NCBI’s Database of Genotypes and Phenotypes: dbGaP

By K. Tryka, Luning Hao, Anne Sturcke, Y. Jin, Zhen Y. Wang, Lora Ziyabari, Moira Lee, N. Popova, N. Sharopova, Masato Kimura and 1 more. Nucleic Acids Res., 2013

505 citations recorded by the source corpus.

The Database of Genotypes and Phenotypes (dbGap, http://www.ncbi.nlm.nih.gov/gap) is a National Institutes of Health-sponsored repository charged to archive, curate and distribute information produced by studies investigating the interaction of genotype and phenotype. Information in dbGaP is organized as a hierarchical structure and includes the accessioned objects, phenotypes (as variables and datasets), various molecular assay data (SNP and Expression Array data, Sequence and Epigenomic marks), analyses and documents. Publicly accessible metadata about submitted studies, summary level data, and documents related to studies can be accessed freely on the dbGaP website. Individual-level data are accessible via Controlled Access application to scientists across the globe.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/151ec57b35f6a7431fdce934a57ae15451079d85

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Citations in the corpus

Variant interpretation using population databases: lessons from gnomAD (2021, background): “Informatics Lab ‐ Space (AnVIL) as well as other repositories (Schatz et al., 2021; Tryka et al., 2014).”
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins (2016, background): “HuGE Navigator Gene-Phenotype Associations (68) MPO Gene-Phenotype Associations (69–72) OMIM Gene-Disease Associations (73, 74) dbGAP Gene-Trait Associations (75, 76) Database, Vol.”
ClinVar: public archive of interpretations of clinically relevant variants (2015, background): “ClinVar’s web display is designed to support the medical professional who wants to determine, at a glance, the level of confidence in any interpretation, what interpretations have been submitted for an allele, whether different submitters agree in their assessments, what disorders may or may not res”
PheKB: a catalog and workflow for creating electronic phenotype algorithms for transportability (2016, methodology): “39,40 Its integration in the phenotyping development workflow within PheKB ensures consistent formatting and coding of shared data sets.”
webTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association study (2021, unknown): “…cohorts include GWAS summary statistics from public databases such as GWAS Catalog (28), LD Hub (36), GRASP (31), PhenoScanner (37) and db-GaP (38), as well as summary statistics curated from consortium websites such as PGC (https://www.med.unc.edu/ pgc), MAGIC…”
RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data (2017, methodology): “As described in our previous study (37), the human disease/trait-associated SNPs were curated from published GWAS data provided by the NHGRI GWAS Catalog (38), Johnson and O’Donnell (39), dbGAP (40) and GAD (41), as well as the SNPs in linkage disequilibrium (LD, r2 ≥ 0.”
The Genome Sequence Archive Family: Toward Explosive Data Growth and Diverse Data Types (2021, methodology): “As an important partner to GSA that provides open access to all released data, GSA-Human features controlled-access and security services for human genetics-related data, which is compatible well with the database of Genotypes and Phenotypes (dbGaP) [10] in the National Center for Biotechnology Info”
The ProteomeXchange consortium at 10 years: 2023 update (2022, unknown): “Resources supporting the storage and dissemination of controlled access DNA/RNA sequencing datasets include the EGA (European Genome-phenome Archive) (57), dbGAP (USA) (58) and the Japanese Genotype-phenotype Archive (JGA) (59).”
The EMBL-EBI search and sequence analysis tools APIs in 2019 (2019, background): “Since the last update, Europe PMC (27) (enriched replacement of Medline), BioSamples (28), Rfam (29), reviewed ChEMBL (25), OLS (30), dbGaP (31), EVA (32), InterPro 7 (12) and bio.”