From 339ed67fb80b65c09161e61b07308afdc02c0a79 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Fri, 13 Jan 2023 10:12:22 -0800 Subject: [PATCH] add add'l xenograft terms (#235) * add addenograft terms * Build jsonld Co-authored-by: nf-osi[bot] --- NF.csv | 6 +++--- NF.jsonld | 27 +++++++++++++++++++++++++++ modules/Template/Template.csv | 6 +++--- 3 files changed, 33 insertions(+), 6 deletions(-) diff --git a/NF.csv b/NF.csv index e94dc145..c06787c1 100644 --- a/NF.csv +++ b/NF.csv @@ -776,12 +776,12 @@ concentrationNaCl,"Numeric value for NaCl concentration","",,FALSE,,parameter,,, concentrationNaClUnit,"Unit used for the NaCl concentration, e.g. mM","mg/mL,mM",,FALSE,,parameter,,,,concentrationNaClUnit,Property,Sample,annotationProperty,,,, Component,"Category of metadata manifest; provide the same one for all items/rows.",,,TRUE,https://w3id.org/biolink/vocab/category,,,,,,,,,,,, genomicsAssayTemplateNormalized,"Generic template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) WITHOUT full individual and biospecimen data. To link individual and biospecimen metadata, an additional “biospecimenTemplate_Default” must be additionally completed with either specimenID or aliquotID available for joining. This is a two-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,specimenID,aliquotID,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template_Normalized,Class,Template,Template,Assay_Template,,, -genomicsAssayTemplate,"Generic denormalized template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) along with individual, biospecimen and experimental metadata. This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,isXenograft,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template,Class,Template,Template,Assay_Template,,, -genomicsAssayTemplateExtended,"Template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) with extended properties for capturing additional metadata such as gene perturbation parameters or experimental conditions and time points. This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,isXenograft,experimentalCondition,experimentalTimepoint,runType,libraryPrep,genePerturbed,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template_Extended,Class,Template,Template,Assay_Template,,, +genomicsAssayTemplate,"Generic denormalized template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) along with individual, biospecimen and experimental metadata. This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,isXenograft,transplantationType,transplantationRecipientSpecies,transplantationRecipientTissue,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template,Class,Template,Template,Assay_Template,,, +genomicsAssayTemplateExtended,"Template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) with extended properties for capturing additional metadata such as gene perturbation parameters or experimental conditions and time points. This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,isXenograft,transplantationType,transplantationRecipientSpecies,transplantationRecipientTissue,experimentalCondition,experimentalTimepoint,runType,libraryPrep,genePerturbed,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template_Extended,Class,Template,Template,Assay_Template,,, WGSTemplate,"Template for describing raw data from Whole Genome Sequencing (WGS)",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,WGS_Template,Class,Template,Template,Assay_Template,,, WESTemplate,"Template for describing raw data from Whole Exome Sequencing (WES)",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,runType,targetCaptureKitID,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,WES_Template,Class,Template,Template,Assay_Template,,, RNASeqTemplate,"Template for describing raw data from (bulk) RNA-sequencing",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,runType,libraryPrep,targetDepth,comments",TRUE,Sage Bionetworks,template,,,,RNA_Seq_Template,Class,Template,Template,Assay_Template,,, -ScRNASeqTemplate,"Template for describing raw data from single-cell RNA-sequencing (scRNA-seq)",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,isXenograft,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,ScRNA_Seq_Template,Class,Template,Template,Assay_Template,,, +ScRNASeqTemplate,"Template for describing raw data from single-cell RNA-sequencing (scRNA-seq)",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,isXenograft,transplantationType,transplantationRecipientSpecies,transplantationRecipientTissue,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,ScRNA_Seq_Template,Class,Template,Template,Assay_Template,,, ProcessedAlignedReadsTemplate,"Template for describing aligned reads output data (i.e. BAM)",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,averageInsertSize,averageReadLength,averageBaseQuality,pairsOnDifferentChr,readsDuplicatedPercent,readsMappedPercent,meanCoverage,proportionCoverage10x,proportionCoverage30x,readDepth,totalReads,workflow,genomicReference,comments",TRUE,Sage Bionetworks,template,,,,Processed_Aligned_Reads_Template,Class,Template,Template,Assay_Template,,, ProcessedVariantCallsTemplate,"Template for describing either germline or variant calls output data (i.e. VCF/MAF)",,"Component,Filename,resourceType,progressReportNumber,specimenID,dataType,assay,individualID,isFilteredReads,workflow,comments",TRUE,Sage Bionetworks,template,,,,Processed_Variant_Calls_Template,Class,Template,Template,Assay_Template,,, ProcessedExpressionTemplate,"Template for describing expression output data",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,individualID,specimenID,parentSpecimenID,modelSystemName,workflow,expressionUnit,comments",TRUE,Sage Bionetworks,template,,,,Processed_Expression_Template,Class,Template,Template,Assay_Template,,, diff --git a/NF.jsonld b/NF.jsonld index 5609289f..fdc3ad9d 100644 --- a/NF.jsonld +++ b/NF.jsonld @@ -17887,6 +17887,15 @@ { "@id": "bts:IsXenograft" }, + { + "@id": "bts:TransplantationType" + }, + { + "@id": "bts:TransplantationRecipientSpecies" + }, + { + "@id": "bts:TransplantationRecipientTissue" + }, { "@id": "bts:RunType" }, @@ -17945,6 +17954,15 @@ { "@id": "bts:IsXenograft" }, + { + "@id": "bts:TransplantationType" + }, + { + "@id": "bts:TransplantationRecipientSpecies" + }, + { + "@id": "bts:TransplantationRecipientTissue" + }, { "@id": "bts:ExperimentalCondition" }, @@ -18183,6 +18201,15 @@ { "@id": "bts:IsXenograft" }, + { + "@id": "bts:TransplantationType" + }, + { + "@id": "bts:TransplantationRecipientSpecies" + }, + { + "@id": "bts:TransplantationRecipientTissue" + }, { "@id": "bts:RunType" }, diff --git a/modules/Template/Template.csv b/modules/Template/Template.csv index 41d8d022..7264ea50 100644 --- a/modules/Template/Template.csv +++ b/modules/Template/Template.csv @@ -1,11 +1,11 @@ Attribute,Description,Valid Values,DependsOn,Required,Source,Parent,Properties,DependsOn Component,Validation Rules,.ID,.Type,.Module,.Root,.SubOf,.Range,.Cardinality,.EditorNote genomicsAssayTemplateNormalized,"Generic template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) WITHOUT full individual and biospecimen data. To link individual and biospecimen metadata, an additional “biospecimenTemplate_Default” must be additionally completed with either specimenID or aliquotID available for joining. This is a two-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,specimenID,aliquotID,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template_Normalized,Class,Template,Template,Assay_Template,,, -genomicsAssayTemplate,"Generic denormalized template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) along with individual, biospecimen and experimental metadata. This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,isXenograft,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template,Class,Template,Template,Assay_Template,,, -genomicsAssayTemplateExtended,"Template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) with extended properties for capturing additional metadata such as gene perturbation parameters or experimental conditions and time points. This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,isXenograft,experimentalCondition,experimentalTimepoint,runType,libraryPrep,genePerturbed,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template_Extended,Class,Template,Template,Assay_Template,,, +genomicsAssayTemplate,"Generic denormalized template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) along with individual, biospecimen and experimental metadata. This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,isXenograft,transplantationType,transplantationRecipientSpecies,transplantationRecipientTissue,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template,Class,Template,Template,Assay_Template,,, +genomicsAssayTemplateExtended,"Template for describing raw data from a genomic type assay (RNA-seq, Exome-seq, etc) with extended properties for capturing additional metadata such as gene perturbation parameters or experimental conditions and time points. This is a one-step template.",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,isXenograft,transplantationType,transplantationRecipientSpecies,transplantationRecipientTissue,experimentalCondition,experimentalTimepoint,runType,libraryPrep,genePerturbed,comments",TRUE,Sage Bionetworks,template,,,,Genomics_Assay_Template_Extended,Class,Template,Template,Assay_Template,,, WGSTemplate,"Template for describing raw data from Whole Genome Sequencing (WGS)",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,WGS_Template,Class,Template,Template,Assay_Template,,, WESTemplate,"Template for describing raw data from Whole Exome Sequencing (WES)",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,runType,targetCaptureKitID,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,WES_Template,Class,Template,Template,Assay_Template,,, RNASeqTemplate,"Template for describing raw data from (bulk) RNA-sequencing",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,runType,libraryPrep,targetDepth,comments",TRUE,Sage Bionetworks,template,,,,RNA_Seq_Template,Class,Template,Template,Assay_Template,,, -ScRNASeqTemplate,"Template for describing raw data from single-cell RNA-sequencing (scRNA-seq)",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,isXenograft,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,ScRNA_Seq_Template,Class,Template,Template,Assay_Template,,, +ScRNASeqTemplate,"Template for describing raw data from single-cell RNA-sequencing (scRNA-seq)",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,isXenograft,transplantationType,transplantationRecipientSpecies,transplantationRecipientTissue,runType,libraryPrep,comments",TRUE,Sage Bionetworks,template,,,,ScRNA_Seq_Template,Class,Template,Template,Assay_Template,,, ProcessedAlignedReadsTemplate,"Template for describing aligned reads output data (i.e. BAM)",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,platform,individualID,parentSpecimenID,averageInsertSize,averageReadLength,averageBaseQuality,pairsOnDifferentChr,readsDuplicatedPercent,readsMappedPercent,meanCoverage,proportionCoverage10x,proportionCoverage30x,readDepth,totalReads,workflow,genomicReference,comments",TRUE,Sage Bionetworks,template,,,,Processed_Aligned_Reads_Template,Class,Template,Template,Assay_Template,,, ProcessedVariantCallsTemplate,"Template for describing either germline or variant calls output data (i.e. VCF/MAF)",,"Component,Filename,resourceType,progressReportNumber,specimenID,dataType,assay,individualID,isFilteredReads,workflow,comments",TRUE,Sage Bionetworks,template,,,,Processed_Variant_Calls_Template,Class,Template,Template,Assay_Template,,, ProcessedExpressionTemplate,"Template for describing expression output data",,"Component,Filename,resourceType,progressReportNumber,dataType,assay,individualID,specimenID,parentSpecimenID,modelSystemName,workflow,expressionUnit,comments",TRUE,Sage Bionetworks,template,,,,Processed_Expression_Template,Class,Template,Template,Assay_Template,,,