Github Action: Updated dictionary term files and term pages

Author: github-actions[bot]

_data/ADKP.csv

@@ -1,2 +1,3 @@
 Key,Key Description,Valid Values,columnType,Parent,module
 ModelSystemType,Type of model system,"animal, cerebral organoid, immortalized cell line, iPSC, organoid, primary cell culture, Not assigned",BOOLEAN,ManifestColumn,ADKP
+isModelSystem,Boolean flag indicating whether or not a file has data from a model system,"True, False, Not assigned",BOOLEAN,ManifestColumn,ADKP

_data/DataModel.csv

@@ -1,5 +1,7 @@
 Key,Key Description,columnType,Source,module
+analysis_results_metadata_template,Template for analysis and results,,Sage Bionetworks, template
 ModelSystemType,Type of model system,BOOLEAN,Sage Bionetworks,ADKP
+isModelSystem,Boolean flag indicating whether or not a file has data from a model system,BOOLEAN,Sage Bionetworks,ADKP
 DNAextraction,"DNA extraction kit method. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",STRING,,ManifestColumn
 acquisitionBatchID,"Acquisition batch identifier, provided by the data contributor to Sage Bionetworks. The batch identifier(s) must be stored in a data dictionary .csv file uploaded to Synapse",STRING,,ManifestColumn
 acquisitionBatchSize,The number of samples,STRING,,ManifestColumn
@@ -146,11 +148,11 @@ useSummaryFile,Was a summary statitics file uploded to Synapse?,STRING,,Manifest
 useTreatment,Was a treatment applied to the sample?,BOOLEAN,,ManifestColumn
 vacuumPressure,The recorded vacuum pressure value,NUMBER,,ManifestColumn
 vacuumPressureUnit,Unit of vacuum pressure value,STRING,,ManifestColumn
-valueReported,The count or gene count for the transcript,NUMBER,,ManifestColumn
+valueReported,The count or gene count for the transcript,STRING,,ManifestColumn
 variantCount,The number of variants analysed in the discovery stage (after QC). Example - 52500,STRING,,ManifestColumn
 visitCode,"Indicate which longitudinal visit for the individual the data comes from, provided by the data contributor's data dictionary",NUMBER,,ManifestColumn
 Component,,,,Unknown
-Filename,,,,Unknown
+Filename,,STRING,,Unknown
 accessReqs,,,,Unknown
 ackContext,,,,Unknown
 acknowledgment,,,,Unknown

_data/ManifestColumn.csv

@@ -97,7 +97,7 @@ reagentName,The reagent name is an alternative to the Reagent ID.,,STRING,Manife
 reagentWeblink,An internet address that may provide details of an assay reagent.,,STRING,ManifestColumn,ManifestColumn
 referenceTranscriptID,"The ID for the transcript/gene. Either the NCBI ID or the Ensembl ID must be provided. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,STRING,ManifestColumn,ManifestColumn
 reportedTrait,"The trait under investigation. Please describe the trait concisely but with enough detail to be clear to a non-specialist. Avoid the use of abbreviations; if these are necessary, please define them or their source in the readme file. Example - Reticulocyte count",,STRING,ManifestColumn,ManifestColumn
-repositoryName,"The public repository name for the transcript (for example, Ensembl or NCBI Gene)","ArrayExpress,Broad Single Cell Portal,dbGAP,ENA,Ensembl,FlowRepository,GenBank,GENCODEv38 GRCh38, GEO,GISAID,IEDB,ImmPort,MassIVE,MetaboLights,Metabolomics Workbench,MGnify,NCBI Gene,PRIDE,SRA,UniProt",STRING,ManifestColumn,ManifestColumn
+repositoryName,"The public repository name for the transcript (for example, Ensembl or NCBI Gene)","ArrayExpress,Broad Single Cell Portal,dbGAP,ENA,Ensembl,FlowRepository,GenBank,GENCODEv38 GRCh38, GEO,GISAID,IEDB,ImmPort,MassIVE,MetaboLights,Metabolomics Workbench,MGnify,NCBI Gene,PRIDE,SRA,Synapse,UniProt,Other,Unknown,Not collected,Not applicable,Not specified",STRING,ManifestColumn,ManifestColumn
 resourceType,The type of resource being stored and annotated,"experimentalData,metadata,tool,analysis,computationalNotebook, Not assigned",STRING_LIST,ManifestColumn,ManifestColumn
 resultUnit,The unit for the result value,"FPKM,raw count, Not applicable,Not collected,Not specified,RPKM,TPM,Unknown",STRING,ManifestColumn,ManifestColumn
 rnaBatchID,"Isolation batch identifier, provided by the data contributor to Sage Bionetworks. The batch identifier(s) must be stored in a data dictionary .csv file uploaded to Synapse. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,STRING,ManifestColumn,ManifestColumn
@@ -145,6 +145,6 @@ useSummaryFile,Was a summary statitics file uploded to Synapse?,,STRING,Manifest
 useTreatment,Was a treatment applied to the sample?,,BOOLEAN,ManifestColumn,ManifestColumn
 vacuumPressure,The recorded vacuum pressure value,,NUMBER,ManifestColumn,ManifestColumn
 vacuumPressureUnit,Unit of vacuum pressure value,"AFU,AI,AU/ml,bp g/dl,DK units/ml,g/l,gm,HAU,IU,iu/l,IU/ml,Kallikrein Inactivator Unit per Milliliter,kg,l,M,mg,mg/dl,mg/l,mg/ml,miu/ml,ml,mM,MOI,ng,ng/dl,ng/ml,ng/nl,ng/ul,nl,nM,Not specified,NPX,optical density,PFU,PFUe,pg,pg/mg creatinine,pg/ml,pg/nl,pg/ul,pl,pM,Pound,TCID50,ug,ug/dl,ug/l,ug/ml,ug/ul,uiu/ml,ul,uM,umol/l,units/ml",STRING,ManifestColumn,ManifestColumn
-valueReported,The count or gene count for the transcript,,NUMBER,ManifestColumn,ManifestColumn
+valueReported,The count or gene count for the transcript,,STRING,ManifestColumn,ManifestColumn
 variantCount,The number of variants analysed in the discovery stage (after QC). Example - 52500,,STRING,ManifestColumn,ManifestColumn
 visitCode,"Indicate which longitudinal visit for the individual the data comes from, provided by the data contributor's data dictionary",,NUMBER,ManifestColumn,ManifestColumn

_data/Unknown.csv

@@ -1,6 +1,6 @@
 Key,Key Description,Valid Values,columnType,Parent,module
 Component,,,,,Unknown
-Filename,,,,,Unknown
+Filename,,,STRING,,Unknown
 accessReqs,,,,,Unknown
 ackContext,,,,,Unknown
 acknowledgment,,,,,Unknown
@@ -10,7 +10,7 @@ experimentalBatchSize,,,,,Unknown
 grantNumber,Grant number including activity code institute code and serial number (e.g. U01MH103392),"U19AG063893,U24AG051129,U19AG023122,UH2AG064706,UH3AG064706,UH2AG064704,UH3AG064704,R01AG061844, Not assigned",STRING_LIST,ManifestColumn,Unknown
 isFeatured,,,,,Unknown
 isReleased,,,,,Unknown
-metadataType,"For files of dataSubtype: metadata, a description of the type of metadata in the file","individual,biospecimen,assay,Not Assigned",STRING_LIST,ManifestColumn,Unknown
+metadataType,"For files of dataSubtype: metadata, a description of the type of metadata in the file","individual,biospecimen,assay,supplementary files,Not Assigned",STRING_LIST,ManifestColumn,Unknown
 methods,,,,,Unknown
 newsRelease,,,,,Unknown
 processingBatchSize,,,,,Unknown

_data/analysis_results_metadata_template.csv

@@ -0,0 +1,4 @@
+Attribute,Description,Required,columnType,DependsOn,Source,Parent,Valid Values
+analysisType,Type of analysis,False,STRING_LIST,,Sage Bionetworks,ManifestColumn,"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"
+dataTypeAll,,True,STRING_LIST,,Sage Bionetworks,ManifestColumn,
+assay,The analysis or technology used to generate the data in this file,True,STRING,,sage.annotations-experimentalData.assay-0.0.26,ManifestColumn,"10x multiome, 16SrRNAseq, active avoidance learning behavior, anxiety-related behavior, ATACSeq, atomicForceMicroscopy, autoradiography, Baker Lipidomics, Biocrates Bile Acids, Biocrates p180, Biocrates Q500, bisulfiteSeq, Blood Chemistry Measurement, brightfieldMicroscopy, cellViabilityAssay, ChIPSeq, CITESeq, contextual conditioning behavior, CUT&Tag, DIA, DNA optical mapping, electrochemiluminescence, elevated plus maze test, elevated T maze apparatus method, ELISA, errBisulfiteSeq, exomeSeq, FIA-MSMS, FitBark, frailty assessment, Genotyping, HI-C, HiChIPseq, high content screen, HPLC, HPLC-MSMS, Immunocytochemistry, immunofluorescence, immunohistochemistry, in vivo bioluminescence, ISOSeq, jumpingLibrary, kinesthetic behavior, label free mass spectrometry, Laser Speckle Imaging, LC-MS, LC-MSMS, LC-SRM, Leiden Oxylipins, lentiMPRA, LFP, liquid chromatography-electrochemical detection, lncrnaSeq, locomotor activation behavior, long-read rnaSeq, LTP, MDMS-SL, memory behavior, Metabolon, methylationArray, MIB/MS, microRNAcounts, mirnaArray, mirnaSeq, MRI, mRNAcounts, MudPIT, m6A-rnaSeq, nextGenerationTargetedSequencing, Nightingale NMR, NOMe-Seq, novelty response behavior, open field test, oxBS-Seq, pharmacodynamics, pharmacokinetics, photograph, polymeraseChainReaction, Positron Emission Tomography, proximity extension assay, questionnaire, Rader Lipidomics, Real Time PCR, Ribo-Seq, rotarod performance test, rnaArray, rnaSeq, RPPA, sandwich ELISA, Sanger sequencing, scale, scATACSeq, scCGIseq, scirnaSeq, scrnaSeq, scwholeGenomeSeq, SiMoA, snpArray, snATACSeq, snrnaSeq, spontaneous alternation, STARRSeq, TMT quantitation, tractionForceMicroscopy, UPLC-MSMS, UPLC-ESI-QTOF-MS, UC Davis GCTOF, UCSD Untargeted Metabolomics, Vernier Caliper, von Frey test, westernBlot, wheel running, whole-cell patch clamp, wholeGenomeSeq, Wishart Catecholamines, Wishart High Value Metabolites, Zeno Electronic Walkway, Not collected, Not specified, Not applicable, Other, Unknown"

_data/assay_RNAseq_template.csv

@@ -2,18 +2,18 @@ Attribute,Description,Required,columnType,DependsOn,Source,Parent,Valid Values
 measurementTechnique,"The name of the measurement technique describing the assay method. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,,ManifestColumn,
 readLengthUnits,The units of measurement. Provide a value or Unknown Not collected Not applicable Not specified ,True,STRING,,,ManifestColumn,
 referenceTranscriptID,"The ID for the transcript/gene. Either the NCBI ID or the Ensembl ID must be provided. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,,ManifestColumn,
-repositoryName,"The public repository name for the transcript (for example, Ensembl or NCBI Gene)",True,STRING,,,ManifestColumn,"ArrayExpress,Broad Single Cell Portal,dbGAP,ENA,Ensembl,FlowRepository,GenBank,GENCODEv38 GRCh38, GEO,GISAID,IEDB,ImmPort,MassIVE,MetaboLights,Metabolomics Workbench,MGnify,NCBI Gene,PRIDE,SRA,UniProt"
+repositoryName,"The public repository name for the transcript (for example, Ensembl or NCBI Gene)",True,STRING,,,ManifestColumn,"ArrayExpress,Broad Single Cell Portal,dbGAP,ENA,Ensembl,FlowRepository,GenBank,GENCODEv38 GRCh38, GEO,GISAID,IEDB,ImmPort,MassIVE,MetaboLights,Metabolomics Workbench,MGnify,NCBI Gene,PRIDE,SRA,Synapse,UniProt,Other,Unknown,Not collected,Not applicable,Not specified"
 resultUnit,The unit for the result value,True,STRING,,,ManifestColumn,"FPKM,raw count, Not applicable,Not collected,Not specified,RPKM,TPM,Unknown"
 sampleType,"The type of sample collected or the term used to describe the source of a biospecimen used for a laboratory test. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,,ManifestColumn,
 technologyPlatformVersion,"The specific version (application, manufacturer, model, lab, etc.) of a technology that is used to carry out a laboratory or computational experiment. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,,ManifestColumn,
 transcriptType,The type of transcript reported,True,STRING,,,ManifestColumn,"lincRNA,mRNA,total RNA minus rRNA,Not applicable,Not collected,Not specified,Other,snRNA,Unknown"
-valueReported,The count or gene count for the transcript,True,NUMBER,,,ManifestColumn,
+valueReported,The count or gene count for the transcript,True,STRING,,,ManifestColumn,
 Component,,False,,,,,
-Filename,,False,,,,,
+Filename,,False,STRING,,,,
 specimenID,"Identifying string linked to a particular sample or specimen, provide by the data contributor",True,STRING,,sage.annotations-experimentalData.specimenID-0.0.2,ManifestColumn,
 platformLocation,"The name of the laboratory, facility, vendor, company, or location where the data generation platform was located, provided by the data contributor. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,sage.annotations-experimentalData.platformLocation-0.0.2,ManifestColumn,
 isStranded,Whether or not the library is stranded.,True,BOOLEAN,,sage.annotations-ngs.isStranded-0.0.2,ManifestColumn,"FALSE,TRUE"
-libraryPreparationMethod,"Method by which library was prepared. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,sage.annotations-ngs.libraryPreparationMethod-0.0.10,ManifestColumn,"10x, Accel-NGS 2S Plus, Accel-NGS Methyl-Seq, CEL-seq, Drop-Seq, NEBNext, NexteraXT, Omni-ATAC, sac-seq, Smart-seq1, Smart-seq2, Smart-seq4, SMRTbell, TruSeq, Ultralow Methyl-Seq, Illumina DNA PCR-Free Prep Kit, Qiagen PreAnalytiX PAXgene Blood miRNA Kit, Unknown, Not collected, Not applicable, Not specified"
+libraryPreparationMethod,"Method by which library was prepared. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,sage.annotations-ngs.libraryPreparationMethod-0.0.10,ManifestColumn,"10x, Accel-NGS 2S Plus, Accel-NGS Methyl-Seq, CEL-seq, Drop-Seq, NEBNext, NexteraXT, Omni-ATAC, sac-seq, Smart-seq1, Smart-seq2, Smart-seq4, SMRTbell, TruSeq, Ultralow Methyl-Seq, Illumina DNA PCR-Free Prep Kit, Qiagen PreAnalytiX PAXgene Blood miRNA Kit, Qiagen Rneasy Extraction Kit, Unknown, Not collected, Not applicable, Not specified"
 libraryVersion,"Library Version- for example, rnaSeq 10x library version. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,sage.annotations-ngs.libraryVersion-0.0.2,ManifestColumn,
 readLength,The length of the read. Provide a value or Unknown Not collected Not applicable Not specified ,True,STRING,,sage.annotations-ngs.readLength-0.0.2,ManifestColumn,
 readStrandOrigin,The strand from which the read originates in a strand-specific protocol.,True,STRING,,sage.annotations-ngs.readStrandOrigin-0.0.2,ManifestColumn,"forward, reverse, stranded, unstranded, Unknown, Not collected, Not specified, Not applicable"

_data/assay_bsSeq_template.csv

@@ -15,15 +15,15 @@ sequencingBatchSize,The number of samples. Provide a value or Unknown Not collec
 sequencingBatchSizeUnit,The unit of measurement for number of samples in a batch. Provide a value or Unknown Not collected Not applicable Not specified,True,STRING,,,ManifestColumn,
 technologyPlatformVersion,"The specific version (application, manufacturer, model, lab, etc.) of a technology that is used to carry out a laboratory or computational experiment. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,,ManifestColumn,
 Component,,False,,,,,
-Filename,,False,,,,,
+Filename,,False,STRING,,,,
 specimenID,"Identifying string linked to a particular sample or specimen, provide by the data contributor",True,STRING,,sage.annotations-experimentalData.specimenID-0.0.2,ManifestColumn,
 platformLocation,"The name of the laboratory, facility, vendor, company, or location where the data generation platform was located, provided by the data contributor. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,sage.annotations-experimentalData.platformLocation-0.0.2,ManifestColumn,
 directionalBSseqLibrary,Indicates whether or not the bisulfiteSeq library is directional,True,STRING,,sage.annotations-ngs.directionalBSseqLibrary-0.0.2,ManifestColumn,"TRUE, FALSE, Unknown, Not collected, Not applicable, Not specified"
 gDNAconc,gDNA Concentration in ng. Provide a value or Unknown Not collected Not applicable Not specified,True,STRING,,sage.annotations-experimentalData.gDNAconc-0.0.3,ManifestColumn,
 isStranded,Whether or not the library is stranded.,True,BOOLEAN,,sage.annotations-ngs.isStranded-0.0.2,ManifestColumn,"FALSE,TRUE"
 lambdaDNAconc,Lambda DNA spike-in concentration in ng. Provide a value or Unknown Not collected Not applicable Not specified ,True,STRING,,sage.annotations-experimentalData.lambdaDNAconc-0.0.2,ManifestColumn,
 libraryPrep,"The general strategy by which the library was prepared. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,sage.annotations-ngs.libraryPrep-0.0.13,ManifestColumn,"amplicon, cellHashing, Chromium Single Cell 3', DNALibraryConstruction, EndItDNAEndRepairKit, KapaHyperPrep, lncRNAenrichment, methylSeq, miRNAenrichment, multiome, MULTIseq, PCRfree, polyAselection, proximity ligation, rRNAdepletion, snIsoSeq, SPLITseq, STARRSeq, SureCell, totalRNA, Unknown, Not collected, Not applicable, Not specified"
-libraryPreparationMethod,"Method by which library was prepared. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,sage.annotations-ngs.libraryPreparationMethod-0.0.10,ManifestColumn,"10x, Accel-NGS 2S Plus, Accel-NGS Methyl-Seq, CEL-seq, Drop-Seq, NEBNext, NexteraXT, Omni-ATAC, sac-seq, Smart-seq1, Smart-seq2, Smart-seq4, SMRTbell, TruSeq, Ultralow Methyl-Seq, Illumina DNA PCR-Free Prep Kit, Qiagen PreAnalytiX PAXgene Blood miRNA Kit, Unknown, Not collected, Not applicable, Not specified"
+libraryPreparationMethod,"Method by which library was prepared. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,sage.annotations-ngs.libraryPreparationMethod-0.0.10,ManifestColumn,"10x, Accel-NGS 2S Plus, Accel-NGS Methyl-Seq, CEL-seq, Drop-Seq, NEBNext, NexteraXT, Omni-ATAC, sac-seq, Smart-seq1, Smart-seq2, Smart-seq4, SMRTbell, TruSeq, Ultralow Methyl-Seq, Illumina DNA PCR-Free Prep Kit, Qiagen PreAnalytiX PAXgene Blood miRNA Kit, Qiagen Rneasy Extraction Kit, Unknown, Not collected, Not applicable, Not specified"
 libraryVersion,"Library Version- for example, rnaSeq 10x library version. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,sage.annotations-ngs.libraryVersion-0.0.2,ManifestColumn,
 meanCoverage,Total number of bases covered by ATAC-seq reads/size of genome. Provide a value or Unknown Not collected Not applicable Not specified,True,STRING,,sage.annotations-qc.meanCoverage-0.0.2,ManifestColumn,
 pcrCycles,Number of PCR cycles to amplify transposased DNA fragments. Provide a value or Unknown Not collected Not applicable Not specified ,True,STRING,,sage.annotations-experimentalData.pcrCycles-0.0.2,ManifestColumn,

_data/assay_metabolomics_template.csv

@@ -33,7 +33,7 @@ technologyPlatformVersion,"The specific version (application, manufacturer, mode
 vacuumPressure,The recorded vacuum pressure value,False,NUMBER,,,ManifestColumn,
 vacuumPressureUnit,Unit of vacuum pressure value,False,STRING,,,ManifestColumn,"AFU,AI,AU/ml,bp g/dl,DK units/ml,g/l,gm,HAU,IU,iu/l,IU/ml,Kallikrein Inactivator Unit per Milliliter,kg,l,M,mg,mg/dl,mg/l,mg/ml,miu/ml,ml,mM,MOI,ng,ng/dl,ng/ml,ng/nl,ng/ul,nl,nM,Not specified,NPX,optical density,PFU,PFUe,pg,pg/mg creatinine,pg/ml,pg/nl,pg/ul,pl,pM,Pound,TCID50,ug,ug/dl,ug/l,ug/ml,ug/ul,uiu/ml,ul,uM,umol/l,units/ml"
 Component,,False,,,,,
-Filename,,False,,,,,
+Filename,,False,STRING,,,,
 acquistionSoftwareVersion,,False,,,,,
 batchSizeUnit,,False,,,,,
 experimentalBatchSize,,False,,,,,