Merge pull request #242 from nf-osi/allaway/new-cagan-terms

Allaway/new cagan terms
nf-osi · Jan 25, 2023 · 34d061d · 34d061d
2 parents ae76ba7 + 560320b
commit 34d061d
Show file tree

Hide file tree

Showing 4 changed files with 112 additions and 2 deletions.
diff --git a/NF.csv b/NF.csv
@@ -103,6 +103,11 @@ Optokinetic reflex assay,"The optokinetic reflex (OKR), which serves to stabiliz
 SUSHI,"Fast super-resolution method that exploits sparsity in the underlying vasculature and statistical independence within the measured signals to detect slow-flowing blood, facilitating noninvasive perfusion measurements.",,,FALSE,https://pubmed.ncbi.nlm.nih.gov/30295619/,assay,,,,Optokinetic_Reflex_Assay,Class,Assay,Assay,Assay,,,
 3D confocal imaging,"Confocal microscopy with 3D reconstruction of the sample tissue.",,,FALSE,https://pubmed.ncbi.nlm.nih.gov/34331281,assay,,,,3D_Confocal_Imaging,Class,Assay,Assay,Imaging_Assay,,,
 3D electron microscopy,"Three-dimensional (3D) reconstruction of single, transparent objects from a collection of projection images recorded with a transmission electron microscope. It offers the opportunity to obtain 3D information on structural cellular arrangements with a high resolution.",,,FALSE,http://purl.obolibrary.org/obo/MI_0410,assay,,,,3D_Electron_Microscopy,Class,Assay,Assay,Imaging_Assay,,,
+cell competition,"An assay in which two or more labeled populations of cells or organoids are mixed, allowed to grow, possibly in the presence of a drug or other perturbagen. The relative quantity of the cell populations is measured at the end of the experiment.",,,FALSE,https://pubmed.ncbi.nlm.nih.gov/22113311/,assay,,,,Competitive_Cell_Growth,Class,Assay,Assay,Imaging_Assay,,,
+body size trait measurement,"Any measurable or observable characteristic related to the overall physical magnitude of an organism.",,,FALSE,http://purl.obolibrary.org/obo/VT_0100005,assay,,,,Body_Size_Trait_Measurement,Class,Assay,Assay,Imaging_Assay,,,
+twin spot assay,"Two individual and genetically different populations of cells that originate from the same mitotic recombination event; twin spots allow a direct and reliable comparison between mutant and wild-type clones, and the size of the wild-type twin can serve as a reference for comparison with the homozygous mutant clones.",,,FALSE,https://pubmed.ncbi.nlm.nih.gov/29378809/,assay,,,,Twin_Spot_Assay,Class,Assay,Assay,Imaging_Assay,,,
+perineurial cell thickness,"Measuring the thickness of the cells in the perineurium, e.g. in developing Drosophila melanogaster.",,,FALSE,http://purl.obolibrary.org/obo/MI_0410,assay,,,,Perineurial_Cell_Thickness,Class,Assay,Assay,Imaging_Assay,,,
+survival,"Any quantitative measurement of survival of or in an individual or study population.",,,FALSE,http://purl.obolibrary.org/obo/MI_0410,assay,,,,Perineurial_Cell_Thickness,Class,Assay,Assay,Imaging_Assay,,,
 channel,Fluorescent color labeling for an array,"Cy5, Cy3","",TRUE,"",array,,"","",Channel,"",Assay,Assay_Parameter,"","","",""
 photograph,An image recorded by a camera.,"","",FALSE,http://purl.obolibrary.org/obo/NCIT_C86035,assay,,"","",Photograph,"",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,"","","",""
@@ -212,7 +217,7 @@ 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,,,
 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,"elevated plus maze test, open field test, rotarod performance test, mRNAcounts, high content screen, Immunocytochemistry, immunofluorescence, autoradiography, electrochemiluminescence, Real Time PCR, in vivo tumor growth, scale, Blood Chemistry Measurement, in vivo bioluminescence, immunohistochemistry, NOMe-Seq, FIA-MSMS, UPLC-MSMS, HPLC-MSMS, liquid chromatography-electrochemical detection, rnaSeq, mirnaSeq, LC-MSMS, LC-MS, lncrnaSeq, Whole Exome Sequencing, Sanger sequencing, ChIPSeq, rnaArray, snpArray, methylationArray, mirnaArray, bisulfiteSeq, ATACSeq, HI-C, errBisulfiteSeq, ISOSeq, westernBlot, wholeGenomeSeq, polymeraseChainReaction, cellViabilityAssay, atomicForceMicroscopy, brightfieldMicroscopy, tractionForceMicroscopy, nextGenerationTargetedSequencing, jumpingLibrary, MIB/MS, scCGIseq, MudPIT, questionnaire, DNA optical mapping, oxBS-Seq, Ribo-Seq, Positron Emission Tomography, RPPA, ELISA, LTP, LFP, whole-cell patch clamp, sandwich ELISA, Laser Speckle Imaging, Genotyping, TMT quantitation, label free mass spectrometry, cell count, reporter gene assay, Single Cell RNA Sequencing, spatial transcriptomics, Conventional MRI, Functional MRI, Magnetic Resonance Spectroscopy, 2D Incucyte, 2D CellTiter-Glo, 3D microtissue viability, in vivo PDX viability, 2D AlamarBlue fluorescence, 2D AlamarBlue absorbance, rheometry, FTIR Spectroscopy, differential scanning calorimetry, Gel filtration chromatography, Massively Parallel Reporter Assay,Riccardi and Ablon scales,Spatial Frequency Domain Imaging,Optical Coherence Tomography,CUT&RUN,High Frequency Ultrasound, 3D Imaging,Dynamic Light Scattering,Static Light Scattering,flow cytometry,Pattern electroretinogram,Optokinetic reflex assay,SUSHI,3D confocal imaging,3D electron microscopy",,TRUE,,experimentalData,,,,assayType,Property,Assay,annotationProperty,,Assay,one,
+assay,The technology used to generate the data in this file,"elevated plus maze test, open field test, rotarod performance test, mRNAcounts, high content screen, Immunocytochemistry, immunofluorescence, autoradiography, electrochemiluminescence, Real Time PCR, in vivo tumor growth, scale, Blood Chemistry Measurement, in vivo bioluminescence, immunohistochemistry, NOMe-Seq, FIA-MSMS, UPLC-MSMS, HPLC-MSMS, liquid chromatography-electrochemical detection, rnaSeq, mirnaSeq, LC-MSMS, LC-MS, lncrnaSeq, Whole Exome Sequencing, Sanger sequencing, ChIPSeq, rnaArray, snpArray, methylationArray, mirnaArray, bisulfiteSeq, ATACSeq, HI-C, errBisulfiteSeq, ISOSeq, westernBlot, wholeGenomeSeq, polymeraseChainReaction, cellViabilityAssay, atomicForceMicroscopy, brightfieldMicroscopy, tractionForceMicroscopy, nextGenerationTargetedSequencing, jumpingLibrary, MIB/MS, scCGIseq, MudPIT, questionnaire, DNA optical mapping, oxBS-Seq, Ribo-Seq, Positron Emission Tomography, RPPA, ELISA, LTP, LFP, whole-cell patch clamp, sandwich ELISA, Laser Speckle Imaging, Genotyping, TMT quantitation, label free mass spectrometry, cell count, reporter gene assay, Single Cell RNA Sequencing, spatial transcriptomics, Conventional MRI, Functional MRI, Magnetic Resonance Spectroscopy, 2D Incucyte, 2D CellTiter-Glo, 3D microtissue viability, in vivo PDX viability, 2D AlamarBlue fluorescence, 2D AlamarBlue absorbance, rheometry, FTIR Spectroscopy, differential scanning calorimetry, Gel filtration chromatography, Massively Parallel Reporter Assay,Riccardi and Ablon scales,Spatial Frequency Domain Imaging,Optical Coherence Tomography,CUT&RUN,High Frequency Ultrasound, 3D Imaging,Dynamic Light Scattering,Static Light Scattering,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",,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, 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",,FALSE,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,,,,

diff --git a/NF.jsonld b/NF.jsonld
@@ -3770,6 +3770,91 @@
             "sms:required": "sms:false",
             "sms:validationRules": []
         },
+        {
+            "@id": "bts:Cellcompetition",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "An assay in which two or more labeled populations of cells or organoids are mixed, allowed to grow, possibly in the presence of a drug or other perturbagen. The relative quantity of the cell populations is measured at the end of the experiment.",
+            "rdfs:label": "Cellcompetition",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Assay"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "cell competition",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
+        {
+            "@id": "bts:Bodysizetraitmeasurement",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "Any measurable or observable characteristic related to the overall physical magnitude of an organism.",
+            "rdfs:label": "Bodysizetraitmeasurement",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Assay"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "body size trait measurement",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
+        {
+            "@id": "bts:Twinspotassay",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "Two individual and genetically different populations of cells that originate from the same mitotic recombination event; twin spots allow a direct and reliable comparison between mutant and wild-type clones, and the size of the wild-type twin can serve as a reference for comparison with the homozygous mutant clones.",
+            "rdfs:label": "Twinspotassay",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Assay"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "twin spot assay",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
+        {
+            "@id": "bts:Perineurialcellthickness",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "Measuring the thickness of the cells in the perineurium, e.g. in developing Drosophila melanogaster.",
+            "rdfs:label": "Perineurialcellthickness",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Assay"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "perineurial cell thickness",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
+        {
+            "@id": "bts:Survival",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "Any quantitative measurement of survival of or in an individual or study population.",
+            "rdfs:label": "Survival",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Assay"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "survival",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
         {
             "@id": "bts:Channel",
             "@type": "rdfs:Class",
@@ -5960,6 +6045,21 @@
                 },
                 {
                     "@id": "bts:3Delectronmicroscopy"
+                },
+                {
+                    "@id": "bts:Cellcompetition"
+                },
+                {
+                    "@id": "bts:Bodysizetraitmeasurement"
+                },
+                {
+                    "@id": "bts:Twinspotassay"
+                },
+                {
+                    "@id": "bts:Perineurialcellthickness"
+                },
+                {
+                    "@id": "bts:Survival"
                 }
             ],
             "sms:displayName": "assay",

diff --git a/modules/Assay/Assay.csv b/modules/Assay/Assay.csv
@@ -103,3 +103,8 @@ Optokinetic reflex assay,"The optokinetic reflex (OKR), which serves to stabiliz
 SUSHI,"Fast super-resolution method that exploits sparsity in the underlying vasculature and statistical independence within the measured signals to detect slow-flowing blood, facilitating noninvasive perfusion measurements.",,,FALSE,https://pubmed.ncbi.nlm.nih.gov/30295619/,assay,,,,Optokinetic_Reflex_Assay,Class,Assay,Assay,Assay,,,
 3D confocal imaging,"Confocal microscopy with 3D reconstruction of the sample tissue.",,,FALSE,https://pubmed.ncbi.nlm.nih.gov/34331281,assay,,,,3D_Confocal_Imaging,Class,Assay,Assay,Imaging_Assay,,,
 3D electron microscopy,"Three-dimensional (3D) reconstruction of single, transparent objects from a collection of projection images recorded with a transmission electron microscope. It offers the opportunity to obtain 3D information on structural cellular arrangements with a high resolution.",,,FALSE,http://purl.obolibrary.org/obo/MI_0410,assay,,,,3D_Electron_Microscopy,Class,Assay,Assay,Imaging_Assay,,,
+cell competition,"An assay in which two or more labeled populations of cells or organoids are mixed, allowed to grow, possibly in the presence of a drug or other perturbagen. The relative quantity of the cell populations is measured at the end of the experiment.",,,FALSE,https://pubmed.ncbi.nlm.nih.gov/22113311/,assay,,,,Competitive_Cell_Growth,Class,Assay,Assay,Imaging_Assay,,,
+body size trait measurement,"Any measurable or observable characteristic related to the overall physical magnitude of an organism.",,,FALSE,http://purl.obolibrary.org/obo/VT_0100005,assay,,,,Body_Size_Trait_Measurement,Class,Assay,Assay,Imaging_Assay,,,
+twin spot assay,"Two individual and genetically different populations of cells that originate from the same mitotic recombination event; twin spots allow a direct and reliable comparison between mutant and wild-type clones, and the size of the wild-type twin can serve as a reference for comparison with the homozygous mutant clones.",,,FALSE,https://pubmed.ncbi.nlm.nih.gov/29378809/,assay,,,,Twin_Spot_Assay,Class,Assay,Assay,Imaging_Assay,,,
+perineurial cell thickness,"Measuring the thickness of the cells in the perineurium, e.g. in developing Drosophila melanogaster.",,,FALSE,http://purl.obolibrary.org/obo/MI_0410,assay,,,,Perineurial_Cell_Thickness,Class,Assay,Assay,Imaging_Assay,,,
+survival,"Any quantitative measurement of survival of or in an individual or study population.",,,FALSE,http://purl.obolibrary.org/obo/MI_0410,assay,,,,Perineurial_Cell_Thickness,Class,Assay,Assay,Imaging_Assay,,,