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Terms for ticket NFOSI-191 (#153)
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* Add tom file format

* Add Riccardi and Ablon scales to assay

* Add changes

* Regenerate docs

Co-authored-by: nf-osi[bot] <[email protected]>
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@anngvu @nfosi-service
anngvu and nfosi-service authored May 31, 2022
1 parent baf9182 commit 13398e6
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Showing 28 changed files with 135 additions and 70 deletions.
6 changes: 4 additions & 2 deletions NF.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -87,6 +87,7 @@ 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,,,
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,,,
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,"","","",""
Expand Down Expand Up @@ -187,7 +188,7 @@ NanostringGeoMx,NanostringGeoMx,,,FALSE,,platform,,,,Nanostring_GeoMx,Class,Assa
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,,,
EnVision 2103 Multiplate Reader,EnVision 2103 Multiplate Reader,,,FALSE,,platform,,,,EnVision_2103,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",,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, 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",,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",,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,,,,
Expand Down Expand Up @@ -629,6 +630,7 @@ REC,This is yet another MRI image format generated by Philips scanners. It is an
hdr,"MRI Header file, as in the NIFTI-1 Analyze 7.5 format","","",FALSE,https://nifti.nimh.nih.gov/pub/dist/src/niftilib/nifti1.h,fileFormat,,"","",hdr,Class,Data,File_Format,"","","",""
img,"MRI Data file, as in the NIFTI-1 Analyze 7.5 format","","",FALSE,https://nifti.nimh.nih.gov/pub/dist/src/niftilib/nifti1.h,fileFormat,,"","",img,Class,Data,File_Format,"","","",""
sf,"Salmon’s main output is its quantification file. This file is a plain-text, tab-separated file with a single header line (which names all of the columns).","","",FALSE,https://salmon.readthedocs.io/en/latest/file_formats.html,fileFormat,,"","",sf,Class,Data,File_Format,"","","",""
tom,"The .tom format is a specialized 3D image export format from the Vectra medical imaging systems that can optionally preserve trimmings and/or landmarks.","","",FALSE,http://canfieldupgrade.com/assets/media/VECTRA-M3-User-Guide.pdf,fileFormat,,"","",tom,Class,Data,File_Format,"","","",""
gene symbol,A unique gene name approved by an organism specific nomenclature committee.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C43568,curatedDataType,,,,Gene_Symbol,Class,Data,Metadata,,,,
clinical data,Data obtained through patient examination or treatment.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C15783,curatedDataType,,,,Clinical_Curated_Data,Class,Data,Metadata,,,,
gene function,A term that expresses the function of a gene product.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C48933,curatedDataType,,,,Gene_Function,Class,Data,Metadata,,,,
Expand Down Expand Up @@ -661,7 +663,7 @@ programmingLanguage,A computer programming language,"Python, R, MATLAB, Java, C,
runtimePlatform,"Runtime platform or script interpreter dependencies (e.g. Java v1, Python 2.3).",,,FALSE,Sage Bionetworks,,,,,runtimePlatform,Property,Data,annotationProperty,ngsParameter,,,
documentation,URL to any documentation describing the resource and its use.,,,FALSE,Sage Bionetworks,,,,,documentation,Property,Data,annotationProperty,ngsParameter,,,
resourceType,The type of resource being stored and annotated,"experimentalData, curatedData, result, tool, report, metadata, protocol",,TRUE,,sageCommunity,,,,resourceType,Property,Data,annotationProperty,,Resource,,
fileFormat,"Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software","bash script,bedgraph,ai,idx,idat,bam,bai,excel,powerpoint,tif,png,doc,pdf,hdf,fasta,fastq,sam,vcf,bcf,maf,bed,chp,cel,sif,tsv,csv,txt,plink,bigwig,wiggle,gct,bgzip,zip,seg,html,mov,hyperlink,svs,md,flagstat,gtf,raw,msf,rmd,bed narrowPeak,bed broadPeak,bed gappedPeak,avi,pzfx,fig,xml,tar,R script,abf,bpm,dat,jpg,locs,Sentrix descriptor file,Python script,sav,gzip,sdf,RData,hic,ab1,7z,gff3,json,sqlite,svg,sra,recal,tranches,mtx,tagAlign,dup,DICOM,czi,mzML,SPAR,SDAT,nii,PAR,REC,hdr,img,sf,MATLAB script, MATLAB data",,TRUE,,sageCommunity,,,,fileFormat,Property,Data,annotationProperty,,File_Format,one,
fileFormat,"Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software","bash script,bedgraph,ai,idx,idat,bam,bai,excel,powerpoint,tif,png,doc,pdf,hdf,fasta,fastq,sam,vcf,bcf,maf,bed,chp,cel,sif,tsv,csv,txt,plink,bigwig,wiggle,gct,bgzip,zip,seg,html,mov,hyperlink,svs,md,flagstat,gtf,raw,msf,rmd,bed narrowPeak,bed broadPeak,bed gappedPeak,avi,pzfx,fig,xml,tar,R script,abf,bpm,dat,jpg,locs,Sentrix descriptor file,Python script,sav,gzip,sdf,RData,hic,ab1,7z,gff3,json,sqlite,svg,sra,recal,tranches,mtx,tagAlign,dup,DICOM,czi,mzML,SPAR,SDAT,nii,PAR,REC,hdr,img,sf,MATLAB script, MATLAB data,tom",,TRUE,,sageCommunity,,,,fileFormat,Property,Data,annotationProperty,,File_Format,one,
progressReportNumber,"Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",,FALSE,,template,,,,progressReportNumber,DataProperty,Data,annotationProperty,,,one,
comments,Brief free-text comments that may also be important to understanding the resource.,,,FALSE,Sage Bionetworks,experimentalData,,,,comments,DataProperty,Data,annotationProperty,,,many,
Resource_id,A UUID for a Resource from the NF Research Tools Database,,,FALSE,Sage Bionetworks,dccProperty,,,,Resource_id,Property,Data,annotationProperty,dccProperty,,,
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40 changes: 40 additions & 0 deletions NF.jsonld
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Expand Up @@ -3473,6 +3473,23 @@
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:RiccardiandAblonscales",
"@type": "rdfs:Class",
"rdfs:comment": "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.",
"rdfs:label": "RiccardiandAblonscales",
"rdfs:subClassOf": [
{
"@id": "bts:Assay"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Riccardi and Ablon scales",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:Channel",
"@type": "rdfs:Class",
Expand Down Expand Up @@ -5465,6 +5482,9 @@
},
{
"@id": "bts:MassivelyParallelReporterAssay"
},
{
"@id": "bts:RiccardiandAblonscales"
}
],
"sms:displayName": "assay",
Expand Down Expand Up @@ -14405,6 +14425,23 @@
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:Tom",
"@type": "rdfs:Class",
"rdfs:comment": "The .tom format is a specialized 3D image export format from the Vectra medical imaging systems that can optionally preserve trimmings and/or landmarks.",
"rdfs:label": "Tom",
"rdfs:subClassOf": [
{
"@id": "bts:FileFormat"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "tom",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:Genesymbol",
"@type": "rdfs:Class",
Expand Down Expand Up @@ -15444,6 +15481,9 @@
},
{
"@id": "bts:MATLABdata"
},
{
"@id": "bts:Tom"
}
],
"sms:displayName": "fileFormat",
Expand Down
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