[ensembl-dev] Accessing sequence information without using the Perl API

Cook, Malcolm MEC at stowers.org
Wed Jan 3 22:08:30 GMT 2018

Hello Felix et al,

I used to mirror Ensembl locally and found the best way to "retrieve lists of available species and genome builds " is to take advantage of the fact that that the ensemble employs a consistent naming convention for the mysql databases allowing you to determine the species and builds by querying the The INFORMATION_SCHEMA SCHEMATA Table<https://dev.mysql.com/doc/refman/5.7/en/schemata-table.html>.

For other purposes, the main disadvantage of using direct SQL is that the schema might change and your query is not protected from such change.  Nominally, a published API should protect your source code from such a change.   In practice, such changes rarely happen, and limiting yourself to the Perl API you are probably trading one problem for another.  I found the schema to be well documented, quite stable, worth learning, and the most efficient way to access Ensembl, whether my local mirror, or remotely (at some point Ensembl introduced US mirrors making such querying even faster).  I don't know all the pertinent characteristics of your project, but I would probably go the direct access route in most cases.

Good luck,


From: Dev [mailto:dev-bounces at ensembl.org] On Behalf Of Felix Krueger
Sent: Wednesday, January 3, 2018 2:25 PM
To: dev at ensembl.org
Subject: [ensembl-dev] Accessing sequence information without using the Perl API

Dear all,

I am looking to use the Ensembl API to retrieve lists of available species and genome builds, as well as potentially large numbers of sequence information for sets of coordinates of various genomes. For this Java-based project we cannot use the Perl API, but could potentially use the REST or direct MySQL access. Would anyone be able to give me a pointer to what is likely the best way for me going forward?

Many thanks and a Happy New Year!
Kind regards,

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