DbGaP FHIR API Docs
This is the documentation repository for the dbGaP FHIR API. (API base URL)
dbGaP is the Database of Genotypes and Phenotypes.
FHIR is HL7's REST API standard for electronic medical data.
Prerequisites
You should already have a basic understanding of FHIR - especially before working through the Notebooks. The FHIR Exercises repo from ODSS worked well for our team in the version they had when we used them. (However, by linking to them we do not imply that they are still good or that NCBI or the United States Federal Government endorses them. Use at your own risk. The same goes for all links on this page.)
For the Notebooks, you should also understand how Notebooks work and Pandas dataframes.
Maintenance
The team is focused on adding features and data. So we are not fixing issues in the documentation. This means it is outdated with no commitment to update it. Being optimists, we hope to update it someday, but we cannot say if that time will ever come.
Issues
We are aware that the current documentation is low quality and there is not enough of it. If you report a bug or request a feature, it will probably be overlooked and neglected.
The CSV download for the interactive concept mapping does not handle quoting correctly. You'll need to hand-edit it.
If you have a query that returns after 20 seconds with an error that looks like the below:
{
"error": {
"status": 500,
"message": "error forwarding request",
"api-key": "192.168.0.1"
}
}Then you probably hit the 20-second timeout imposed by our network infrastructure. Removing sorting, simplifying your query, or including fewer sub-queries in a batch can sometimes help.
Contact
If, despite knowing it is nearly equivalent to shouting into the void (see above), you still wish to contact the team, you can reach the technical lead via email: eric (d)o(t) moyer at nih.gov. Your email will then join the thousands of other unopened items languishing in his inbox Limbo.
