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add add'l xenograft terms (#235)
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* add addenograft terms

* Build jsonld

Co-authored-by: nf-osi[bot] <[email protected]>
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@allaway @nfosi-service
allaway and nfosi-service authored Jan 13, 2023
1 parent 71cc853 commit 339ed67
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Showing 3 changed files with 33 additions and 6 deletions.
6 changes: 3 additions & 3 deletions NF.csv
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Expand Up @@ -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,,,
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27 changes: 27 additions & 0 deletions NF.jsonld
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Expand Up @@ -17887,6 +17887,15 @@
{
"@id": "bts:IsXenograft"
},
{
"@id": "bts:TransplantationType"
},
{
"@id": "bts:TransplantationRecipientSpecies"
},
{
"@id": "bts:TransplantationRecipientTissue"
},
{
"@id": "bts:RunType"
},
Expand Down Expand Up @@ -17945,6 +17954,15 @@
{
"@id": "bts:IsXenograft"
},
{
"@id": "bts:TransplantationType"
},
{
"@id": "bts:TransplantationRecipientSpecies"
},
{
"@id": "bts:TransplantationRecipientTissue"
},
{
"@id": "bts:ExperimentalCondition"
},
Expand Down Expand Up @@ -18183,6 +18201,15 @@
{
"@id": "bts:IsXenograft"
},
{
"@id": "bts:TransplantationType"
},
{
"@id": "bts:TransplantationRecipientSpecies"
},
{
"@id": "bts:TransplantationRecipientTissue"
},
{
"@id": "bts:RunType"
},
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6 changes: 3 additions & 3 deletions modules/Template/Template.csv
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@@ -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,,,
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