Merge pull request #50 from eliteportal/update-cohort-in-EL-metadata-…

…dictionary update dictionary site
eliteportal · Aug 21, 2024 · 8b8fb4b · 8b8fb4b
2 parents b845ad7 + b05a0a8
commit 8b8fb4b
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Showing 21 changed files with 7 additions and 3 deletions.
diff --git a/_data/assay_phenotype_human_template.csv b/_data/assay_phenotype_human_template.csv
@@ -9,5 +9,5 @@ ethnicity,Ethnicity of individual,True,STRING,,sage.annotations-demographics.eth
 race,Race of individual,True,STRING,,sage.annotations-demographics.race-0.0.2,ManifestColumn,"American Indian or Alaska Native,Asian,Black or African American,Multiracial,Native Hawaiian or Pacific Islander,Prefer not to answer,White"
 sex,The biological sex of the individual,True,STRING,,sage.annotations-experimentalData.sex-0.0.2,ManifestColumn,"Female,Male,Not applicable,Not collected,Not specified,Other,Unknown"
 age,"Age of the individual (age in years of the individual at first recorded study event (enrollment, visit, observation, sample collection, survey completion, etc.)",True,STRING,,,ManifestColumn,
-cohort,Name of the cohort the individual belongs to,False,STRING,,"http://purl.obolibrary.org/obo/NCIT_C61512,http://purl.obolibrary.org/obo/STATO_0000203",ManifestColumn,"ABC-DS, ACT, ADNI, Banner, BEB-Miller, BLSA, CHDWB, CLINCOR, DiCAD, EHBS, Emory ADRC, Framingham, HBTRC, HPGP, HUP, LBP, MARS, MAYO, MC, MCJ, MCR, MSBB, NYBB, Pitt ADRC, RADC, ROSMAP, SMRI, UK Biobank, UPBB, UPenn, UW ADRC,ABC-DS,ACT,ADNI,Banner,BEB-Miller,Biggs Institute Brain Bank,BLSA,CHDWB,CLINCOR,Columbia ADRC,DiCAD,EFIGA,EHBS,Emory ADRC,FBS,Framingham,HBCC,HBTRC,HPGP,HUP,LBP,MARS,Mayo Clinic,MC,MCJ,MCR,MSBB,NYBB,Pitt ADRC,RADC,ROSMAP,SMRI,UFL,UK Biobank,UPBB,UPenn,UW ADRC,WHICAP"
+cohort,Name of the cohort the individual belongs to,False,STRING,,"http://purl.obolibrary.org/obo/NCIT_C61512,http://purl.obolibrary.org/obo/STATO_0000203",ManifestColumn,"ABC-DS, ACT, ADNI, Banner, BEB-Miller, BLSA, CHDWB,CHS, CLINCOR, DiCAD, EHBS, Emory ADRC, Framingham, HABC, HBTRC, HPGP, HUP, LBP, MARS, MAYO, MC, MCJ, MCR, MSBB, MrOS, NYBB, Pitt ADRC, RADC, ROSMAP, SMRI, SOF, UK Biobank, UPBB, UPenn, UW ADRC,ABC-DS,ACT,ADNI,Banner,BEB-Miller,Biggs Institute Brain Bank,BLSA,CHDWB,CLINCOR,Columbia ADRC,DiCAD,EFIGA,EHBS,Emory ADRC,FBS,Framingham,HBCC,HBTRC,HPGP,HUP,LBP,MARS,Mayo Clinic,MC,MCJ,MCR,MSBB,NYBB,Pitt ADRC,RADC,ROSMAP,SMRI,UFL,UK Biobank,UPBB,UPenn,UW ADRC,WHICAP"
 individualID,"Identifying string linked to the individual or animal being studied, provided by the data contributor",True,STRING,,sage.annotations-experimentalData.individualID-0.0.2,ManifestColumn,
diff --git a/_data/cohort.csv b/_data/cohort.csv
@@ -6,11 +6,13 @@ ABC-DS,,STRING,,ManifestColumn
  BEB-Miller,,STRING,,ManifestColumn
  BLSA,,STRING,,ManifestColumn
  CHDWB,,STRING,,ManifestColumn
+CHS,,STRING,,ManifestColumn
  CLINCOR,,STRING,,ManifestColumn
  DiCAD,,STRING,,ManifestColumn
  EHBS,,STRING,,ManifestColumn
  Emory ADRC,,STRING,,ManifestColumn
  Framingham,,STRING,,ManifestColumn
+ HABC,,STRING,,ManifestColumn
  HBTRC,,STRING,,ManifestColumn
  HPGP,,STRING,,ManifestColumn
  HUP,,STRING,,ManifestColumn
@@ -21,11 +23,13 @@ ABC-DS,,STRING,,ManifestColumn
  MCJ,,STRING,,ManifestColumn
  MCR,,STRING,,ManifestColumn
  MSBB,,STRING,,ManifestColumn
+ MrOS,,STRING,,ManifestColumn
  NYBB,,STRING,,ManifestColumn
  Pitt ADRC,,STRING,,ManifestColumn
  RADC,,STRING,,ManifestColumn
  ROSMAP,,STRING,,ManifestColumn
  SMRI,,STRING,,ManifestColumn
+ SOF,,STRING,,ManifestColumn
  UK Biobank,,STRING,,ManifestColumn
  UPBB,,STRING,,ManifestColumn
  UPenn,,STRING,,ManifestColumn

diff --git a/_data/individual.csv b/_data/individual.csv
@@ -1,5 +1,5 @@
 Key,Key Description,Valid Values,columnType,Parent,module
 age,"Age of the individual (age in years of the individual at first recorded study event (enrollment, visit, observation, sample collection, survey completion, etc.)",,STRING,ManifestColumn,individual
-cohort,Name of the cohort the individual belongs to,"ABC-DS, ACT, ADNI, Banner, BEB-Miller, BLSA, CHDWB, CLINCOR, DiCAD, EHBS, Emory ADRC, Framingham, HBTRC, HPGP, HUP, LBP, MARS, MAYO, MC, MCJ, MCR, MSBB, NYBB, Pitt ADRC, RADC, ROSMAP, SMRI, UK Biobank, UPBB, UPenn, UW ADRC,ABC-DS,ACT,ADNI,Banner,BEB-Miller,Biggs Institute Brain Bank,BLSA,CHDWB,CLINCOR,Columbia ADRC,DiCAD,EFIGA,EHBS,Emory ADRC,FBS,Framingham,HBCC,HBTRC,HPGP,HUP,LBP,MARS,Mayo Clinic,MC,MCJ,MCR,MSBB,NYBB,Pitt ADRC,RADC,ROSMAP,SMRI,UFL,UK Biobank,UPBB,UPenn,UW ADRC,WHICAP",STRING,ManifestColumn,individual
+cohort,Name of the cohort the individual belongs to,"ABC-DS, ACT, ADNI, Banner, BEB-Miller, BLSA, CHDWB,CHS, CLINCOR, DiCAD, EHBS, Emory ADRC, Framingham, HABC, HBTRC, HPGP, HUP, LBP, MARS, MAYO, MC, MCJ, MCR, MSBB, MrOS, NYBB, Pitt ADRC, RADC, ROSMAP, SMRI, SOF, UK Biobank, UPBB, UPenn, UW ADRC,ABC-DS,ACT,ADNI,Banner,BEB-Miller,Biggs Institute Brain Bank,BLSA,CHDWB,CLINCOR,Columbia ADRC,DiCAD,EFIGA,EHBS,Emory ADRC,FBS,Framingham,HBCC,HBTRC,HPGP,HUP,LBP,MARS,Mayo Clinic,MC,MCJ,MCR,MSBB,NYBB,Pitt ADRC,RADC,ROSMAP,SMRI,UFL,UK Biobank,UPBB,UPenn,UW ADRC,WHICAP",STRING,ManifestColumn,individual
 individualID,"Identifying string linked to the individual or animal being studied, provided by the data contributor",,STRING,ManifestColumn,individual
 species,The name of a species (typically a taxonomic group) of organism.,"Human,Mouse",STRING_LIST,ManifestColumn,individual
diff --git a/_data/individual_human_template.csv b/_data/individual_human_template.csv
@@ -14,5 +14,5 @@ ethnicity,Ethnicity of individual,True,STRING,,sage.annotations-demographics.eth
 race,Race of individual,True,STRING,,sage.annotations-demographics.race-0.0.2,ManifestColumn,"American Indian or Alaska Native,Asian,Black or African American,Multiracial,Native Hawaiian or Pacific Islander,Prefer not to answer,White"
 sex,The biological sex of the individual,True,STRING,,sage.annotations-experimentalData.sex-0.0.2,ManifestColumn,"Female,Male,Not applicable,Not collected,Not specified,Other,Unknown"
 age,"Age of the individual (age in years of the individual at first recorded study event (enrollment, visit, observation, sample collection, survey completion, etc.)",True,STRING,,,ManifestColumn,
-cohort,Name of the cohort the individual belongs to,False,STRING,,"http://purl.obolibrary.org/obo/NCIT_C61512,http://purl.obolibrary.org/obo/STATO_0000203",ManifestColumn,"ABC-DS, ACT, ADNI, Banner, BEB-Miller, BLSA, CHDWB, CLINCOR, DiCAD, EHBS, Emory ADRC, Framingham, HBTRC, HPGP, HUP, LBP, MARS, MAYO, MC, MCJ, MCR, MSBB, NYBB, Pitt ADRC, RADC, ROSMAP, SMRI, UK Biobank, UPBB, UPenn, UW ADRC,ABC-DS,ACT,ADNI,Banner,BEB-Miller,Biggs Institute Brain Bank,BLSA,CHDWB,CLINCOR,Columbia ADRC,DiCAD,EFIGA,EHBS,Emory ADRC,FBS,Framingham,HBCC,HBTRC,HPGP,HUP,LBP,MARS,Mayo Clinic,MC,MCJ,MCR,MSBB,NYBB,Pitt ADRC,RADC,ROSMAP,SMRI,UFL,UK Biobank,UPBB,UPenn,UW ADRC,WHICAP"
+cohort,Name of the cohort the individual belongs to,False,STRING,,"http://purl.obolibrary.org/obo/NCIT_C61512,http://purl.obolibrary.org/obo/STATO_0000203",ManifestColumn,"ABC-DS, ACT, ADNI, Banner, BEB-Miller, BLSA, CHDWB,CHS, CLINCOR, DiCAD, EHBS, Emory ADRC, Framingham, HABC, HBTRC, HPGP, HUP, LBP, MARS, MAYO, MC, MCJ, MCR, MSBB, MrOS, NYBB, Pitt ADRC, RADC, ROSMAP, SMRI, SOF, UK Biobank, UPBB, UPenn, UW ADRC,ABC-DS,ACT,ADNI,Banner,BEB-Miller,Biggs Institute Brain Bank,BLSA,CHDWB,CLINCOR,Columbia ADRC,DiCAD,EFIGA,EHBS,Emory ADRC,FBS,Framingham,HBCC,HBTRC,HPGP,HUP,LBP,MARS,Mayo Clinic,MC,MCJ,MCR,MSBB,NYBB,Pitt ADRC,RADC,ROSMAP,SMRI,UFL,UK Biobank,UPBB,UPenn,UW ADRC,WHICAP"
 individualID,"Identifying string linked to the individual or animal being studied, provided by the data contributor",True,STRING,,sage.annotations-experimentalData.individualID-0.0.2,ManifestColumn,
diff --git a/docs/Template/Template.md → docs/template/Template.md b/docs/Template/Template.md → docs/template/Template.md
diff --git a/docs/Template/assay_RNAseq_template.md → docs/template/assay_RNAseq_template.md b/docs/Template/assay_RNAseq_template.md → docs/template/assay_RNAseq_template.md
diff --git a/docs/Template/assay_bsSeq_template.md → docs/template/assay_bsSeq_template.md b/docs/Template/assay_bsSeq_template.md → docs/template/assay_bsSeq_template.md
diff --git a/docs/Template/assay_metabolomics_template.md → docs/template/assay_metabolomics_template.md b/docs/Template/assay_metabolomics_template.md → docs/template/assay_metabolomics_template.md
diff --git a/docs/Template/assay_metagenomics_template.md → docs/template/assay_metagenomics_template.md b/docs/Template/assay_metagenomics_template.md → docs/template/assay_metagenomics_template.md
diff --git a/docs/Template/assay_microbiome_template.md → docs/template/assay_microbiome_template.md b/docs/Template/assay_microbiome_template.md → docs/template/assay_microbiome_template.md
diff --git a/...emplate/assay_phenotype_human_template.md → ...emplate/assay_phenotype_human_template.md b/...emplate/assay_phenotype_human_template.md → ...emplate/assay_phenotype_human_template.md
diff --git a/docs/Template/assay_proteomics_template.md → docs/template/assay_proteomics_template.md b/docs/Template/assay_proteomics_template.md → docs/template/assay_proteomics_template.md
diff --git a/docs/Template/assay_scRNAseq_template.md → docs/template/assay_scRNAseq_template.md b/docs/Template/assay_scRNAseq_template.md → docs/template/assay_scRNAseq_template.md
diff --git a/...assay_whole_genome_sequencing_template.md → ...assay_whole_genome_sequencing_template.md b/...assay_whole_genome_sequencing_template.md → ...assay_whole_genome_sequencing_template.md
diff --git a/docs/Template/biospecimen_human_template.md → docs/template/biospecimen_human_template.md b/docs/Template/biospecimen_human_template.md → docs/template/biospecimen_human_template.md
diff --git a/...emplate/biospecimen_non_human_template.md → ...emplate/biospecimen_non_human_template.md b/...emplate/biospecimen_non_human_template.md → ...emplate/biospecimen_non_human_template.md
diff --git a/docs/Template/file_annotation_template.md → docs/template/file_annotation_template.md b/docs/Template/file_annotation_template.md → docs/template/file_annotation_template.md
diff --git a/docs/Template/genotyping_human_template.md → docs/template/genotyping_human_template.md b/docs/Template/genotyping_human_template.md → docs/template/genotyping_human_template.md
diff --git a/docs/Template/individual_human_template.md → docs/template/individual_human_template.md b/docs/Template/individual_human_template.md → docs/template/individual_human_template.md
diff --git a/...Template/individual_non_human_template.md → ...template/individual_non_human_template.md b/...Template/individual_non_human_template.md → ...template/individual_non_human_template.md
diff --git a/docs/Template/study_folder_template.md → docs/template/study_folder_template.md b/docs/Template/study_folder_template.md → docs/template/study_folder_template.md