Patch/assay mapping (#268)

* Add assays missed in last patch * Reference correct versions and additional mappings * Update registered JSON * Build jsonld * Resolve suggestion of quantitative PCR vs real-time PCR * Build jsonld --------- Co-authored-by: nf-osi[bot] <[email protected]>
nf-osi · Mar 21, 2023 · 343d4e1 · 343d4e1
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Showing 6 changed files with 170 additions and 45 deletions.
diff --git a/NF.csv b/NF.csv
@@ -10,7 +10,6 @@ immunofluorescence,An immunological procedure in which the antibodies are couple
 autoradiography,A radioactivity detection technique using X- ray film to visualize molecules or fragments of molecules that have been radioactively labeled.,,,FALSE,http://purl.obolibrary.org/obo/ERO_0000716,assay,,,,Autoradiography,Class,Assay,Assay,Radio_Assay,,,
 reporter gene assay,"Reporter gene assay measures the gene expression from a reporter gene. The reporter gene is inserted under the control of a foreign promoter or an artificial regulatory element of interest. Reporters include luciferase, beta galactosidase, beta lactamase, chloramphenicol acetyl transferase, or a fluorescent protein.",,,FALSE,http://purl.obolibrary.org/obo/OBI_0002082,assay,,,,Reporter_Gene_Assay,Class,Assay,Assay,RNA_Assay,,,
 electrochemiluminescence,"A method in which electromagnetic radiation, in the form of light emission, is generated from an electrochemical reaction in a solution.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C111193,assay,,,,Electrochemiluminescence,Class,Assay,Assay,RNA_Assay,,,
-real-time PCR,An application of PCR that measures the products generated during each cycle of the polymerase chain reaction process in order to determine the starting amount of template in the reaction.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C51962,assay,,,,Real_Time_PCR,Class,Assay,Assay,RNA_Assay,,,
 in vivo tumor growth,"The growth of a tumor measured using calipers, ruler, or another similar measurement device. See also """"in vivo bioluminescence"""".",,,FALSE,Sage Bionetworks,assay,,,,In_Vivo_Tumor_Growth,Class,Assay,Assay,Volume_Measurement_Assay,,,
 blood chemistry measurement,The determination of the measured concentrations of chemical constituents of the blood by assay in a clinical laboratory.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C47868,assay,,,,Blood_Chemistry_Measurement,Class,Assay,Assay,Clinical_Assay_Template,,,
 in vivo bioluminescence,An imaging assay that allows detection of bioluminescence from a living organism or organisms.,,,FALSE,http://purl.obolibrary.org/obo/ERO_0000651,assay,,,,In_Vivo_Bioluminescence,Class,Assay,Assay,Imaging_Assay,,,
@@ -120,6 +119,11 @@ novelty response behavior assay,"A behavioral assay devised to measure novelty r
 contextual conditioning behavior assay,"A behavioral assay devised to measure contextual conditioning behavior",,,FALSE,,assay,,,,Contextual_Conditioning_Behavior_Assay,Class,Assay,Assay,Behavioral_Assay,,,
 active avoidance learning behavior assay,"A behavioral assay devised to measure active avoidance learning behavior",,,FALSE,,assay,,,,Active_Avoidance_Learning Behavior_Assay,Class,Assay,Assay,Behavioral_Assay,,,
 focus forming assay,"The focus forming assay (FFA) is an immunostaining technique and a variation of the viral plaque assay. Instead of detecting the plaque formation after virus-induced cell lysis these assays detect infected host cells and infectious virus particles before a plaque is formed.",,,FALSE,,assay,,,,Focus_Forming_Assay,Class,Assay,Assay,Viral_Assay,,,See https://www.bpes.co.uk/focus-forming-assay-virus-titer-quantitation/
+blue native PAGE,"Blue native PAGE (BN-PAGE) permits a high-resolution separation of multi-protein complexes under native conditions. ",,,FALSE,http://purl.obolibrary.org/obo/MI_0276,assay,,,,Blue_Native_PAGE,Class,Assay,Assay,Proteomics_Assay,,,
+in vitro tumorigenesis,"An in vitro assay devised to measure tumor formation",,,FALSE,,assay,,,,In_Vitro_Tumorigenesis,Class,Assay,Assay,Tumorigenesis_Assay,,,
+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,,,
 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,"","","",""
@@ -230,7 +234,7 @@ LifeViz Infinity System,"(From vendor) All-in-one 3D imaging system for face, bo
 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,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,real-time PCR,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 assay",,TRUE,,experimentalData,,,,assayType,Property,Assay,annotationProperty,,Assay,one,
+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",,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,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,,
 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
@@ -2159,23 +2159,6 @@
             "sms:required": "sms:false",
             "sms:validationRules": []
         },
-        {
-            "@id": "bts:Real-timePCR",
-            "@type": "rdfs:Class",
-            "rdfs:comment": "An application of PCR that measures the products generated during each cycle of the polymerase chain reaction process in order to determine the starting amount of template in the reaction.",
-            "rdfs:label": "Real-timePCR",
-            "rdfs:subClassOf": [
-                {
-                    "@id": "bts:Assay"
-                }
-            ],
-            "schema:isPartOf": {
-                "@id": "http://schema.biothings.io"
-            },
-            "sms:displayName": "real-time PCR",
-            "sms:required": "sms:false",
-            "sms:validationRules": []
-        },
         {
             "@id": "bts:Invivotumorgrowth",
             "@type": "rdfs:Class",
@@ -4059,6 +4042,91 @@
             "sms:required": "sms:false",
             "sms:validationRules": []
         },
+        {
+            "@id": "bts:BluenativePAGE",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "Blue native PAGE (BN-PAGE) permits a high-resolution separation of multi-protein complexes under native conditions. ",
+            "rdfs:label": "BluenativePAGE",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Assay"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "blue native PAGE",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
+        {
+            "@id": "bts:Invitrotumorigenesis",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "An in vitro assay devised to measure tumor formation",
+            "rdfs:label": "Invitrotumorigenesis",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Assay"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "in vitro tumorigenesis",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
+        {
+            "@id": "bts:Matrigel-basedtumorigenesisassay",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "An assay in which tumor cells are loaded into a Matrigel matrix and measured for tumor formation characteristics",
+            "rdfs:label": "Matrigel-basedtumorigenesisassay",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Assay"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "Matrigel-based tumorigenesis assay",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
+        {
+            "@id": "bts:Calciumretentioncapacityassay",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "The CRC assay assesses Ca2+-related mitochondrial functions",
+            "rdfs:label": "Calciumretentioncapacityassay",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Assay"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "calcium retention capacity assay",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
+        {
+            "@id": "bts:QuantitativePCR",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "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.",
+            "rdfs:label": "QuantitativePCR",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Assay"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "quantitative PCR",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
         {
             "@id": "bts:Channel",
             "@type": "rdfs:Class",
@@ -6012,9 +6080,6 @@
                 {
                     "@id": "bts:Electrochemiluminescence"
                 },
-                {
-                    "@id": "bts:Real-timePCR"
-                },
                 {
                     "@id": "bts:Invivotumorgrowth"
                 },
@@ -6340,7 +6405,19 @@
                     "@id": "bts:Activeavoidancelearningbehaviorassay"
                 },
                 {
-                    "@id": "bts:Focusformingassay"
+                    "@id": "bts:FocusformingassaybluenativePAGE"
+                },
+                {
+                    "@id": "bts:Invitrotumorigenesis"
+                },
+                {
+                    "@id": "bts:Matrigel-basedtumorigenesisassay"
+                },
+                {
+                    "@id": "bts:Calciumretentioncapacityassay"
+                },
+                {
+                    "@id": "bts:QuantitativePCR"
                 }
             ],
             "sms:displayName": "assay",
@@ -21314,6 +21391,23 @@
             "sms:required": "sms:false",
             "sms:validationRules": []
         },
+        {
+            "@id": "bts:FocusformingassaybluenativePAGE",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "FocusformingassaybluenativePAGE",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Assay"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "focus forming assayblue native PAGE",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
         {
             "@id": "bts:Nuclei",
             "@type": "rdfs:Class",