Top level links:
- Main top level page for all documentation
- EnteroBase Features
- Registering on EnteroBase and logging in
- Using the API
- About the underlying pipelines and other internals
- How schemes in EnteroBase work
About the API
- Getting started with the Enterobase API
- Automatic renewal of API tokens
- Understanding the API structure
- Downloading assembles
- Downloading schemes
- Searching strain data
- Searching ST data
- API Reference
API Usage notes
- API requests need to authenticated with a valid API Token.
- The API exists to be used; if you have suggestions for how to make it more useful for you, let us know.
- Please be responsible, do not flood the server with requests. We have now applied rate limiting (3 requests/second) on our end. If you exceed this you will get a 503 response instead of the data you requested. This does not apply to static resources (http://enterobase.warwick.ac.uk/schemes/).
- Do not submit large long running requests - Fetch only what you need.
- Do not try to download 'all' the genome assembly data
- Do not try to download 'all' genotyping data (MLST, cgMLST etc.) through the main API. Please use the static resources (http://enterobase.warwick.ac.uk/schemes/)
- No short reads are available through EnteroBase. You will have to retrieve them from NCBI/EBI/DDBJ.
- Bulk download of rMLST allele sequences and profiles is NOT permitted through this service.
- People who abuse the system, first offense: will be warned, second offense: their API access will be revoked, third offense: Banned from EnteroBase.
The API is designed for rapid live updates of small amounts of data. It is NOT designed large scale dumps of the entire database. Consider that there are > 80,000 Salmonella genomes in EnteroBase (about 1TB); downloading these through the main REST API would be painfully slow and would hurt the service for everyone.
This also applies to fetching genotyping schemes (MLST/wgMLST/cgMLST). wgMLST for Salmonella is now over 22 Gigabytes in size. It will take you over 10 hours to fetch it locus by locus through the API. Please DO NOT DO IT.
There is a specific workflow for downloading genotyping schemes, please read Downloading schemes. If you want download large amounts of data (or you want to set up regular synchronization between you and EnteroBase) please contact me email@example.com
3rd Party acknowledgements
If you use data generated by 3rd party tools in EnteroBase, please cite both EnteroBase and the paper describing the specific tool.