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 - add a 1-2 second pause.
- Do not submit large long running requests - Fetch only what you need.
- Do not try to download 'all' the genome assembly data
- No short reads are available through EnteroBase. You will have to retrieve them from NCBI/EBI/DDBJ.
- Bulk downloading 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. There is a specific method for fetching genotyping schemes (MLST/wgMLST/cgMLST), please read Downloading schemes. If you want download large amounts of data, 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.