- Course overview
- Search within this course
- What is the GWAS Catalog?
- How to access and navigate the GWAS Catalog
- How to search the GWAS Catalog: some guided examples
- Summary Statistics
- Summary
- Try it for yourself
- Quiz: Check your learning
- Your feedback
- Get help and support on the GWAS Catalog
- References
All materials are free cultural works licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, except where further licensing details are provided.
The GWAS Catalog API
While the web interface is human-friendly option for exploratory data access, you may need more flexibility, have many variants to query, or need the data to integrate with another resource. In that case, you may wish to use our API. This requires some programming skills, which we will not cover here, but give a brief overview and links to our documentation pages.
What is an API?
An Application Programming Interface is a utility that allows a machine to interface with a web-based resource, submitting requests and receiving responses. Responses are standardised and machine-readable in JSON format. To parse the returned data, you can use any programming language you like.
Requests are formulated as a URL:
Different arguments can be added to retrieve different data:
Available endpoints are:
By exploring the different endpoints, you can formulate a wide range of requests:
- Search for variants by gene, genomic region etc.
- Search for associations by PubMed ID etc.
- Search for associations by ancestry, array manufacturer etc
- Search iteratively
- Fetch the trait and p-value of all associations for multiple rsIDs
Summary statistics API
A separate API is available to query our summary statistics database. This allows access to all variants included in summary statistics, not only the top loci/lead SNPs.
Further reading
Before using either API, please read the documentation available here:
- GWAS Catalog REST API exercise: https://github.com/EBISPOT/GWAS_Catalog-workshop/blob/master/notebooks/gwas_cat_rest.ipynb
- GWAS Catalog API: https://www.ebi.ac.uk/gwas/rest/docs/api
- Summary stats API: https://www.ebi.ac.uk/gwas/summary-statistics/docs/
