Welcome to ensembldb3 documentation!



ensembldb3 provides python 3 compatible bindings to the Ensembl MySQL databases. It also includes capabilities for administering these databases locally. Specifically, tools for downloading MySQL dumps, installing those locally and removing old releases.

See the EnsemblDb3 project page for the latest version of the code.


ensembldb3 began it’s existence in 2009 as cogent.db.ensembl, a part of Cogent3. With the port of Cogent3 to Python 3 (resulting in Cogent3), it was decided to split the Ensembl querying code out into it’s own project. This will make it easier to increase features and improve the project visibility.


We would greatly appreciate assistance in updating the project to PEP8, or anything else you think needs doing.

Please post a ticket, or comment on an existing one, indicating your intention so we can assist. Then it’s the usual “fork”, “pull request” dance.

If you discover a bug, especially something that worked in Cogent3 but not in ensembldb3, please post a ticket!

When posting a ticket, please provide a minimum working example to reproduce the issue. Also include the versions of the library and other tools (e.g. attach the result of $ pip freeze > libs.txt).


For now, please continue to cite the Cogent3 paper – Knight et al., 2007, Genome Biol, 8, R171.