Merge pull request #83 from eliteportal/file-annotation-template-updates

ameliakallaher · web-flow · commit 4baa88315d6c · 2025-05-14T13:05:01.000-04:00
updates to file annotation template May 2025
diff --git a/EL.data.model.csv b/EL.data.model.csv
diff --git a/EL.data.model.jsonld b/EL.data.model.jsonld
diff --git a/modules/ADKP/isModelSystem.csv b/modules/ADKP/isModelSystem.csv
@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-isModelSystem,,"TRUE,FALSE",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,ADKP,False,BOOLEAN,Sage Bionetworks,,study_folder_template
+ModelSystemType,Type of model system,"animal, cerebral organoid, immortalized cell line, iPSC, organoid, primary cell culture, Not assigned",,,False,ManifestColumn,,ManifestColumn,Sage Bionetworks,ADKP,False,BOOLEAN,Sage Bionetworks,,study_folder_template
diff --git a/modules/ManifestColumn/analysisType.csv b/modules/ManifestColumn/analysisType.csv
@@ -0,0 +1,2 @@
+Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
+analysisType,"Type of analysis","ANOVA,batch effect correction,clustering,data normalization,de-novo assembly,dose response study,enrichment analysis,genome-wide association,mendelian randomization analysis,network analysis,polygenic risk scores, Not assigned",,,False,ManifestColumn,,ManifestColumn,Sage Bionetworks,ManifestColumn,True,STRING_LIST,Sage Bionetworks,,"study_folder_template, file_annotation_template"
diff --git a/modules/ManifestColumn/consortium.csv b/modules/ManifestColumn/consortium.csv
@@ -0,0 +1,2 @@
+Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
+consortium,The name of the consortium,"ELITE, ELITE CDCP, Not assigned",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,ManifestColumn,True,STRING_LIST,Sage Bionetworks,,"study_folder_template, file_annotation_template"
diff --git a/modules/ManifestColumn/dataSubtype.csv b/modules/ManifestColumn/dataSubtype.csv
@@ -0,0 +1,2 @@
+Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
+dataSubtype,"Further qualification of dataType, which may be used to indicate the state of processing of the data, aggregation of the data, or presence of metadata","raw,processed,results,normalized,metadata, Not assigned",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,ManifestColumn,True,STRING_LIST,Sage Bionetworks,,"study_folder_template, file_annotation_template"
diff --git a/modules/ManifestColumn/fileFormat.csv b/modules/ManifestColumn/fileFormat.csv
@@ -0,0 +1,2 @@
+Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
+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","FASTQ, FASTA, SAM, BAM, CRAM, VCF, BCF, GTF, GFF, GFF3, BED, BigBed, WIG, BigWig, CSV, TSV, MTX, H5AD, LOOM, RDS,PED, MAP, BED_PLINK, TPED, TFAM, BEDGRAPH, NARROWPEAK, BROADPEAK, TAGALIGN, OME-TIFF, ND2, CZI, LSM, H5, HDF5, PARQUET, PDB, MMCIF, JSON, YAML, XML, TXT, XLSX, CSV, Not assigned",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,ManifestColumn,True,STRING_LIST,Sage Bionetworks,,"study_folder_template, file_annotation_template"
diff --git a/modules/ManifestColumn/projectShortName.csv b/modules/ManifestColumn/projectShortName.csv
@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-projectShortName,,"LC,ILO,LLFS,LG",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,ManifestColumn,False,STRING,Sage Bionetworks,,study_folder_template
+projectShortName,,"LC,ILO,LLFS,LG, Not assigned",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,ManifestColumn,False,STRING,Sage Bionetworks,,study_folder_template
diff --git a/modules/ManifestColumn/resourceType.csv b/modules/ManifestColumn/resourceType.csv
@@ -0,0 +1,2 @@
+Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
+resourceType,The type of resource being stored and annotated,"experimentalData,metadata,tool,analysis,computationalNotebook, Not assigned",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,ManifestColumn,True,STRING_LIST,Sage Bionetworks,,"study_folder_template, file_annotation_template"
diff --git a/modules/ManifestColumn/studyKey.csv b/modules/ManifestColumn/studyKey.csv
@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-studyKey,,,,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,ManifestColumn,False,STRING,Sage Bionetworks,,study_folder_template
+studyKey,The short acronym for a study name in a URL-friendly format (ex. LLFS_Metabolomics OR ELPSCRNA),,,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,ManifestColumn,False,STRING,Sage Bionetworks,,study_folder_template
diff --git a/modules/Unknown/grantNumber.csv b/modules/Unknown/grantNumber.csv
@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-grantNumber,,,,,,,,,,Unknown,,,,,study_folder_template
+grantNumber,"Grant number including activity code institute code and serial number (e.g. U01MH103392)","U19AG063893,U24AG051129,U19AG023122,UH2AG064706,UH3AG064706,UH2AG064704,UH3AG064704,R01AG061844, Not assigned",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,Unknown,True,STRING_LIST,Sage Bionetworks,,study_folder_template
diff --git a/modules/Unknown/metadataType.csv b/modules/Unknown/metadataType.csv
@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-metadataType,,,,,,,,,,Unknown,,,,,study_folder_template
+metadataType,"For files of dataSubtype: metadata, a description of the type of metadata in the file","individual,biospecimen,assay,Not Assigned",,,False,ManifestColumn,,ManifestColumn,Sage Bionetworks,Unknown,True,STRING_LIST,Sage Bionetworks,,"study_folder_template, file_annotation_template"
diff --git a/modules/biospecimen/isMultiSpecimen.csv b/modules/biospecimen/isMultiSpecimen.csv
@@ -0,0 +1,2 @@
+Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
+isMultiSpecimen,Boolean flag indicating whether or not a file has data for multiple specimens,"true,fasle,Not assigned",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,individual,True,STRING_LIST,Sage Bionetworks,,"study_folder_template,Individual_Human,Individual_non_Human,Biospecimen_human, Biospecimen_non_Human,Phenotype_human,file_annotation_template"
diff --git a/modules/demographics/familyStudyParticipant.csv b/modules/demographics/familyStudyParticipant.csv
@@ -0,0 +1,2 @@
+Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
+familyStudyParticipant,Indicates whether or not a file has data from a human participant involved in a family study (ex. LLFS),"Yes, No, Not Assigned",,,False,ManifestColumn,,ManifestColumn,sage.annotations-demographics.ethnicityfamilyStudyParticipant-0.0.2,demographics,False,STRING,"Sage Bionetworks",,"Individual_Human,Phenotype_human,file_annotation_template"
diff --git a/modules/individual/species.csv b/modules/individual/species.csv
@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-species,The name of a species (typically a taxonomic group) of organism.,"Human,Mouse",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,individual,True,STRING_LIST,Sage Bionetworks,,study_folder_template
+species,The name of a species (typically a taxonomic group) of organism.,"Human,Non Human,Not assigned",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,individual,True,STRING_LIST,Sage Bionetworks,,study_folder_template
diff --git a/modules/template/templates.csv b/modules/template/templates.csv
@@ -1,6 +1,6 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-biospecimen_human_template,Template for Biospecimen_human,,"Filename,individualID,specimenID,specimenType,measurementTechnique,specimenAge,samplingAge,organ,tissue,tissueVolume,tissueWeight,specimenSource,nucleicAcidSource,cellType,fastingState,isPostMortem,Component",,False,Component,,template,Sage Bionetworks,template,,,Sage Bionetworks,,
-biospecimen_non_human_template,Template for Biospecimen_non_Human,,"Filename,individualID,specimenID,specimenType,assay,specimenAge,samplingAge,organ,tissue,tissueVolume,tissueWeight,specimenSource,nucleicAcidSource,cellType,fastingState,isPostMortem,Component",,False,Component,,template,Sage Bionetworks,template,,,Sage Bionetworks,,
+biospecimen_human_template,Template for Biospecimen_human,,"Filename,individualID,specimenID,isMultiSpecimen,specimenType,measurementTechnique,specimenAge,samplingAge,organ,tissue,tissueVolume,tissueWeight,specimenSource,nucleicAcidSource,cellType,fastingState,isPostMortem,Component",,False,Component,,template,Sage Bionetworks,template,,,Sage Bionetworks,,
+biospecimen_non_human_template,Template for Biospecimen_non_Human,,"Filename,individualID,specimenID,isMultiSpecimen,specimenType,assay,specimenAge,samplingAge,organ,tissue,tissueVolume,tissueWeight,specimenSource,nucleicAcidSource,cellType,fastingState,isPostMortem,Component",,False,Component,,template,Sage Bionetworks,template,,,Sage Bionetworks,,
 assay_bsSeq_template,Template for bsSeq,,"Filename,specimenID,sampleType,measurementTechnique,technologyPlatformVersion,platformLocation,referenceTranscriptID,dnaBatchID,dnaBatchSize,dnaBatchSizeUnit,libraryBatchID,libraryPrep,libraryPreparationMethod,libraryVersion,sequencingBatchID,sequencingBatchSize,sequencingBatchSizeUnit,isStranded,readStrandOrigin,readLength,readLengthUnits,runType,totalReads,directionalBSseqLibrary,gDNAconc,lambdaDNAconc,pcrCycles,meanCoverage,conversionRatio,conversionRatioUnits,enrichmentMethod,Component",,False,Component,,template,Sage Bionetworks,template,,,Sage Bionetworks,,
 genotyping_human_template,Template for Genotyping_Human,,"Filename,specimenID,stage,numberIndividuals,sampleType,useReagent,reagentIDs,reagentName,reagentManufacturer,reagentCatalogNumber,reagentLotNumber,reagentWeblink,reagentContact,useTreatment,treatmentIDs,treatmentName,treatmentAmountValue,treatmentAmountUnit,treatmentDurationValue,treatmentDurationUnit,treatmentTemperatureValue,treatmentTemperatureUnit,measurementTechnique,genotypeTechnology,arrayManufacturer,arrayInformation,imputation,imputationPanel,imputationSoftware,variantCount,statisticalModel,adjustedCovariates,reportedTrait,backgroundTrait,useReadMeFile,readmeFile,useSummaryFile,summaryFile,summaryStatisticsAssembly,Component",,False,Component,,template,Sage Bionetworks,template,,,Sage Bionetworks,,
 individual_human_template,Template for Individual_Human,,"Filename,individualID,cohort,studyCode,fieldCenterCode,visitCode,countryCode,consentGroupID,speciesGroup,sex,race,ethnicity,ethnicGroupCode,age,diagnosisStatus,diagnosis,hasMoCA,hasCASI,hasCDR,hasMMSE,hasADLs,Component",,False,Component,,template,Sage Bionetworks,template,,,Sage Bionetworks,,
@@ -14,4 +14,4 @@ assay_RNAseq_template,Template for RNAseq,,"Filename,specimenID,sampleType,measu
 assay_whole_genome_sequencing_template,Template for Whole_Genome_Sequencing,,"Filename,specimenID,sampleType,measurementTechnique,technologyPlatformVersion,platformLocation,referenceTranscriptID,repositoryName,transcriptType,resultUnit,valueReported,rnaBatchID,libraryBatchID,sequencingBatchID,libraryPrep,libraryPreparationMethod,libraryVersion,isStranded,readStrandOrigin,readLength,readLengthUnits,runType,totalReads,Component",,False,Component,,template,Sage Bionetworks,template,,,Sage Bionetworks,,
 assay_scRNAseq_template,Template for scRNAseq,,"Filename,specimenID,sampleType,measurementTechnique,technologyPlatformVersion,platformLocation,referenceTranscriptID,repositoryName,transcriptType,resultUnit,valueReported,rnaBatchID,rnaBatchSize,rnaBatchSizeUnit,libraryBatchID,sequencingBatchID,sequencingBatchSize,sequencingBatchSizeUnit,libraryPrep,libraryPreparationMethod,libraryVersion,isStranded,readStrandOrigin,readLength,readLengthUnits,runType,totalReads,Component",,False,Component,,template,Sage Bionetworks,template,,,Sage Bionetworks,,
 study_folder_template,Annotations for study folders,,"studyKey,studyName,projectShortName,projectFullName,dataTypeAll,species,specimenType,studyAbstract,studyDescription,studyFocus,program,grantNumber,studyWiki,acknowledgment,methods,relatedStudies,studyType,isModelSystem,isFeatured,ackContext,studyMetadata,accessReqs,isReleased,newsRelease,metadataType,Component",,False,Component,,template,Sage Bionetworks,template,,,Sage Bionetworks,,
-file_annotation_template,Base annotations for files in synapse,,"Filename, individualID, specimenID, isMultiSpecimen, assay, fileFormat, consortium, study, grant, resourceType, dataType, dataSubtype, metadataType, analysisType, isModelSystem, chromosome,Component",,False,Component,,template,Sage Bionetworks,template,,,Sage Bionetworks,,
+file_annotation_template,Base annotations for files in synapse,,"Filename, individualID, specimenID, isMultiSpecimen, species, familyStudyParticipant, assay, fileFormat, consortium, projectShortName, studyKey, grant, resourceType, dataTypeAll, dataSubtype, metadataType, analysisType, ModelSystemType, Component",,False,Component,,template,Sage Bionetworks,template,,,Sage Bionetworks,,

Original file line number	Diff line number	Diff line change
`@@ -1,2 +1,2 @@`
`1`	`1`	`Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn`
`2`		`-isModelSystem,,"TRUE,FALSE",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,ADKP,False,BOOLEAN,Sage Bionetworks,,study_folder_template`
	`2`	`+ModelSystemType,Type of model system,"animal, cerebral organoid, immortalized cell line, iPSC, organoid, primary cell culture, Not assigned",,,False,ManifestColumn,,ManifestColumn,Sage Bionetworks,ADKP,False,BOOLEAN,Sage Bionetworks,,study_folder_template`
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,2 @@`
	`1`	`+Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn`
	`2`	`+analysisType,"Type of analysis","ANOVA,batch effect correction,clustering,data normalization,de-novo assembly,dose response study,enrichment analysis,genome-wide association,mendelian randomization analysis,network analysis,polygenic risk scores, Not assigned",,,False,ManifestColumn,,ManifestColumn,Sage Bionetworks,ManifestColumn,True,STRING_LIST,Sage Bionetworks,,"study_folder_template, file_annotation_template"`
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`@@ -0,0 +1,2 @@`
	`1`	`+Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn`
	`2`	`+consortium,The name of the consortium,"ELITE, ELITE CDCP, Not assigned",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,ManifestColumn,True,STRING_LIST,Sage Bionetworks,,"study_folder_template, file_annotation_template"`
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`@@ -0,0 +1,2 @@`
	`1`	`+Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn`
	`2`	`+dataSubtype,"Further qualification of dataType, which may be used to indicate the state of processing of the data, aggregation of the data, or presence of metadata","raw,processed,results,normalized,metadata, Not assigned",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,ManifestColumn,True,STRING_LIST,Sage Bionetworks,,"study_folder_template, file_annotation_template"`
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`@@ -0,0 +1,2 @@`
	`1`	`+Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn`
	`2`	+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","FASTQ, FASTA, SAM, BAM, CRAM, VCF, BCF, GTF, GFF, GFF3, BED, BigBed, WIG, BigWig, CSV, TSV, MTX, H5AD, LOOM, RDS,PED, MAP, BED_PLINK, TPED, TFAM, BEDGRAPH, NARROWPEAK, BROADPEAK, TAGALIGN, OME-TIFF, ND2, CZI, LSM, H5, HDF5, PARQUET, PDB, MMCIF, JSON, YAML, XML, TXT, XLSX, CSV, Not assigned",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,ManifestColumn,True,STRING_LIST,Sage Bionetworks,,"study_folder_template, file_annotation_template"
Original file line number	Diff line number	Diff line change
`@@ -1,2 +1,2 @@`
`1`	`1`	`Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn`
`2`		`-projectShortName,,"LC,ILO,LLFS,LG",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,ManifestColumn,False,STRING,Sage Bionetworks,,study_folder_template`
	`2`	`+projectShortName,,"LC,ILO,LLFS,LG, Not assigned",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,ManifestColumn,False,STRING,Sage Bionetworks,,study_folder_template`
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`@@ -0,0 +1,2 @@`
	`1`	`+Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn`
	`2`	`+resourceType,The type of resource being stored and annotated,"experimentalData,metadata,tool,analysis,computationalNotebook, Not assigned",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,ManifestColumn,True,STRING_LIST,Sage Bionetworks,,"study_folder_template, file_annotation_template"`
Original file line number	Diff line number	Diff line change
`@@ -1,2 +1,2 @@`
`1`	`1`	`Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn`
`2`		`-studyKey,,,,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,ManifestColumn,False,STRING,Sage Bionetworks,,study_folder_template`
	`2`	`+studyKey,The short acronym for a study name in a URL-friendly format (ex. LLFS_Metabolomics OR ELPSCRNA),,,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,ManifestColumn,False,STRING,Sage Bionetworks,,study_folder_template`