Add spatial transcriptomics (#163)

* Add spatial transcriptomics * Update annotationProperty.csv * Add changes * Minor RNA-Seq correction * Add changes Co-authored-by: nf-osi[bot] <[email protected]> Co-authored-by: anngvu <[email protected]>
nf-osi · Jun 6, 2022 · 77e0d16 · 77e0d16
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Showing 4 changed files with 24 additions and 2 deletions.
diff --git a/NF.csv b/NF.csv
@@ -86,6 +86,7 @@ combinationScreen,,,,FALSE,,drugScreenType,,,,Combination_Screen,Class,Assay,Ass
 compoundScreen,,,,FALSE,,assay,,,,Compound_Screen,Class,Assay,Assay,Drug_Screen,,,
 array,,,,FALSE,,assay,,,,Array,Class,Assay,Assay,Assay,,,
 Single Cell RNA Sequencing,A procedure that can determine the nucleotide sequence for all of the RNA transcripts in an amplified nucleotide sample that was derived from a single cell.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C171152,assay,,,,ScRNA_Seq,Class,Assay,Assay,RNA-Seq,,,
+spatial transcriptomics,"assay that allows visualization and quantitative analysis of the transcriptome with spatial resolution in individual tissue sections",,,FALSE,http://www.ebi.ac.uk/efo/EFO_0008994,assay,,,,Spatial_Transcriptomics,Class,Assay,Assay,RNA-Seq,,,
 Massively Parallel Reporter Assay,An assay in which multiplexing the construction and interrogation of larger libraries of reporter constructs allows measurement of the transcriptional regulatory activities of thousands to hundreds of thousands of DNA sequences.,,,FALSE,http://purl.obolibrary.org/obo/OBI_0002675,assay,,,,Massively_Parallel_Reporter_Assay,Class,Assay,Assay,Reporter_Gene_Assay,,,
 Riccardi and Ablon scales,"The Riccardi and Ablon scales score severity and visibility of disease, respectively, and are commonly used as a combined assessment for NF1 patients in clinical settings. See https://doi.org/10.1001/archderm.137.11.1421 for example usage.",,,FALSE,https://doi.org/10.1001/archderm.137.11.1421,assay,,,,Riccardi_Ablon_Scales,Class,Assay,Assay,Clinical_Assay,,,
 Spatial Frequency Domain Imaging,"Spatial Frequency Domain Imaging (SFDI) is a non-contact, depth-varying and wide-field optical imaging technique for measuring optical properties in a wide field-of-view on a pixel-by-pixel basis. Relevant applications include including burn assessment, skin tissue evaluation, tumor tissue detection, brain tissue monitoring.",,,FALSE,https://doi.org/10.3390/photonics8050162,assay,,,,Spatial_Frequency_Domain_Imaging,Class,Assay,Assay,Imaging_Assay,,,Note that term has no matches in OLS as of June 2022.
@@ -192,7 +193,7 @@ EnVision 2103 Multiplate Reader,EnVision 2103 Multiplate Reader,,,FALSE,,platfor
 Vectra H1 3D Imaging System,"(From vendor) Handheld imaging system for clinical-quality 3D imaging; applications for facial aesthetics and clinical documention.",,,FALSE,https://www.canfieldsci.com/imaging-systems/vectra-h1-3d-imaging-system/,platform,,,,Vectra_H1,Class,Assay,Platform,Platform,,,
 Vevo 3100 Imaging System,"(From vendor) A micro-ultrasound imaging system for anatomical, hemodynamic, functional, and molecular data all in one platform.",,,FALSE,https://www.visualsonics.com/product/imaging-systems/vevo-3100,platform,,,,Vectra_H1,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, 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",,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",,TRUE,,experimentalData,,,,assayType,Property,Assay,annotationProperty,,Assay,one,
 platform,"A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","HiSeq3000, HiSeq2500, HiSeq4000, NextSeq500, HiSeq2000, MiSeq, Zeiss LSM 980, Affy5.0, Affy6.0, PacBioRSII, GAIIx, Illumina_HumanOmni1-Quadv1.0, Illumina_1M, Illumina_h650, Illumina_Omni2pt5M, Illumina_Omni5M, Illumina MouseWG-6 v2.0 expression beadchip, Perlegen300Karray, Agilent44Karray, IlluminaWholeGenomeDASL, IlluminaHumanHap300, NanostringnCounter, LTQOrbitrapXL, IlluminaHumanMethylation450, Illumina Infinium MethylationEPIC BeadChip, AffymetrixU133AB, Affymetrix Human Gene 1.0 ST Array, AffymetrixU133Plus2, HiSeqX, Bionano Irys, Infinium HumanOmniExpressExome, NextSeq 550, NextSeq 1000, NextSeq 2000, PacBio Sequel IIe System, PacBio Sequel II System, NanostringGeoMx, 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",,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group&anchor=platform,experimentalData,,,,platform,Property,Assay,annotationProperty,,Platform,,
 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,,,,

diff --git a/NF.jsonld b/NF.jsonld
@@ -3456,6 +3456,23 @@
             "sms:required": "sms:false",
             "sms:validationRules": []
         },
+        {
+            "@id": "bts:Spatialtranscriptomics",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "assay that allows visualization and quantitative analysis of the transcriptome with spatial resolution in individual tissue sections",
+            "rdfs:label": "Spatialtranscriptomics",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Assay"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "spatial transcriptomics",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
         {
             "@id": "bts:MassivelyParallelReporterAssay",
             "@type": "rdfs:Class",
@@ -5509,6 +5526,9 @@
                 {
                     "@id": "bts:SingleCellRNASequencing"
                 },
+                {
+                    "@id": "bts:Spatialtranscriptomics"
+                },
                 {
                     "@id": "bts:ConventionalMRI"
                 },

diff --git a/modules/Assay/Assay.csv b/modules/Assay/Assay.csv
@@ -86,6 +86,7 @@ combinationScreen,,,,FALSE,,drugScreenType,,,,Combination_Screen,Class,Assay,Ass
 compoundScreen,,,,FALSE,,assay,,,,Compound_Screen,Class,Assay,Assay,Drug_Screen,,,
 array,,,,FALSE,,assay,,,,Array,Class,Assay,Assay,Assay,,,
 Single Cell RNA Sequencing,A procedure that can determine the nucleotide sequence for all of the RNA transcripts in an amplified nucleotide sample that was derived from a single cell.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C171152,assay,,,,ScRNA_Seq,Class,Assay,Assay,RNA-Seq,,,
+spatial transcriptomics,"assay that allows visualization and quantitative analysis of the transcriptome with spatial resolution in individual tissue sections",,,FALSE,http://www.ebi.ac.uk/efo/EFO_0008994,assay,,,,Spatial_Transcriptomics,Class,Assay,Assay,RNA-Seq,,,
 Massively Parallel Reporter Assay,An assay in which multiplexing the construction and interrogation of larger libraries of reporter constructs allows measurement of the transcriptional regulatory activities of thousands to hundreds of thousands of DNA sequences.,,,FALSE,http://purl.obolibrary.org/obo/OBI_0002675,assay,,,,Massively_Parallel_Reporter_Assay,Class,Assay,Assay,Reporter_Gene_Assay,,,
 Riccardi and Ablon scales,"The Riccardi and Ablon scales score severity and visibility of disease, respectively, and are commonly used as a combined assessment for NF1 patients in clinical settings. See https://doi.org/10.1001/archderm.137.11.1421 for example usage.",,,FALSE,https://doi.org/10.1001/archderm.137.11.1421,assay,,,,Riccardi_Ablon_Scales,Class,Assay,Assay,Clinical_Assay,,,
 Spatial Frequency Domain Imaging,"Spatial Frequency Domain Imaging (SFDI) is a non-contact, depth-varying and wide-field optical imaging technique for measuring optical properties in a wide field-of-view on a pixel-by-pixel basis. Relevant applications include including burn assessment, skin tissue evaluation, tumor tissue detection, brain tissue monitoring.",,,FALSE,https://doi.org/10.3390/photonics8050162,assay,,,,Spatial_Frequency_Domain_Imaging,Class,Assay,Assay,Imaging_Assay,,,Note that term has no matches in OLS as of June 2022.

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, 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",,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",,TRUE,,experimentalData,,,,assayType,Property,Assay,annotationProperty,,Assay,one,
 platform,"A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","HiSeq3000, HiSeq2500, HiSeq4000, NextSeq500, HiSeq2000, MiSeq, Zeiss LSM 980, Affy5.0, Affy6.0, PacBioRSII, GAIIx, Illumina_HumanOmni1-Quadv1.0, Illumina_1M, Illumina_h650, Illumina_Omni2pt5M, Illumina_Omni5M, Illumina MouseWG-6 v2.0 expression beadchip, Perlegen300Karray, Agilent44Karray, IlluminaWholeGenomeDASL, IlluminaHumanHap300, NanostringnCounter, LTQOrbitrapXL, IlluminaHumanMethylation450, Illumina Infinium MethylationEPIC BeadChip, AffymetrixU133AB, Affymetrix Human Gene 1.0 ST Array, AffymetrixU133Plus2, HiSeqX, Bionano Irys, Infinium HumanOmniExpressExome, NextSeq 550, NextSeq 1000, NextSeq 2000, PacBio Sequel IIe System, PacBio Sequel II System, NanostringGeoMx, 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",,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group&anchor=platform,experimentalData,,,,platform,Property,Assay,annotationProperty,,Platform,,
 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,,,,