Enterobase API Usage¶
Please see the Enterobase Terms and Conditions.
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 > 400,000 `Salmonella` genomes in EnteroBase (about 4TB); downloading these through the main REST API would be painfully slow and would hurt the service for everyone.
If you simply wish to download assemblies this can be done efficiently for 1000s of assemblies by using the GUI as described in Downloading assemblies If you would like to discuss assembly downloads in more detail please contact us (firstname.lastname@example.org)
Download of scheme information without using the API, including bulk transfer using ftp is described here: Downloading schemes from the website There is a specific method for fetching genotyping schemes (MLST/wgMLST/cgMLST), please read Downloading EnteroBase genotyping schemes through the API.
If you wish to use the API please contact us, explaining the purpose for which you wish to use the API (email@example.com)
- 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 read data 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.
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.