Curator_updates

modules/ManifestColumn/analysisType.csv

@@ -1,2 +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"
+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,Sage Bionetworks,,"study_folder_template, file_annotation_template"

modules/ManifestColumn/consortium.csv

@@ -1,2 +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"
+consortium,The name of the consortium,"ELITE, ELITE CDCP, Not assigned",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,ManifestColumn,True,STRING,Sage Bionetworks,,"study_folder_template, file_annotation_template"

modules/ManifestColumn/dataModelVersion.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-dataModelVersion,Version of the data model,,,,False,,,ManifestColumn,,ManifestColumn,,,,,
+dataModelVersion,Version of the data model,,,,False,,,ManifestColumn,,ManifestColumn,,STRING,,,

modules/ManifestColumn/dataSubtype.csv

@@ -1,2 +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"
+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,Sage Bionetworks,,"study_folder_template, file_annotation_template"

modules/ManifestColumn/dataTypeAll.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-dataTypeAll,,"clinical,drugScreen,electrophysiology,epigenetics,geneExpression,genomeAssembly,genomicVariants,imaging,lipidomics,metabolomics,metagenomics,Not applicable,Not collected,Not specified,Other,phenotype,proteomics,Unknown,wearableData",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,ManifestColumn,True,STRING_LIST,Sage Bionetworks,,study_folder_template
+dataTypeAll,,"clinical,drugScreen,electrophysiology,epigenetics,geneExpression,genomeAssembly,genomicVariants,imaging,lipidomics,metabolomics,metagenomics,Not applicable,Not collected,Not specified,Other,phenotype,proteomics,Unknown,wearableData",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,ManifestColumn,True,STRING,Sage Bionetworks,,study_folder_template

modules/ManifestColumn/fileFormat.csv

@@ -1,2 +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"
+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,Sage Bionetworks,,"study_folder_template, file_annotation_template"

modules/ManifestColumn/resourceType.csv

@@ -1,2 +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"
+resourceType,The type of resource being stored and annotated,"experimentalData,metadata,tool,analysis,computationalNotebook, Not assigned",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,ManifestColumn,True,STRING,Sage Bionetworks,,"study_folder_template, file_annotation_template"

modules/Unknown/Component.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-Component,,,,,,,,,,Unknown,,,,,"assay_RNAseq_template,assay_bsSeq_template,assay_metabolomics_template,assay_metagenomics_template,assay_microbiome_template,assay_phenotype_human_template,assay_proteomics_template,assay_scRNAseq_template,assay_whole_genome_sequencing_template,biospecimen_human_template,biospecimen_non_human_template,file_annotation_template,genotyping_human_template,individual_human_template,individual_non_human_template,study_folder_template"
+Component,,,,,,,,,,Unknown,,STRING,,,"assay_RNAseq_template,assay_bsSeq_template,assay_metabolomics_template,assay_metagenomics_template,assay_microbiome_template,assay_phenotype_human_template,assay_proteomics_template,assay_scRNAseq_template,assay_whole_genome_sequencing_template,biospecimen_human_template,biospecimen_non_human_template,file_annotation_template,genotyping_human_template,individual_human_template,individual_non_human_template,study_folder_template"

modules/Unknown/accessReqs.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-accessReqs,,,,,,,,,,Unknown,,,,,study_folder_template
+accessReqs,,,,,,,,,,Unknown,,STRING,,,study_folder_template

modules/Unknown/ackContext.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-ackContext,,,,,,,,,,Unknown,,,,,study_folder_template
+ackContext,,,,,,,,,,Unknown,,STRING,,,study_folder_template

modules/Unknown/acknowledgment.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-acknowledgment,,,,,,,,,,Unknown,,,,,study_folder_template
+acknowledgment,,,,,,,,,,Unknown,,STRING,,,study_folder_template

modules/Unknown/acquistionSoftwareVersion.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-acquistionSoftwareVersion,,,,,,,,,,Unknown,,,,,assay_metabolomics_template
+acquistionSoftwareVersion,,,,,,,,,,Unknown,,STRING,,,assay_metabolomics_template

modules/Unknown/batchSizeUnit.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-batchSizeUnit,,,,,,,,,,Unknown,,,,,assay_metabolomics_template
+batchSizeUnit,,,,,,,,,,Unknown,,STRING,,,assay_metabolomics_template

modules/Unknown/experimentalBatchSize.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-experimentalBatchSize,,,,,,,,,,Unknown,,,,,assay_metabolomics_template
+experimentalBatchSize,,,,,,,,,,Unknown,,INTEGER,,,assay_metabolomics_template

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,"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
+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,Sage Bionetworks,,study_folder_template

modules/Unknown/isFeatured.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-isFeatured,,,,,,,,,,Unknown,,,,,study_folder_template
+isFeatured,,,,,,,,,,Unknown,,BOOLEAN,,,study_folder_template

modules/Unknown/isReleased.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-isReleased,,,,,,,,,,Unknown,,,,,study_folder_template
+isReleased,,,,,,,,,,Unknown,,BOOLEAN,,,study_folder_template

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,"For files of dataSubtype: metadata, a description of the type of metadata in the file","individual,biospecimen,assay,supplementary files,Not Assigned",,,False,ManifestColumn,,ManifestColumn,Sage Bionetworks,Unknown,True,STRING_LIST,Sage Bionetworks,,"study_folder_template, file_annotation_template"
+metadataType,"For files of dataSubtype: metadata, a description of the type of metadata in the file","individual,biospecimen,assay,supplementary files,Not Assigned",,,False,ManifestColumn,,ManifestColumn,Sage Bionetworks,Unknown,True,STRING,Sage Bionetworks,,"study_folder_template, file_annotation_template"

modules/Unknown/methods.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-methods,,,,,,,,,,Unknown,,,,,study_folder_template
+methods,,,,,,,,,,Unknown,,STRING,,,study_folder_template

modules/Unknown/newsRelease.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-newsRelease,,,,,,,,,,Unknown,,,,,study_folder_template
+newsRelease,,,,,,,,,,Unknown,,STRING,,,study_folder_template

modules/Unknown/processingBatchSize.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-processingBatchSize,,,,,,,,,,Unknown,,,,,assay_metabolomics_template
+processingBatchSize,,,,,,,,,,Unknown,,INTEGER,,,assay_metabolomics_template

modules/Unknown/processingBatchSizeUnit.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-processingBatchSizeUnit,,,,,,,,,,Unknown,,,,,assay_metabolomics_template
+processingBatchSizeUnit,,,,,,,,,,Unknown,,STRING,,,assay_metabolomics_template

modules/Unknown/projectFullName.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-projectFullName,,,,,,,,,,Unknown,,,,,study_folder_template
+projectFullName,,,,,,,,,,Unknown,,STRING,,,study_folder_template

modules/Unknown/relatedStudies.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-relatedStudies,,,,,,,,,,Unknown,,,,,study_folder_template
+relatedStudies,,,,,,,,,,Unknown,,STRING,,,study_folder_template

modules/Unknown/sampleBatchSize.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-sampleBatchSize,,,,,,,,,,Unknown,,,,,assay_metabolomics_template
+sampleBatchSize,,,,,,,,,,Unknown,,INTEGER,,,assay_metabolomics_template

modules/Unknown/sampleBatchSizeUnit.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-sampleBatchSizeUnit,,,,,,,,,,Unknown,,,,,assay_metabolomics_template
+sampleBatchSizeUnit,,,,,,,,,,Unknown,,STRING,,,assay_metabolomics_template

modules/Unknown/studyAbstract.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-studyAbstract,,,,,,,,,,Unknown,,,,,study_folder_template
+studyAbstract,,,,,,,,,,Unknown,,STRING,,,study_folder_template

modules/Unknown/studyDescription.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-studyDescription,,,,,,,,,,Unknown,,,,,study_folder_template
+studyDescription,,,,,,,,,,Unknown,,STRING,,,study_folder_template

modules/Unknown/studyFocus.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-studyFocus,,,,,,,,,,Unknown,,,,,study_folder_template
+studyFocus,,,,,,,,,,Unknown,,STRING,,,study_folder_template

modules/Unknown/studyMetadata.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-studyMetadata,,,,,,,,,,Unknown,,,,,study_folder_template
+studyMetadata,,,,,,,,,,Unknown,,STRING,,,study_folder_template

modules/Unknown/studyName.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-studyName,,,,,,,,,,Unknown,,,,,study_folder_template
+studyName,,,,,,,,,,Unknown,,STRING,,,study_folder_template

modules/Unknown/studyType.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-studyType,,,,,,,,,,Unknown,,,,,study_folder_template
+studyType,,,,,,,,,,Unknown,,STRING,,,study_folder_template

modules/Unknown/studyWiki.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-studyWiki,,,,,,,,,,Unknown,,,,,study_folder_template
+studyWiki,,,,,,,,,,Unknown,,STRING,,,study_folder_template

modules/biospecimen/isMultiSpecimen.csv

@@ -1,2 +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"
+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,Sage Bionetworks,,"study_folder_template,Individual_Human,Individual_non_Human,Biospecimen_human, Biospecimen_non_Human,Phenotype_human,file_annotation_template"

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.,"Cross-Species Avian,Cross-Species Mammalian,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.,"Cross-Species Avian,Cross-Species Mammalian,Human,Mouse",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,individual,True,STRING,Sage Bionetworks,,study_folder_template