[Source]: Database of Genotypes and Phenotypes (dbGaP)

[gtsueng]

Source Name

Database of Genotypes and Phenotypes (dbGaP)

Source URL

https://www.ncbi.nlm.nih.gov/gap/

Source Description

The database of Genotypes and Phenotypes (dbGaP) was developed to archive and distribute the data and results from studies that have investigated the interaction of genotype and phenotype in Humans.

Source Abstract

Database of Genotypes and Phenotypes (dbGaP) is a NIH supported IID repository that includes multiomic data.

Source Genre

IID

Source Access

No access issue, account not needed for public access records. Study-level records may be treated as Dataset records the way SRA is handled. FTP for public accessible records: https://ftp.ncbi.nlm.nih.gov/dbgap/studies/

Example records

• A study record via their browser: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000001.v3.p1
• xml version from FTP: https://ftp.ncbi.nlm.nih.gov/dbgap/studies/phs000001/phs000001.v3.p1/GapExchange_phs000001.v3.p1.xml

Source Funding

NIH/NLM

Source Relevance

This resource was prioritized by the NIAID/ODSET team

Related WBS task

• [ ] Check here if this repository is funded by NIAID (https://github.com/NIAID-Data-Ecosystem/nde-roadmap/issues/11)
• [ ] Check here if this repository only has IID data (https://github.com/NIAID-Data-Ecosystem/nde-roadmap/issues/12)
• [X] Check here if this is a generalist repository with IID data (https://github.com/NIAID-Data-Ecosystem/nde-roadmap/issues/12)

For internal use only. Assignee, please select the status of this issue

• [ ] Not yet started
• [ ] In process
• [ ] Blocked
• [ ] Will not include

Status Description

No response

Source to-do list

• [X] License check- Can this source be included?
• [X] Class check- Does this source have the right class of research output for inclusions?
• [X] NIAID Review- Does NIAID approve of the inclusion of this source?
• [X] Data access check- Have data access issues been resolved?
• [X] Structured data check- Does this source have structured data?
• [ ] Mapping check- Has the properties from this source been mapped to the schema?
• [ ] Parser check- Has the parser been written?
• [ ] Parsed data check- Has a sanity check on the data obtained from this source been performed?
• [ ] Merge data- Has the crawler/plugin been successfully integrated with the system?
• [ ] Issues could not be resolved - Add as a single record via the DDE