 -/- Exon 52 R2550X #5", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13467,7 +13547,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "HEK293 NF1 -/- clone 2", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13484,7 +13564,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "HEK293 NF1 -/- with R1306X mNf1 cDNA", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13501,7 +13581,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "HEK293 NF1 -/- with R192X mNf1 cDNA", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13518,7 +13598,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "HEK293 NF1 -/- with R1947X mNf1 cDNA", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13535,7 +13615,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "HEK293 NF1 -/- with R2550X mNf1 cDNA", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13552,7 +13632,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "HEK293 NF1 -/- with R461X mNf1 cDNA", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13569,7 +13649,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "HEK293 NF1 -/- with R681X mNf1 cDNA", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13586,7 +13666,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "HEK293 NF1 -/- with R816X mNf1 cDNA", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13603,7 +13683,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "HEK293 NF1 -/- with WT mNf1 cDNA", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13620,7 +13700,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "HEK293 NF1 -/- with WT tagged mNf1 cDNA", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13637,7 +13717,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "HeLa SilenciX NF1", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13654,7 +13734,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "JH-2-002-CL", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13671,7 +13751,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "JH-2-079-CL", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13688,7 +13768,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "JH-2-103-CL", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13705,7 +13785,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "JHU 2-002-CL", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13722,7 +13802,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "JHU 2-002-PDX", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13739,7 +13819,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "JHU 2-079-CL", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13756,7 +13836,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "JHU 2-079-PDX", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13773,7 +13853,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "JHU 2-103-CL", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13790,7 +13870,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "JHU 2-103-PDX", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13807,7 +13887,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "KCL024", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13824,7 +13904,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "KCL025", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13841,7 +13921,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Lis42_NF1_1N", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13858,7 +13938,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Lis47_NF1_2N", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13875,7 +13955,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "M3 MPNST", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13892,7 +13972,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "NCC-MPNST1-C1", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13909,7 +13989,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "NCC-MPNST2-C1", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13926,7 +14006,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "NCC-MPNST3-C1", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13943,7 +14023,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "NCC-MPNST3-X2-C1", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13960,7 +14040,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "NCC-MPNST4-C1", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13977,7 +14057,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "NCC-MPNST5-C1", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -13994,7 +14074,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "NF1", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14011,7 +14091,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "NF1-R68X Embryonic cells", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14028,7 +14108,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "NF2-/- AC007-hTERT", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14045,7 +14125,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Nf1-/- Epithelial lung cells", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14062,7 +14142,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Nf1-/- HEK 293", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14079,7 +14159,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Nf1-/- skin-derived precursor cells", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14096,7 +14176,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Nf1Arg681*/+ ES", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14113,7 +14193,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Nf1Arg681*/Arg681* ES", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14130,7 +14210,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Nf1Arg681*/Arg681* MEFs", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14147,7 +14227,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Nf2-/- Schwann SC (mouse) (PMID26554010)", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14164,7 +14244,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "S462", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14181,7 +14261,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "S462.TY", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14198,7 +14278,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "S520", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14215,7 +14295,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "SC4 [Mouse schwannoma]", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14232,7 +14312,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "ST88-14", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14249,7 +14329,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "STS-26T", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14266,7 +14346,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "SZ-NF1", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14283,7 +14363,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "SZ-NF2", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14300,7 +14380,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "SZ-NF4", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14317,7 +14397,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Schwann cell NF1 -/- (iPN97.4 #24)", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14334,7 +14414,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Schwann cell NF1 -/- with R681X mNf1 cDNA", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14351,7 +14431,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Schwann cell NF1 -/- with R816X mNf1 cDNA", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14368,7 +14448,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Schwann cell NF1 -/- with WT tagged mNf1 cDNA", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14385,7 +14465,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Schwann cell i28cNF NF1 -/- (#14)", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14402,7 +14482,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "ScienCell Schwann cells", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14419,7 +14499,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "T265", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14436,7 +14516,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "WT ES", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14453,7 +14533,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "YST-1", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14470,7 +14550,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "cNF00.10a", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14487,7 +14567,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "cNF04.9a", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14504,7 +14584,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "cNF97.2a", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14521,7 +14601,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "cNF97.2b", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14538,7 +14618,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "cNF98.4c", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14555,7 +14635,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "cNF98.4d", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14572,7 +14652,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "hTERT NF1 ipNF00.6", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14589,7 +14669,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "hTERT NF1 ipNF03.3", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14606,7 +14686,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "hTERT NF1 ipNF04.4", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14623,7 +14703,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "hTERT NF1 ipNF05.5", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14640,7 +14720,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "hTERT NF1 ipNF05.5 (Mixed clones)", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14657,7 +14737,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "hTERT NF1 ipNF95.11b C", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14674,7 +14754,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "hTERT NF1 ipNF95.11b C/T", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14691,7 +14771,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "hTERT NF1 ipNF95.6", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14708,7 +14788,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "hTERT NF1 ipn02.3 2λ", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14725,7 +14805,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "hTERT NF1 ipn06.2 A", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14742,7 +14822,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "hTERT NF1 ipnNF09.4", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14759,7 +14839,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "hTERT NF1 ipnNF95.11c", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14776,7 +14856,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "hTERT NF1 sipnNF95.12B", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14793,7 +14873,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "hTERT SC ipn02.8", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14810,7 +14890,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "hTERT SC ipn97.4", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14827,7 +14907,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "hTERT ipn02.3 2λ", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14844,7 +14924,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "hTERT ipn02.8", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14861,7 +14941,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "hiPSC", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14878,7 +14958,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "hiPSC-SCP", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14895,7 +14975,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "human foreskin fibroblasts", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14912,7 +14992,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "i28cNF", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14929,7 +15009,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "i21cNF", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14946,7 +15026,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "i18cNF", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14963,7 +15043,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "cNF18.1a", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14980,7 +15060,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "cNF97.5", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -14997,7 +15077,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "cNF99.1", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15014,7 +15094,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "icNF99.1", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15031,7 +15111,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "iPSC NF1 +/- BJFF.6 bkgd", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15048,7 +15128,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "iPSC NF1 WT", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15065,7 +15145,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "iPSC Y489C; Exon 13 cryptic splice", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15082,7 +15162,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "icNF00.10a", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15099,7 +15179,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "icNF04.9a", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15116,7 +15196,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "icNF97.2a", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15133,7 +15213,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "icNF97.2b", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15150,7 +15230,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "icNF98.4c", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15167,7 +15247,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "icNF98.4d", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15184,7 +15264,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "sNF02.2", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15201,7 +15281,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "sNF94.3", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15218,7 +15298,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "sNF96.2", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15235,7 +15315,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "sc93.1", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15252,7 +15332,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "NMS-2", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15269,7 +15349,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "HS-PSS", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15286,7 +15366,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "HS-Sch-2", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15303,7 +15383,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Neurofibromatosis type 1", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15320,7 +15400,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Neurofibromatosis type 2", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15337,7 +15417,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Schwannomatosis", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15354,7 +15434,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Not Applicable", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15388,7 +15468,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "cancer", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15405,7 +15485,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "neuro", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15422,7 +15502,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "neurofibromatosis", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15439,7 +15519,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "-/-", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15456,7 +15536,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "+/-", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15473,7 +15553,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "+/+", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15490,7 +15570,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Unknown", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15507,7 +15587,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "-/-", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15524,7 +15604,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "+/-", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15541,7 +15621,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "+/+", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15558,7 +15638,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Unknown", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15575,7 +15655,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "R816X", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15592,7 +15672,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Polymeric nanoparticles", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15609,7 +15689,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "DNA", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15626,7 +15706,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "C57BL/6J", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15643,7 +15723,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "NOD scid gamma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15660,7 +15740,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "NRG", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15677,7 +15757,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "B6;129S2-Trp53tm1Tyj Nf1tm1Tyj/J", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15694,7 +15774,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "B6;129-Trp53tm1Tyj Nf1tm1Tyj Suz12Gt(Betageo)1Khe/KcichJ", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15711,7 +15791,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "B6.129S2-Nf1tm1Tyj/J", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15728,7 +15808,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "B6.129S1-Nf1tm1Cbr/J", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15745,7 +15825,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "B6.129(Cg)-Nf1tm1Par/J", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15762,7 +15842,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Prss56Cre;R26mT", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15779,7 +15859,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Nf1-OPG", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15796,7 +15876,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Nf1-OPG-Arg816", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15813,7 +15893,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Male", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15830,7 +15910,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Female", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15847,7 +15927,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Unknown", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15864,7 +15944,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Homo sapiens", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15881,7 +15961,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Mus musculus", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:ModelSystemName" @@ -15903,7 +15983,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Mus musculus (humanized)", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:ModelSystemName" @@ -15925,7 +16005,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Rattus norvegicus", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:ModelSystemName" @@ -15947,7 +16027,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Drosophila melanogaster", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:ModelSystemName" @@ -15969,7 +16049,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Rhesus macaque", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -15986,7 +16066,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Pan troglodytes", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16003,7 +16083,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Gallus gallus", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16020,7 +16100,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Sus scrofa", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:ModelSystemName" @@ -16042,7 +16122,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Oryctolagus cuniculus", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:ModelSystemName" @@ -16064,7 +16144,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Danio rerio", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:ModelSystemName" @@ -16086,7 +16166,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Human", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16103,7 +16183,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Mouse", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16120,7 +16200,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "10x_v2", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16137,7 +16217,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "FACS", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16154,7 +16234,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Fluidigm C1", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16171,7 +16251,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "drop-seq", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16188,7 +16268,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "inDrop", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16205,7 +16285,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "mouth pipette", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16222,7 +16302,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "enzymatic", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16239,7 +16319,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "mechanical", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16256,7 +16336,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Viably frozen", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16273,7 +16353,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "nerve tissue", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16290,7 +16370,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "optic nerve", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16307,7 +16387,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "serum", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16324,7 +16404,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "plasma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16341,7 +16421,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "splenocyte", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16358,7 +16438,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "blood", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16375,7 +16455,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "primary tumor", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:TumorType" @@ -16397,7 +16477,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "embryonic tissue", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16414,7 +16494,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "meninges", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16431,7 +16511,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "bone marrow", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16448,7 +16528,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Buccal Mucosa", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16465,7 +16545,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Dorsal Root Ganglion", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16482,7 +16562,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "cerebral cortex", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16499,7 +16579,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "sciatic nerve", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16516,7 +16596,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "unspecified", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16533,7 +16613,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "whole brain", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16550,7 +16630,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Buffy Coat", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16567,7 +16647,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "normal", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16584,7 +16664,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "connective tissue", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16601,7 +16681,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "tumor-adjacent normal", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16618,7 +16698,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "PDX tissue", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16635,7 +16715,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "CDX tissue", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16652,7 +16732,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "organoid", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16669,7 +16749,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "spheroid", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16686,7 +16766,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "microtissue", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16703,7 +16783,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "retina", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16720,7 +16800,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Teratoma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16737,7 +16817,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Cutaneous Neurofibroma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16754,7 +16834,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Subcutaneous Neurofibroma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16771,7 +16851,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Plexiform Neurofibroma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16788,7 +16868,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Atypical Neurofibroma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16805,7 +16885,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Malignant Peripheral Nerve Sheath Tumor", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16822,7 +16902,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Glioma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16839,7 +16919,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Low-Grade Glioma NOS", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16856,7 +16936,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Pilocytic Astrocytoma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16873,7 +16953,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Atypical Pilocytic Astrocytoma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16890,7 +16970,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Pilomyxoid Astrocytoma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16907,7 +16987,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Diffuse Astrocytoma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16924,7 +17004,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Glioblastoma Multiforme", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16941,7 +17021,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Anaplastic Pilocytic Astrocytoma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16958,7 +17038,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Pleomorphic Xanthoastrocytoma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16975,7 +17055,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Oligoastrocytoma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -16992,7 +17072,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "High-Grade Glioma NOS", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17009,7 +17089,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Unknown", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17026,7 +17106,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Anaplastic Astrocytoma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17043,7 +17123,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Glioblastoma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17060,7 +17140,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Schwannoma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17077,7 +17157,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Meningioma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17094,7 +17174,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Massive Soft Tissue Neurofibroma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17111,7 +17191,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Diffuse Infiltrating Neurofibroma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17128,7 +17208,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Localized Neurofibroma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17145,7 +17225,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Neurofibroma with Degenerative Atypia", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17162,7 +17242,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Neurofibroma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17179,7 +17259,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Anaplastic Pleomorphic Xanthoastrocytoma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17196,7 +17276,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Ganglioglioma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17213,7 +17293,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Anaplastic Ganglioglioma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17230,7 +17310,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Optic Pathway Glioma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17247,7 +17327,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Not Applicable", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17264,7 +17344,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Colorectal Adenocarcinoma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17281,7 +17361,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Colorectal Carcinoma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17298,7 +17378,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Recurrent MPNST", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17315,7 +17395,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Juvenile Myelomonocytic Leukemia", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17332,7 +17412,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Sarcoma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17349,7 +17429,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Fibromatosis", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17366,7 +17446,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Fibrosarcoma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17383,7 +17463,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Necrotic Neoplasm", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17400,7 +17480,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Hemorrhagic Neoplasm", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17417,7 +17497,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "NF1-Associated Tumor", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17434,7 +17514,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "NF2-Associated Tumor", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17451,7 +17531,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "ANNUBP", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17468,7 +17548,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "tumor", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17485,7 +17565,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "metastatic tumor", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17502,7 +17582,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "metastatic/recurrent tumor", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17519,7 +17599,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "recurrent tumor", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17536,7 +17616,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "Melanoma", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17684,7 +17764,7 @@ } ], "sms:displayName": "tumorType", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17721,7 +17801,7 @@ } ], "sms:displayName": "diagnosis", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17848,7 +17928,7 @@ } ], "sms:displayName": "bodyPart", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17924,7 +18004,7 @@ } ], "sms:displayName": "organ", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -17941,7 +18021,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "individualIdSource", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -18044,7 +18124,7 @@ } ], "sms:displayName": "tissue", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -18069,7 +18149,7 @@ } ], "sms:displayName": "isCellLine", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -18094,7 +18174,7 @@ } ], "sms:displayName": "isPrimaryCell", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -18218,7 +18298,7 @@ } ], "sms:displayName": "cellType", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [ "list like" ] @@ -18298,7 +18378,7 @@ } ], "sms:displayName": "sex", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -18367,7 +18447,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "individualID", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Sex" @@ -18407,7 +18487,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "parentSpecimenID", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:SpecimenID" @@ -18456,7 +18536,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "specimenID", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -18473,7 +18553,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "specimenIDSource", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -18490,7 +18570,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "aliquotID", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -18941,7 +19021,7 @@ } ], "sms:displayName": "modelSystemName", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [ "list like" ] @@ -18980,7 +19060,7 @@ } ], "sms:displayName": "nf2Genotype", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -19017,7 +19097,7 @@ } ], "sms:displayName": "nf1Genotype", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -19060,7 +19140,7 @@ } ], "sms:displayName": "nf1Variant", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -19106,7 +19186,7 @@ } ], "sms:displayName": "specimenPreparationMethod", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -19123,7 +19203,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "age", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:AgeUnit" @@ -19158,7 +19238,7 @@ } ], "sms:displayName": "ageUnit", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -19200,7 +19280,7 @@ } ], "sms:displayName": "isXenograft", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -19234,7 +19314,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "sampleType", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -19263,7 +19343,7 @@ } ], "sms:displayName": "materialType", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -19280,7 +19360,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "pH", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -19297,7 +19377,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "concentrationMaterial", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -19325,7 +19405,7 @@ } ], "sms:displayName": "concentrationMaterialUnit", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -19342,7 +19422,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "concentrationNaCl", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -19367,7 +19447,7 @@ } ], "sms:displayName": "concentrationNaClUnit", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -20802,7 +20882,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "updateMilestoneReport", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Component" @@ -20833,7 +20913,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "template", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:validationRules": [] }, { @@ -20876,7 +20956,7 @@ } ], "sms:displayName": "individualTemplate", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Component" @@ -20957,7 +21037,7 @@ } ], "sms:displayName": "biospecimenTemplateNormalized", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Component" @@ -21012,7 +21092,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "biospecimenTemplate", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Component" @@ -21060,7 +21140,7 @@ } ], "sms:displayName": "dataFileComponent", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Filename" @@ -21105,7 +21185,7 @@ } ], "sms:displayName": "experimentComponent", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:ExperimentalCondition" @@ -21141,7 +21221,7 @@ } ], "sms:displayName": "genePerturbComponent", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:GenePerturbed" @@ -21183,7 +21263,7 @@ } ], "sms:displayName": "fileComponent", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Filename" @@ -21246,7 +21326,7 @@ } ], "sms:displayName": "ngsComponent", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:RunType" @@ -21295,7 +21375,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "LightScatteringAssayTemplate", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Component" @@ -21353,7 +21433,7 @@ "@id": "http://schema.biothings.io" }, "sms:displayName": "FlowCytometryTemplate", - "sms:required": "sms:true", + "sms:required": "sms:false", "sms:requiresDependency": [ { "@id": "bts:Component" diff --git a/modules/Assay/Assay.csv b/modules/Assay/Assay.csv index f3c75a5b..5557c4ce 100644 --- a/modules/Assay/Assay.csv +++ b/modules/Assay/Assay.csv @@ -40,7 +40,7 @@ western blot,A multistep process in which a mixture of proteins is separated by whole genome sequencing,Laboratory technique to sequence the complete DNA sequence of an organism's genome at a single time,,,FALSE,http://edamontology.org/topic_3673,assay,,,,Whole_Genome_Seq,Class,Assay,Assay,DNA_Assay,,, polymerase chain reaction,"A rapid technique for in vitro amplification of specific DNA or RNA sequences, allowing small quantities of short sequences to be analyzed without cloning",,,FALSE,http://purl.obolibrary.org/obo/MMO_0000459,assay,,,,Polymerase_Chain_Reaction,Class,Assay,Assay,RNA_Assay,,, cell viability assay,This assay type measures the cellular state of living or dying by measuring an indicator of life or death,,,FALSE,http://www.bioassayontology.org/bao#BAO_0003009,assay,,,,Cell_Viability_Assay,Class,Assay,Assay,Cell_Assay,,, -2D Incucyte,Cell viability assay on a 2D monolayer model.,,,FALSE,,assay,,,,2D_Incucyte_Assay,Class,Assay,Assay,Cell_Viability_Assay,,, +2D Incucyte,Cell viability assay on a 2D monolayer model.,,,FALSE,https://www.essenbioscience.com/en/resources/documents/,assay,,,,2D_Incucyte_Assay,Class,Assay,Assay,Cell_Viability_Assay,,, 2D CellTiter-Glo,Cell viability assay based on detection of ATP.,,,FALSE,https://www.promega.com/products/cell-health-assays/cell-viability-and-cytotoxicity-assays/celltiter_glo-2_0-assay/?catNum=G9241,assay,,,,2D_Cell_Titer_Glo_Assay,Class,Assay,Assay,Cell_Viability_Assay,,, 3D microtissue viability,Cell viability assay on a 3D microtissue model.,,,FALSE,https://www.ncbi.nlm.nih.gov/books/NBK343426/,assay,,,,3D_Microtissue_Viability_Assay,Class,Assay,Assay,Cell_Viability_Assay,,, 2D AlamarBlue fluorescence,"Cell viability assay based on detection of AlamarBlue (resazurin). Living cells reduce blue, non-fluorescent resazurin to the red, fluorescent molecule resorufin. The amount of fluorescence or absorbance is proportional to the number of living cells and corresponds to the cell’s metabolic activity. For the fluorescence-based assay, color change and fluorescence can be detected using 560/590 nm (excitation/emission).",,,FALSE,https://www.thermofisher.com/us/en/home/life-science/cell-analysis/fluorescence-microplate-assays/microplate-assays-cell-viability/alamarblue-assay-cell-viability.html,assay,,,,2D_AlamarBlue_Fluorescence,Class,Assay,Assay,Cell_Viability_Assay,,, @@ -124,5 +124,6 @@ in vitro tumorigenesis,"An in vitro assay devised to measure tumor formation",,, Matrigel-based tumorigenesis assay,"An assay in which tumor cells are loaded into a Matrigel matrix and measured for tumor formation characteristics",,,FALSE,,assay,,,,Matrigel-based_Tumorigenesis_Assay,Class,Assay,Assay,Tumorigenesis_Assay,,,See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3230200/ calcium retention capacity assay,"The CRC assay assesses Ca2+-related mitochondrial functions",,,FALSE,,assay,,,,Calcium_Retention_Capacity_Assay,Class,Assay,Assay,Cell_Assay,,,See https://pubmed.ncbi.nlm.nih.gov/29781984/ quantitative PCR,"Quantitative PCR (Q-PCR) is used to measure the quantity of a PCR product (commonly in real-time). It quantitatively measures starting amounts of DNA, cDNA, or RNA.",,,FALSE,http://purl.obolibrary.org/obo/MI_1195,assay,,,,Quantitative_PCR,Class,Assay,Assay,RNA_Assay,,, -clinical data, "Data pertaining to the medical well-being or status of a patient. Category also includes clinical reports and individual patient data.",,, FALSE,http://purl.obolibrary.org/obo/NCIT_C15783,assay,,,,Clinical_Data_Assay,Class,Assay,Assay,Assay,,, +clinical data,"Data pertaining to the medical well-being or status of a patient. Category also includes clinical reports and individual patient data.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C15783,assay,,,,Clinical_Data_Assay,Class,Assay,Assay,Assay,,, photograph,An image recorded by a camera.,"","",FALSE,http://purl.obolibrary.org/obo/NCIT_C86035,assay,,"","",Photograph,"",Assay,Assay,"","","","" +cAMP-Glo Max Assay,"The cAMP-Glo Max Assay from Promega is a bioluminescent assay used for the quantification of cyclic AMP (cAMP) in cell-based assays. It utilizes a luminescent luciferase-based detection system to detect the levels of cAMP in cell lysates, which can be used to study G protein-coupled receptor (GPCR) signaling and other intracellular signaling pathways.",,,FALSE,https://www.promega.com/products/cell-signaling/gpcr-signaling/camp_glo-max-assay/?catNum=V1681,assay,,,,cAMP_Glo_Max,Class,Assay,Assay,Assay,,, diff --git a/modules/Assay/Assay_Parameter.csv b/modules/Assay/Assay_Parameter.csv index 719455f1..d9fba994 100644 --- a/modules/Assay/Assay_Parameter.csv +++ b/modules/Assay/Assay_Parameter.csv @@ -44,3 +44,4 @@ forward,Read 1 (or unpaired read) comes from the forward strand and read 2 (if a reverse,read 1 (or unpaired read) comes from the reverse strand and read 2 (if applicable) comes from the forward strand; equivalent to Tophat 'fr-firststrand' type,"","",FALSE,Sage Bionetworks,readStrandOrigin,,"","",Reverse_Read,Class,Assay,Assay_Parameter,Read_Strand_Origin,"","","" singleEnd,A library preparation that results in the creation of a library of 5' ends of DNA.,"","",FALSE,Sage Bionetworks,runType,,"","",Single_End,Class,Assay,Assay_Parameter,Run_Type,"","","" pairedEnd,A library preparation that results in the creation of a library of the 5' and 3' ends of DNA or cDNA fragments using adaptors and endonucleases. The preparation may or may not include cloning process.,"","",FALSE,http://purl.obolibrary.org/obo/OBI_0001852,runType,,"","",Paired_End,Class,Assay,Assay_Parameter,Run_Type,"","","" +KAPA mRNA HyperPrep Kit,The KAPA mRNA HyperPrep Kit is a highly efficient library preparation kit designed for generating stranded RNA-seq libraries with low input amounts and reduced bias.,,,FALSE,https://sequencing.roche.com/global/en/products/group/kapa-rna-hyperprep-kits.html,libraryPreparationMethod,,,,KAPA_mRNA_HyperPrep,Class,Assay,Assay_Parameter,Library_Prep,,, diff --git a/modules/Assay/Platform.csv b/modules/Assay/Platform.csv index e8114247..a8eadf5f 100644 --- a/modules/Assay/Platform.csv +++ b/modules/Assay/Platform.csv @@ -55,4 +55,3 @@ LifeViz Micro System,"(From vendor) Portable 3D imaging system for skin microstr LifeViz Infinity System,"(From vendor) All-in-one 3D imaging system for face, body and breast.",,,FALSE,https://www.quantificare.com/3d-photography-systems_old/lifeviz-infinity/,platform,,,,LifeViz_Infinity_System,Class,Assay,Platform,Platform,,, Promega GloMax Discover,"(From vendor) Microplate reader with high-performance luminescence, fluorescence, UV-Visible absorbance, BRET and FRET, two-color filtered luminescence and kinetic measurement capabilities.",,,FALSE,https://www.promega.com/products/microplate-readers-fluorometers-luminometers/microplate-readers/glomax-discover-system/?catNum=GM3000,platform,,,,Promega_GloMax_Discover,Class,Assay,Platform,Platform,,, BGISEQ-500,"(From vendor) BGISEQ-500 is an industry leading high-throughput sequencing solution, powered by combinatorial Probe-Anchor Synthesis (cPAS) and improved DNA Nanoballs (DNB™) technology.",,,FALSE,https://www.bgi.com/wp-content/uploads/sites/4/2017/05/GLOBAL_BGISEQ-500_WholeGenomeSeq_ServiceOverview_04-17.pdf,platform,,,,BGISEQ_500,Class,Assay,Platform,Platform,,, - diff --git a/modules/Assay/annotationProperty.csv b/modules/Assay/annotationProperty.csv index 295e5d0e..24547fcf 100644 --- a/modules/Assay/annotationProperty.csv +++ b/modules/Assay/annotationProperty.csv @@ -1,7 +1,7 @@ Attribute,Description,Valid Values,DependsOn,Required,Source,Parent,Properties,DependsOn Component,Validation Rules,.ID,.Type,.Module,.Root,.SubOf,.Range,.Cardinality,.EditorNote drugScreenType,String describing general class of drug screen,"singleMolecule, smallMoleculeLibraryScreen, combinationLibraryScreen, combinationScreen",,FALSE,,compoundScreen,,,,drugScreenType,Property,Assay,annotationProperty,,,, -assay,The technology used to generate the data in this file,"HPLC,elevated plus maze test,open field test,rotarod performance test,mRNA counts,high content screen,immunocytochemistry,immunofluorescence,autoradiography,reporter gene assay,electrochemiluminescence,in vivo tumor growth,blood chemistry measurement,in vivo bioluminescence,immunohistochemistry,NOMe-seq,FIA-MSMS,ultra high-performance liquid chromatography/tandem mass spectrometry,high-performance liquid chromatography/tandem mass spectrometry,liquid chromatography-electrochemical detection,RNA-seq,miRNA-seq,liquid chromatography/tandem mass spectrometry,liquid chromatography/mass spectrometry,lncRNA-seq,whole exome sequencing,Sanger sequencing,ChIP-seq,RNA array,SNP array,methylation array,miRNA array,bisulfite sequencing,ATAC-seq,HI-C,ERR bisulfite sequencing,ISO-seq,western blot,whole genome sequencing,polymerase chain reaction,cell viability assay,2D Incucyte,2D CellTiter-Glo,3D microtissue viability,2D AlamarBlue fluorescence,2D AlamarBlue absorbance,in vivo PDX viability,atomic force microscopy,brightfield microscopy,traction force microscopy,phase-contrast microscopy,next generation targeted sequencing,MIB/MS,scCGI-seq,MudPIT,questionnaire,DNA optical mapping,oxBS-seq,ribo-seq,positron emission tomography,RPPA,ELISA,long term potentiation assay,local field potential recording,whole-cell patch clamp,sandwich ELISA,laser speckle imaging,genotyping,TMT quantitation,mass spectrometry,label free mass spectrometry,cell count,immunoassay,conventional MRI,functional MRI,magnetic resonance spectroscopy,FTIR spectroscopy,rheometry,gel filtration chromatography,differential scanning calorimetry,single molecule drug screen assay,small molecule library screen,combination library screen,combination screen,compound screen,array,single-cell RNA-seq,spatial transcriptomics,massively parallel reporter assay,Riccardi and Ablon scales,spatial frequency domain imaging,optical coherence tomography,CUT&RUN,3D imaging,high frequency ultrasound,dynamic light scattering,static light scattering,light scattering assay,flow cytometry,pattern electroretinogram,optokinetic reflex assay,SUSHI,3D confocal imaging,3D electron microscopy,cell competition,body size trait measurement,twin spot assay,perineurial cell thickness,survival,gait measurement,sorbitol dehydrogenase activity level assay,T cell receptor repertoire sequencing,cell proliferation,oxygen consumption assay,reactive oxygen species assay,ATPase activity assay,novelty response behavior assay,contextual conditioning behavior assay,active avoidance learning behavior assay,focus forming assayblue native PAGE,in vitro tumorigenesis,Matrigel-based tumorigenesis assay,calcium retention capacity assay,quantitative PCR,photograph",,TRUE,,experimentalData,,,,assayType,Property,Assay,annotationProperty,,Assay,one, -platform,"A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","Illumina HiSeq 3000, Illumina HiSeq 2500, Illumina HiSeq 4000, Illumina NextSeq 500, Illumina HiSeq 2000, Illumina MiSeq, Zeiss LSM 980, Affymetrix Genome-Wide Human SNP 5.0 Array, Affymetrix Genome-Wide Human SNP 6.0 Array, PacBio RS II, Illumina Genome Analyzer IIx, Illumina HumanOmni1-Quadv1.0, Illumina 1M, Illumina h650, Illumina Omni2pt5M, Illumina Omni5M, Illumina MouseWG-6 v2.0 expression beadchip, Perlegen 300Karray, Agilent 44Karray, Illumina WholeGenome DASL, Illumina HumanHap300, Nanostring Counter, LTQ Orbitrap XL, Illumina HumanMethylation450, Illumina Infinium MethylationEPIC BeadChip v1.0 (850k),Illumina Infinium MethylationEPIC BeadChip v2.0 (935k), Affymetrix U133AB, Affymetrix Human Gene 1.0 ST Array, Affymetrix Human Genome U133 Plus 2.0 Array, Illumina HiSeq X, Bionano Irys, Infinium HumanOmniExpressExome, Illumina NextSeq 550, Illumina NextSeq 1000, Illumina NextSeq 2000, PacBio Sequel IIe System, PacBio Sequel II System, Nanostring GeoMx, LI-COR Odyssey CLx, Spectramax M Series, Olympus DP80, Orbitrap Fusion Lumos Tribrid, Illumina NovaSeq 6000, Chromium X,EnVision 2103 Multiplate Reader,Vectra H1 3D Imaging System,Vevo 3100 Imaging System,10x Visium Spatial Gene Expression,Cherry Imaging TRACE Platform,Cherry Imaging FACE Platform,LifeViz Micro System,LifeViz Infinity System,BGISEQ-500",,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group&anchor=platform,experimentalData,,,,platform,Property,Assay,annotationProperty,,Platform,, +assay,The technology used to generate the data in this file,"HPLC,elevated plus maze test,open field test,rotarod performance test,mRNA counts,high content screen,immunocytochemistry,immunofluorescence,autoradiography,reporter gene assay,electrochemiluminescence,in vivo tumor growth,blood chemistry measurement,in vivo bioluminescence,immunohistochemistry,NOMe-seq,FIA-MSMS,ultra high-performance liquid chromatography/tandem mass spectrometry,high-performance liquid chromatography/tandem mass spectrometry,liquid chromatography-electrochemical detection,RNA-seq,miRNA-seq,liquid chromatography/tandem mass spectrometry,liquid chromatography/mass spectrometry,lncRNA-seq,whole exome sequencing,Sanger sequencing,ChIP-seq,RNA array,SNP array,methylation array,miRNA array,bisulfite sequencing,ATAC-seq,HI-C,ERR bisulfite sequencing,ISO-seq,western blot,whole genome sequencing,polymerase chain reaction,cell viability assay,2D Incucyte,2D CellTiter-Glo,3D microtissue viability,2D AlamarBlue fluorescence,2D AlamarBlue absorbance,in vivo PDX viability,atomic force microscopy,brightfield microscopy,traction force microscopy,phase-contrast microscopy,next generation targeted sequencing,MIB/MS,scCGI-seq,MudPIT,questionnaire,DNA optical mapping,oxBS-seq,ribo-seq,positron emission tomography,RPPA,ELISA,long term potentiation assay,local field potential recording,whole-cell patch clamp,sandwich ELISA,laser speckle imaging,genotyping,TMT quantitation,mass spectrometry,label free mass spectrometry,cell count,immunoassay,conventional MRI,functional MRI,magnetic resonance spectroscopy,FTIR spectroscopy,rheometry,gel filtration chromatography,differential scanning calorimetry,single molecule drug screen assay,small molecule library screen,combination library screen,combination screen,compound screen,array,single-cell RNA-seq,spatial transcriptomics,massively parallel reporter assay,Riccardi and Ablon scales,spatial frequency domain imaging,optical coherence tomography,CUT&RUN,3D imaging,high frequency ultrasound,dynamic light scattering,static light scattering,light scattering assay,flow cytometry,pattern electroretinogram,optokinetic reflex assay,SUSHI,3D confocal imaging,3D electron microscopy,cell competition,body size trait measurement,twin spot assay,perineurial cell thickness,survival,gait measurement,sorbitol dehydrogenase activity level assay,T cell receptor repertoire sequencing,cell proliferation,oxygen consumption assay,reactive oxygen species assay,ATPase activity assay,novelty response behavior assay,contextual conditioning behavior assay,active avoidance learning behavior assay,focus forming assayblue native PAGE,in vitro tumorigenesis,Matrigel-based tumorigenesis assay,calcium retention capacity assay,quantitative PCR,photograph,cAMP-Glo Max Assay",,TRUE,,experimentalData,,,,assayType,Property,Assay,annotationProperty,,Assay,one, +platform,"A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","Illumina HiSeq 3000, Illumina HiSeq 2500, Illumina HiSeq 4000, Illumina NextSeq 500, Illumina HiSeq 2000, Illumina MiSeq, Zeiss LSM 980, Affymetrix Genome-Wide Human SNP 5.0 Array, Affymetrix Genome-Wide Human SNP 6.0 Array, PacBio RS II, Illumina Genome Analyzer IIx, Illumina HumanOmni1-Quadv1.0, Illumina 1M, Illumina h650, Illumina Omni2pt5M, Illumina Omni5M, Illumina MouseWG-6 v2.0 expression beadchip, Perlegen 300Karray, Agilent 44Karray, Illumina WholeGenome DASL, Illumina HumanHap300, Nanostring Counter, LTQ Orbitrap XL, Illumina HumanMethylation450, Illumina Infinium MethylationEPIC BeadChip v1.0 (850k),Illumina Infinium MethylationEPIC BeadChip v2.0 (935k), Affymetrix U133AB, Affymetrix Human Gene 1.0 ST Array, Affymetrix Human Genome U133 Plus 2.0 Array, Illumina HiSeq X, Bionano Irys, Infinium HumanOmniExpressExome, Illumina NextSeq 550, Illumina NextSeq 1000, Illumina NextSeq 2000, PacBio Sequel IIe System, PacBio Sequel II System, Nanostring GeoMx, LI-COR Odyssey CLx, Spectramax M Series, Olympus DP80, Orbitrap Fusion Lumos Tribrid, Illumina NovaSeq 6000, Chromium X,EnVision 2103 Multiplate Reader,Vectra H1 3D Imaging System,Vevo 3100 Imaging System,10x Visium Spatial Gene Expression,Cherry Imaging TRACE Platform,Cherry Imaging FACE Platform,LifeViz Micro System,LifeViz Infinity System,BGISEQ-500",,TRUE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group&anchor=platform,experimentalData,,,,platform,Property,Assay,annotationProperty,,Platform,, targetCaptureKitID,"A unique identifier for the kit used to construct a genomic library using target capture-based techniques, which should be composed of the vendor name, kit name and kit version.",,,TRUE,http://purl.obolibrary.org/obo/NCIT_C177583,experimentalData,,,,targetCaptureKitID,Property,Assay,annotationProperty,,,,"For WES processing, the target BED used could be provided based on the target capture kit." libraryID,,,,TRUE,,experimentalData,,,,libraryID,Property,Assay,annotationProperty,,,, assayTarget,The HUGO gene symbol that represents the target analyte assayed.,,,FALSE,Sage Bionetworks,experimentalData,,,,assayTarget,Property,Assay,annotationProperty,,,, @@ -11,11 +11,11 @@ reporterSubstance,A gene which produces an easily assayed phenotype. Often used immunoAssayType,Type of immuno assay,"ChIP-seq, ATAC-seq",,TRUE,,immunoAssay,,,,immunoAssayType,Property,Assay,annotationProperty,,,, runType,Is the sequencing run single or paired end?,"singleEnd, pairedEnd","readPair,isStranded,readPairOrientation,readStrandOrigin,readLength,readDepth",FALSE,Sage Bionetworks,ngs,,,,runType,Property,Assay,annotationProperty,ngsParameter,Run_Type,, readPair,The read of origin,,,FALSE,,ngs,,,int,readPair,Property,Assay,annotationProperty,ngsParameter,Read_Pair,, -isStranded,Whether or not the library is stranded (Yes; No),"Yes, No",,FALSE,,ngs,,,,isStranded,Property,Assay,annotationProperty,ngsParameter,,, -readPairOrientation,The relative orientation of the reads in a paired-end protocol,"inward, outward, matching, fr-firststrand",,FALSE,,ngs,,,,readPairOrientation,Property,Assay,annotationProperty,ngsParameter,Read_Pair_Orientation,, +isStranded,Whether or not the library is stranded (Yes; No),"Yes, No",,TRUE,,ngs,,,,isStranded,Property,Assay,annotationProperty,ngsParameter,,, +readPairOrientation,The relative orientation of the reads in a paired-end protocol,"inward, outward, matching, fr-firststrand",,TRUE,,ngs,,,,readPairOrientation,Property,Assay,annotationProperty,ngsParameter,Read_Pair_Orientation,, readStrandOrigin,The strand from which the read originates in a strand-specific protocol,"forward, reverse",,FALSE,,ngs,,,,readStrandOrigin,Property,Assay,annotationProperty,ngsParameter,Read_Strand_Origin,, libraryPrep,The general strategy by which the library was prepared,"rRNAdepletion, polyAselection, lncRNAenrichment, miRNAenrichment","libraryPreparationMethod,nucleicAcidSource,dissociationMethod",FALSE,,ngs,,,,libraryPrep,Property,Assay,annotationProperty,ngsParameter,Library_Prep,, -libraryPreparationMethod,Method by which library was prepared,"10x, CEL-seq, Drop-Seq, Smart-seq2, TruSeq, Smart-seq4, Omni-ATAC, NEBNext mRNA Library Prep Reagent Set for Illumina, IDT xGen Exome Research Panel, TruSeq standard total RNA library kit, Illumina TruSeq DNA Nano, KAPA HyperPrep Kit PCR-free,KAPA RNA HyperPrep Kit with RiboErase (HMR),GTAC@WUSTL in-house prep",,FALSE,,ngs,,,,libraryPreparationMethod,Property,Assay,annotationProperty,ngsParameter,Library_Preparation_Method,, +libraryPreparationMethod,Method by which library was prepared,"10x, CEL-seq, Drop-Seq, Smart-seq2, TruSeq, Smart-seq4, Omni-ATAC, NEBNext mRNA Library Prep Reagent Set for Illumina, IDT xGen Exome Research Panel, TruSeq standard total RNA library kit, Illumina TruSeq DNA Nano, KAPA HyperPrep Kit PCR-free,KAPA RNA HyperPrep Kit with RiboErase (HMR),GTAC@WUSTL in-house prep, KAPA mRNA HyperPrep Kit",,TRUE,,ngs,,,,libraryPreparationMethod,Property,Assay,annotationProperty,ngsParameter,Library_Preparation_Method,, nucleicAcidSource,Source of the extracted nucleic acid used in the experiment,"bulk cell, single cell, bulk nuclei, single nucleus, mitochondria",,FALSE,Sage Bionetworks,ngs,,,,nucleicAcidSource,Property,Assay,annotationProperty,ngsParameter,Nucleic_Acid_Source,, dissociationMethod,Procedure by which a biological specimen is dissociated into individual cells or a cell suspension,"10x_v2, FACS, Fluidigm C1, drop-seq, inDrop, mouth pipette, bulk, enzymatic, mechanical, none",,FALSE,https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0009088,ngs,,,,dissociationMethod,Property,Assay,annotationProperty,ngsParameter,Dissociation_Method,, readLength,Number of base pairs (bp) sequenced for a read,,,TRUE,,ngs,,,,readLength,DataProperty,Assay,annotationProperty,ngsParameter,,, diff --git a/modules/Data/File_Format.csv b/modules/Data/File_Format.csv index 0a9b1a58..6cabdf26 100644 --- a/modules/Data/File_Format.csv +++ b/modules/Data/File_Format.csv @@ -90,3 +90,5 @@ hdr,"MRI Header file, as in the NIFTI-1 Analyze 7.5 format","","",FALSE,https:// img,"MRI Data file, as in the NIFTI-1 Analyze 7.5 format","","",FALSE,https://nifti.nimh.nih.gov/pub/dist/src/niftilib/nifti1.h,fileFormat,,"","",img,Class,Data,File_Format,"","","","" sf,"Salmon’s main output is its quantification file. This file is a plain-text, tab-separated file with a single header line (which names all of the columns).","","",FALSE,https://salmon.readthedocs.io/en/latest/file_formats.html,fileFormat,,"","",sf,Class,Data,File_Format,"","","","" tom,"The .tom format is a specialized 3D image export format from the Vectra medical imaging systems that can optionally preserve trimmings and/or landmarks.","","",FALSE,http://canfieldupgrade.com/assets/media/VECTRA-M3-User-Guide.pdf,fileFormat,,"","",tom,Class,Data,File_Format,"","","","" +fcs,"Format standard of a digital entity that is conformant with the Flow Cytometry Data File Standard",,,FALSE,http://purl.obolibrary.org/obo/OBI_0000327,fileFormat,,"","",fcs,Class,Data,File_Format,"","","","" +NWB,"Neurodata Without Borders (NWB) is a data standard for neurophysiology data, designed to store data including from intracellular and extracellular electrophysiology experiments, data from optical physiology experiments, and tracking and stimulus data.","","",FALSE,https://www.nwb.org/,fileFormat,,"","",NWB,Class,Data,File_Format,"","","","" diff --git a/modules/Data/annotationProperty.csv b/modules/Data/annotationProperty.csv index 9f82975f..9b4e5d5e 100644 --- a/modules/Data/annotationProperty.csv +++ b/modules/Data/annotationProperty.csv @@ -6,13 +6,13 @@ dataSubtype,"Further qualification of dataType, which may be used to indicate th metadataType,"For files of dataSubtype: metadata, a description of the type of metadata in the file.","individual, biospecimen, assay, data dictionary, manifest, protocol",,FALSE,,experimentalData,,,,metadataType,Property,Data,annotationProperty,,,, dataType,"A type of experimental, clinical, or other data. This typically refers to a high-level data type that can be related to an assay type. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`.","Volume, Weight, Pharmacokinetic Study, genomicVariants,behavior process, metabolomics, image, geneExpression, isoformExpression, proteomics, particle characterization, kinomics, drugScreen, drugCombinationScreen, cellularPhysiology, chromatinActivity, surveyData, network, clinical, immunoassay, electrophysiology, raw counts, mask image,AlignedReads,SomaticVariants,AnnotatedSomaticVariants,StructuralVariants,GermlineVariants,AnnotatedGermlineVariants,characteristic",dataSubtype,TRUE,,experimentalData,,,,dataType,Property,Data,annotationProperty,,Data,one, expressionUnit,Measure used for transcript expression quantification,"TPM,RPKM,FPKM,Counts,Other",,TRUE,,experimentalData,,,,expressionUnit,DataProperty,Data,annotationProperty,,,, -failedQC,"Whether the sample or data failed QC checks (Yes, No)","Yes, No",,TRUE,,experimentalData,,,,failedQC,DataProperty,Data,annotationProperty,,, +failedQC,"Whether the sample or data failed QC checks (Yes, No)","Yes, No",,TRUE,,experimentalData,,,,failedQC,DataProperty,Data,annotationProperty,,,, Filename,The name of the file.,,"entityId,fileFormat",TRUE,Sage Bionetworks,NF,,,,fileName,Class,Data,annotationProperty,fileName,,one,Automatically filled when using the curator app. programmingLanguage,A computer programming language,"Python, R, MATLAB, Java, C, C++, C#, Javascript, bash",,FALSE,Sage Bionetworks,,,,,programmingLanguage,Property,Data,annotationProperty,ngsParameter,,, runtimePlatform,"Runtime platform or script interpreter dependencies (e.g. Java v1, Python 2.3).",,,FALSE,Sage Bionetworks,,,,,runtimePlatform,Property,Data,annotationProperty,ngsParameter,,, documentation,URL to any documentation describing the resource and its use.,,,FALSE,Sage Bionetworks,,,,,documentation,Property,Data,annotationProperty,ngsParameter,,, resourceType,The type of resource being stored and annotated,"experimentalData, curatedData, result, tool, report, metadata, protocol, workflow report,weblink",,TRUE,,sageCommunity,,,,resourceType,Property,Data,annotationProperty,,Resource,, -fileFormat,"Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software","bash script,bedgraph,ai,idx,idat,bam,bai,excel,powerpoint,tif,png,doc,pdf,hdf,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,mzML,SPAR,SDAT,nii,PAR,REC,hdr,img,sf,MATLAB script, MATLAB data,tom",,TRUE,,sageCommunity,,,,fileFormat,Property,Data,annotationProperty,,File_Format,one, +fileFormat,"Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software","bash script,bedgraph,ai,idx,idat,bam,bai,excel,powerpoint,tif,png,doc,pdf,hdf,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,mzML,SPAR,SDAT,nii,PAR,REC,hdr,img,sf,MATLAB script, MATLAB data,tom,fcs,NWB",,TRUE,,sageCommunity,,,,fileFormat,Property,Data,annotationProperty,,File_Format,one, progressReportNumber,"Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",,FALSE,,template,,,,progressReportNumber,DataProperty,Data,annotationProperty,,,one, comments,Brief free-text comments that may also be important to understanding the resource.,,,FALSE,Sage Bionetworks,experimentalData,,,,comments,DataProperty,Data,annotationProperty,,,many, Resource_id,A UUID for a Resource from the NF Research Tools Database,,,FALSE,Sage Bionetworks,dccProperty,,,,Resource_id,Property,Data,annotationProperty,dccProperty,,, @@ -31,4 +31,4 @@ contentSize,(Files only) File size calculated by the platform.,,,FALSE,Sage Bion type,"Refers to the type of the resource on the platform, e.g. “file”.",,,FALSE,Sage Bionetworks,synapseProperty,,,,type,Property,Data,annotationProperty,synapseProperty,,, concreteType,Refers to the class model the data platform uses for representing the resource. This is a low-level field set by the platform and is not a user annotation.,,,FALSE,Sage Bionetworks,synapseProperty,,,,concreteType,Property,Data,annotationProperty,synapseProperty,,, author,"The author of the resource; preferably use an ORCID ID, GitHub profile link, etc., if available and a text name if not.",,,FALSE,Sage Bionetworks,,,,,,Property,Data,annotationProperty,,,, -license,Link to a license or name of license applicable for the resource.,,,,,,,,,,,,,,,, +license,Link to a license or name of license applicable for the resource.,,,FALSE,Sage Bionetworks,,,,,,Property,Data,annotationProperty,,,, diff --git a/utils/lint.clj b/utils/lint.clj new file mode 100644 index 00000000..da6dfa51 --- /dev/null +++ b/utils/lint.clj @@ -0,0 +1,41 @@ +(require '[clojure.data.csv :as csv] + '[clojure.java.io :as io] + '[babashka.cli :as cli] + '[clojure.string :as str]) + +(def cli-options {:files {}}) + +(def opts (cli/parse-opts *command-line-args* {:coerce {:files [] }})) + +(defn output-notice-fix [line file] + [{:type "::notice" :file file :msg "Missing EOL was fixed for you" :col 1 :line line}]) + +(defn fix-eol-at-eof! [lines file] + (when (false? (str/ends-with? (slurp file) "\n")) + (spit file "\n" :append true) + (output-notice-fix (count lines) file))) + +(defn output-error-fields [lines file] + (let [n (count (first lines))] + (->> lines + (keep-indexed #(when (not= n (count %2)) %1)) + (map (fn [idx] {:type "::error" :file file :msg (str "Number of fields is not " n) :col 1 :line (inc idx) }))))) + +(defn lint [rows file] + (concat (output-error-fields rows file) (fix-eol-at-eof! rows file))) + +(defn gh-workflow-format [coll] + (map #(str (% :type) " file=" (% :file) ",line=" (% :line) ",col=" (% :col) "::" (% :msg)) coll)) + +(defn gh-workflow-print [msg] + (when (seq msg) + (println (first msg)) + (recur (rest msg)))) + +(doseq [file (opts :files)] + (println (str "Processing " file)) + (let [rows (with-open [reader (io/reader file)] (doall (csv/read-csv reader)))] + (->> + (lint rows file) + (gh-workflow-format) + (gh-workflow-print)))) diff --git a/scripts/toolsdb_sync.R b/utils/toolsdb_sync.R similarity index 100% rename from scripts/toolsdb_sync.R rename to utils/toolsdb_sync.R