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Merge pull request #79 from anngvu/feature-pdx-supp
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Add organoid and spheroid to tissue, cellType to PDX template
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@allaway
allaway authored Nov 2, 2021
2 parents 42b5a95 + d879d93 commit 71c2bf6
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6 changes: 4 additions & 2 deletions NF.csv
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Expand Up @@ -182,7 +182,7 @@ bodyPart,"Sample location referring to a named area of the body, inclusive of gr
organ,A unique macroscopic (gross) anatomic structure that performs specific functions. It is composed of various tissues. An organ is part of an anatomic system or a body region.,"lymph node, kidney, skin, mammary gland, nerves, brain, blood, breast, colon, lung, liver, prostate, pancreas, ovary, spleen, bone marrow, Bursa Of Fabricius, nose",,FALSE,,experimentalData,,,
dataType,"A type of experimental, clinical, or other data. This typically refers to a high-level data type, that is paired with a specific assay. For example, a file of dataType of ""genomicVariants"" might have an assay value of ""whole genome sequencing"". ","Volume, Weight, Pharmacokinetic Study, genomicVariants, behavior process, metabolomics, image, geneExpression, isoformExpression, proteomics, kinomics, drugScreen, drugCombinationScreen, cellularPhysiology, chromatinActivity, surveyData, network, clinical, immunoassay, electrophysiology, raw counts, mask image",,FALSE,,experimentalData,,,
individualIdSource,Database or repository to which individual ID maps,,,FALSE,,experimentalData,,,
tissue,A tissue is a mereologically maximal collection of cells that together perform physiological function.,"nerve tissue,optic nerve,serum,plasma,splenocyte,blood,primary tumor,embryonic tissue,meninges,bone marrow,Buccal Mucosa,Dorsal Root Ganglion,unspecified,whole brain,Buffy Coat,cerebral cortex,sciatic nerve,connective tissue,tumor-adjacent normal, PDX tissue, CDX tissue, metastatic/recurrent tumor, recurrent tumor, metastatic tumor",,FALSE,,experimentalData,,,
tissue,A tissue is a mereologically maximal collection of cells that together perform physiological function.,"nerve tissue,optic nerve,serum,plasma,splenocyte,blood,primary tumor,embryonic tissue,meninges,bone marrow,Buccal Mucosa,Dorsal Root Ganglion,unspecified,whole brain,Buffy Coat,cerebral cortex,sciatic nerve,connective tissue,tumor-adjacent normal, PDX tissue, CDX tissue, metastatic/recurrent tumor, recurrent tumor, metastatic tumor, organoid, spheroid",,FALSE,,experimentalData,,,
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",,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group&anchor=platform,experimentalData,,,
isCellLine,Boolean flag indicating whether or not sample source is a cell line. (Note: TRUE = Yes; FALSE = No),"TRUE, FALSE",,FALSE,,experimentalData,,,
isPrimaryCell,Boolean flag indicating whether or not cellType is primary (Note: TRUE = Yes; FALSE = No),"TRUE, FALSE",,FALSE,,experimentalData,,,
Expand Down Expand Up @@ -579,7 +579,7 @@ array,,,,FALSE,,,,,
sageCommunity,,,,FALSE,,,,,
ngs,next gen sequencing/genomics attributes.,"runType,readPair,isStranded,readPairOrientation,readStrandOrigin,libraryPrep,libraryPreparationMethod,libraryPreparationMethod,dissociationMethod,readLength,nucleicAcidSource",,FALSE,,,,,
progressReportNumber,"Indicates which milestone you're annotating data files for. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ""progress report"" timeline. An example: if submitting data for your 6-month milestone report for NTAP, progressReportNumber=1. Also if you are submitting data associated with your first milestone, progressReportNumber =1","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",,FALSE,,template,,,
pdxGenomicsAssay,Extends genomicsAssay for PDX experiments,,"Filename,progressReportNumber,fileFormat,resourceType,dataType,dataSubtype,assay,individualID,sex,species,transplantationRecipientSpecies,transplantationRecipientTissue,transplantationType,modelSystemName,genePerturbationType,genePerturbationTechnology,genePerturbed,diagnosis,specimenID,bodyPart,tissue,nf1Genotype,nf2Genotype,isCellLine,tumorType,specimenPreparationMethod,experimentalCondition,experimentalTimepoint,timePointUnit,platform,runType,readPair,isStranded,readPairOrientation,readStrandOrigin,libraryPrep,libraryPreparationMethod,dissociationMethod,nucleicAcidSource,readLength,readDepth,comments",FALSE,,template,,,
pdxGenomicsAssay,Extends genomicsAssay for PDX experiments,,"Filename,progressReportNumber,fileFormat,resourceType,dataType,dataSubtype,assay,individualID,sex,species,transplantationRecipientSpecies,transplantationRecipientTissue,transplantationType,modelSystemName,genePerturbationType,genePerturbationTechnology,genePerturbed,diagnosis,specimenID,bodyPart,tissue,cellType,nf1Genotype,nf2Genotype,isCellLine,tumorType,specimenPreparationMethod,experimentalCondition,experimentalTimepoint,timePointUnit,platform,runType,readPair,isStranded,readPairOrientation,readStrandOrigin,libraryPrep,libraryPreparationMethod,dissociationMethod,nucleicAcidSource,readLength,readDepth,comments",FALSE,,template,,,
specimenPreparationMethod,Term that represents the method used to preserve the sample before preparing the sample for sequencing,"Fresh collected, Flash frozen, FFPE, Cryopreserved, OCT, RNAlater, formalin-fixed, ethanol, Viably frozen",,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=sample&anchor=preservation_method,ngs,,,
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,,,
updateMilestoneReport,Defines a metadata template for updating milestone report values in NF studies -- currently a supported feature for NTAP and GFF.,,"Filename,progressReportNumber",TRUE,,template,,,
Expand Down Expand Up @@ -620,3 +620,5 @@ tumor,"General term for tumor sample – use when it is unknown when a more spec
metastatic tumor,"For neoplasms, a non-infiltrating and non-metastasizing neoplastic process that is characterized by the absence of morphologic features associated with malignancy (e.g., severe atypia, nuclear pleomorphism, tumor cell necrosis, and abnormal mitoses).",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C14172,tissue,,,
metastatic/recurrent tumor,A tumor with metastatic/recurrent characteristic.,,,FALSE,,tissue,,,
recurrent tumor,A tumor described with recurrent characteristic.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C4798,tissue,,,
organoid,Organoids are three-dimensional cell culture models that self-organize into complex organ-like tissues.,,,FALSE,https://www.nature.com/articles/s41378-020-00185-3 ,tissue,,,
spheroid,"Spheroids are 3D culture systems that can be used to model multicellular tumors; more broadly, spheroids can be defined as cell aggregates cultured on nonadherent substrates. ",,,FALSE,https://www.nature.com/articles/s41378-020-00185-3 ,tissue,,,
43 changes: 43 additions & 0 deletions NF.jsonld
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Expand Up @@ -5976,6 +5976,12 @@
},
{
"@id": "bts:Metastatictumor"
},
{
"@id": "bts:Organoid"
},
{
"@id": "bts:Spheroid"
}
],
"sms:displayName": "tissue",
Expand Down Expand Up @@ -14617,6 +14623,9 @@
{
"@id": "bts:Tissue"
},
{
"@id": "bts:CellType"
},
{
"@id": "bts:Nf1Genotype"
},
Expand Down Expand Up @@ -15400,6 +15409,40 @@
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:Organoid",
"@type": "rdfs:Class",
"rdfs:comment": "Organoids are three-dimensional cell culture models that self-organize into complex organ-like tissues.",
"rdfs:label": "Organoid",
"rdfs:subClassOf": [
{
"@id": "bts:Tissue"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "organoid",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:Spheroid",
"@type": "rdfs:Class",
"rdfs:comment": "Spheroids are 3D culture systems that can be used to model multicellular tumors; more broadly, spheroids can be defined as cell aggregates cultured on nonadherent substrates. ",
"rdfs:label": "Spheroid",
"rdfs:subClassOf": [
{
"@id": "bts:Tissue"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "spheroid",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:TRUE",
"@type": "rdfs:Class",
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