Update assay module and document (#165)

* Add platform related to issue #164 * Fix assay ID for doc-gen * Add changes * Regen docs for new spatial assays/platforms Co-authored-by: nf-osi[bot] <[email protected]>
nf-osi · Jun 7, 2022 · ef2c06c · ef2c06c
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Showing 6 changed files with 94 additions and 68 deletions.
diff --git a/NF.csv b/NF.csv
@@ -90,7 +90,7 @@ spatial transcriptomics,"assay that allows visualization and quantitative analys
 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.
-Optical Coherence Tomography,"Optical Coherence Tomography (OCT) combines the principles of ultrasound with the imaging performance of a microscope. OCT uses infrared light waves that reflect off the internal microstructure within the biological tissues. The frequencies and bandwidths of infrared light are orders of magnitude higher than medical ultrasound signals, resulting in greatly increased image resolution, 8-25 times greater than any existing modality. In addition to providing high-level resolutions for the evaluation of microanatomic structures OCT is also able to provide information regarding tissue composition",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C20828,assay,,,,Array,Class,Assay,Assay,Imaging_Assay,,,
+Optical Coherence Tomography,"Optical Coherence Tomography (OCT) combines the principles of ultrasound with the imaging performance of a microscope. OCT uses infrared light waves that reflect off the internal microstructure within the biological tissues. The frequencies and bandwidths of infrared light are orders of magnitude higher than medical ultrasound signals, resulting in greatly increased image resolution, 8-25 times greater than any existing modality. In addition to providing high-level resolutions for the evaluation of microanatomic structures OCT is also able to provide information regarding tissue composition",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C20828,assay,,,,Optical_Coherence_Tomography,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,"","","",""
@@ -189,12 +189,13 @@ PacBio Sequel IIe System,PacBio Sequel IIe System,,,FALSE,,platform,,,,PacBio_Se
 PacBio Sequel II System,PacBio Sequel II System,,,FALSE,,platform,,,,PacBio_Sequel_II_System,Class,Assay,Platform,Platform,,,
 NanostringGeoMx,NanostringGeoMx,,,FALSE,,platform,,,,Nanostring_GeoMx,Class,Assay,Platform,Platform,,,
 Chromium X,"(From 10x Genomics) Single-cell platform that can analyze hundreds to hundreds of thousands of cells in single run for e.g. gene expression, chromatin accessibility, cell surface proteins, immune clonotype, antigen specificity, CRISPR perturbation screens).",,,FALSE,https://www.10xgenomics.com/chromium-x,platform,,,,Chromium_X,Class,Assay,Platform,Platform,,,
+10x Visium Spatial Gene Expression,"10x Genomics product that includes special slides, reagents and technology to allow whole transcriptome profiling with morphological (spatial) context in FFPE or fresh-frozen tissues. Vendor ref: https://www.10xgenomics.com/products/spatial-gene-expression",,,FALSE,http://www.ebi.ac.uk/efo/EFO_0010961,platform,,,,10x_Visium_Spatial_Gene_Expression,Class,Assay,Platform,Platform,,,
 EnVision 2103 Multiplate Reader,EnVision 2103 Multiplate Reader,,,FALSE,,platform,,,,EnVision_2103,Class,Assay,Platform,Platform,,,
 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, 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,,
+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,10x Visium Spatial Gene Expression",,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,,,,
 proteinExtractSource,Source of the extracted protein used in the experiment,"cell lysate, nuclei, mitochondria, cytoplasm",,TRUE,http://purl.obolibrary.org/obo/OBI_0000894,experimentalData,,,,proteinExtractSource,Property,Assay,annotationProperty,,,,

diff --git a/NF.jsonld b/NF.jsonld
@@ -5229,6 +5229,23 @@
             "sms:required": "sms:false",
             "sms:validationRules": []
         },
+        {
+            "@id": "bts:10xVisiumSpatialGeneExpression",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "10x Genomics product that includes special slides, reagents and technology to allow whole transcriptome profiling with morphological (spatial) context in FFPE or fresh-frozen tissues. Vendor ref: https://www.10xgenomics.com/products/spatial-gene-expression",
+            "rdfs:label": "10xVisiumSpatialGeneExpression",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Platform"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "10x Visium Spatial Gene Expression",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
         {
             "@id": "bts:EnVision2103MultiplateReader",
             "@type": "rdfs:Class",
@@ -5736,6 +5753,9 @@
                 },
                 {
                     "@id": "bts:Vevo3100ImagingSystem"
+                },
+                {
+                    "@id": "bts:10xVisiumSpatialGeneExpression"
                 }
             ],
             "sms:displayName": "platform",