Merge pull request #219 from nf-osi/feat/facs

Add flow cytometry
nf-osi · Nov 30, 2022 · 8256578 · 8256578
2 parents 58677df + f354372
commit 8256578
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Showing 4 changed files with 24 additions and 2 deletions.
diff --git a/NF.csv b/NF.csv
@@ -97,6 +97,7 @@ High Frequency Ultrasound,"High frequency ultrasound (HFUS) is an imaging modali
 Dynamic Light Scattering,"Dynamic Light Scattering (DLS), also known as photocorrelation spectroscopy, is a method for determining the size distribution of a sample of small particles in solution by illuminating the sample with a light source (usually a laser) and measuring the time-dependent fluctuations in the intensity of the scattered light caused by Brownian motion.",,Assay,FALSE,http://purl.obolibrary.org/obo/CHMO_0000167,assay,,,,Dynamic_Light_Scattering,Class,Assay,Assay,Light_Scattering_Assay,,,
 Static Light Scattering,"Static Light Scattering is a method for determining structure by measuring the total or time-averaged scattering intensity of scattered visible light as a function of angle.",,Assay,FALSE,http://purl.obolibrary.org/obo/CHMO_0000180,assay,,,,Static_Light_Scattering,Class,Assay,Assay,Light_Scattering_Assay,,,
 Light Scattering Assay,"A method for determining structure by measuring the change in direction or energy of scattered visible light. Light is scattered by the electrons surrounding the atomic nuclei in the sample.",,Assay,FALSE,http://purl.obolibrary.org/obo/CHMO_0000166,assay,,,,Light_Scattering_Assay,Class,Assay,Assay,Spectroscopy,,,
+flow cytometry,"A cytometry assay in which an input cell population is put in solution, is passed by a laser, and optical sensors are used to detect scattering of the laser light and/or fluorescence of specific markers to count and characterize the particles in solution",,,FALSE,http://purl.obolibrary.org/obo/OBI_0000916,assay,,,,Flow_Cytometry_Assay,Class,Assay,Assay,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,"","","",""
@@ -205,7 +206,7 @@ Cherry Imaging FACE Platform,"(From vendor) A micro-ultrasound imaging system fo
 LifeViz Micro System,"(From vendor) Portable 3D imaging system for skin microstructure analysis.",,,FALSE,https://www.quantificare.com/3d-photography-systems_old/lifeviz-micro/,platform,,,,LifeViz_Micro_System,Class,Assay,Platform,Platform,,,
 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,,,
 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",,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",,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
@@ -3668,6 +3668,23 @@
             ],
             "sms:validationRules": []
         },
+        {
+            "@id": "bts:Flowcytometry",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "A cytometry assay in which an input cell population is put in solution, is passed by a laser, and optical sensors are used to detect scattering of the laser light and/or fluorescence of specific markers to count and characterize the particles in solution",
+            "rdfs:label": "Flowcytometry",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Assay"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "flow cytometry",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
         {
             "@id": "bts:Channel",
             "@type": "rdfs:Class",
@@ -5823,6 +5840,9 @@
                 },
                 {
                     "@id": "bts:StaticLightScattering"
+                },
+                {
+                    "@id": "bts:Flowcytometry"
                 }
             ],
             "sms:displayName": "assay",

diff --git a/modules/Assay/Assay.csv b/modules/Assay/Assay.csv
@@ -97,3 +97,4 @@ High Frequency Ultrasound,"High frequency ultrasound (HFUS) is an imaging modali
 Dynamic Light Scattering,"Dynamic Light Scattering (DLS), also known as photocorrelation spectroscopy, is a method for determining the size distribution of a sample of small particles in solution by illuminating the sample with a light source (usually a laser) and measuring the time-dependent fluctuations in the intensity of the scattered light caused by Brownian motion.",,Assay,FALSE,http://purl.obolibrary.org/obo/CHMO_0000167,assay,,,,Dynamic_Light_Scattering,Class,Assay,Assay,Light_Scattering_Assay,,,
 Static Light Scattering,"Static Light Scattering is a method for determining structure by measuring the total or time-averaged scattering intensity of scattered visible light as a function of angle.",,Assay,FALSE,http://purl.obolibrary.org/obo/CHMO_0000180,assay,,,,Static_Light_Scattering,Class,Assay,Assay,Light_Scattering_Assay,,,
 Light Scattering Assay,"A method for determining structure by measuring the change in direction or energy of scattered visible light. Light is scattered by the electrons surrounding the atomic nuclei in the sample.",,Assay,FALSE,http://purl.obolibrary.org/obo/CHMO_0000166,assay,,,,Light_Scattering_Assay,Class,Assay,Assay,Spectroscopy,,,
+flow cytometry,"A cytometry assay in which an input cell population is put in solution, is passed by a laser, and optical sensors are used to detect scattering of the laser light and/or fluorescence of specific markers to count and characterize the particles in solution",,,FALSE,http://purl.obolibrary.org/obo/OBI_0000916,assay,,,,Flow_Cytometry_Assay,Class,Assay,Assay,Assay,,,
diff --git a/modules/Assay/annotationProperty.csv b/modules/Assay/annotationProperty.csv
@@ -1,6 +1,6 @@
 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,"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",,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",,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,,,,