6 Finding unharmonized TOPMed study phenotypes on dbGaP
6.1 Ways to get TOPMed phenotype data
- Get DCC harmonized phenotypes from the Exchange Area
- Get (harmonized or unharmonized) phenotypes directly from the studies (transfer via the Exchange Area)
- Get unharmonized phenotypes from dbGaP
6.2 dbGaP accession lingo
- study accession: A unique identifier, phs, that specifies a study on dbGaP
- parent accession: The phs that holds the subject, sample, and phenotype data for a study
- child accession: The phs that holds the genotype or other omics data for a project within a parent study
- TOPMed accession: The phs that will hold TOPMed sequence data
- Currently a separate parent phs
- Will eventually be made into a child phs connected to the original parent phs
- dataset accession: A unique identifier, pht, that specifies a dataset within a study
- variable accession: A unique identifier, phv, that specifies a variable
6.3 dbGaP advanced search tools
6.3.1 Entrez advanced search
Search strings for Entrez
# All variables within four studies
(phs000007[Belongs To] OR phs000286[Belongs To] OR phs000284[Belongs To] OR phs000462[Belongs To])
# All variables with "bmi" in the variable name within four studies
(phs000007[Belongs To] OR phs000286[Belongs To] OR phs000284[Belongs To] OR phs000462[Belongs To]) AND bmi[Variable Name]
# All variables with "bmi" in the variable description within four studies
(phs000007[Belongs To] OR phs000286[Belongs To] OR phs000284[Belongs To] OR phs000462[Belongs To]) AND bmi[Variable Description]
# All variables with "bmi" in the variable name or description within four studies
(phs000007[Belongs To] OR phs000286[Belongs To] OR phs000284[Belongs To] OR phs000462[Belongs To]) AND (bmi[Variable Description] OR bmi[Variable Name])6.3.2 Faceted advanced search
Saved URLs for Faceted search examples