Category Archives: API and schemas

3-day Ensembl API workshop, 22-24 May 2013, Hinxton, UK

Posted on May 7, 2013 by Bert Overduin

In May the Ensembl team will again provide a 3-day Ensembl Perl API workshop on the Wellcome Trust Genome Campus in Hinxton, United Kingdom. Although this workshop is primarily meant for campus employees, external participants are also more than welcome … Continue reading →

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Database Port Changes

Posted on May 2, 2013 by Andy (Core)

You may have noticed that release 71 saw us make useastdb.ensembl.org accessible on port 3306 alongside the traditional Ensembl DB port 5306. This is in response to comments from users that many institutions and businesses do not allow access to … Continue reading →

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Variants in regulatory regions

Posted on January 24, 2013 by Anja (Variation)

From release 70 we store and display information on the type of consequence a variant has on overlapping regulatory regions (Ensembl regulatory features and Ensembl motif features) for human and mouse. Web display One of the major benefits of this is that we … Continue reading →

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Ensembl REST API – Ensembl Data from Any Language

Posted on September 27, 2012 by Andy (Core)

We are pleased to announce the beta release of our programming language agnostic REST API, for Release 68 data, at beta.rest.ensembl.org. Our initial release provides access to: Sequences (genomic, cDNA, CDS and protein) VEP (Variant Effect Predictor) Homologies Gene Trees … Continue reading →

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Importing VCF files

Posted on May 14, 2012 by Will (Variation)

Variant Call Format (VCF) has become the standard portable data format for variation data. Ensembl provides various tools for handling VCF files, such as the ability to upload and view VCF data on the genome browser, and the Variant Effect … Continue reading →

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Stable ID Changes in the Ensembl Core Schema

Posted on December 12, 2011 by Andy (Core)

Ensembl 65 brought a major change to our core data model; we decided to merge the stable id tables with their parent tables. The relationship between a stable id record and its parent record was 1:1 making these tables an … Continue reading →

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API reference gets a refresh

Posted on July 4, 2011 by Kieron (Vertebrate Genomics)

With some satisfaction, I am happy to announce the arrival of a new documentation resource with Release 63, intended to assist programmers in getting the most out of EnsEMBL. Using a custom filter and the open source tool Doxygen we … Continue reading →

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Changes to mysqlimport

Posted on September 28, 2010 by Anne (Webteam)

Owing to problems with BLOB data in some tables, we have had to change the way these tables are dumped, which in turn means a change to the mysqlimport parameters. It has been necessary to escape the table fields when … Continue reading →

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Go, go, go …. the new Ensembl ontology database and API

Posted on July 2, 2009 by Bert Overduin

Starting with release 55 of Ensembl we provide an ensembl_ontology database. It replaces the older ensembl_go database which used to be loaded straight from the public table dumps provided by the Gene Ontology group (and hence wasn’t really an Ensembl … Continue reading →

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Accessing the Ensembl data with Perl

Posted on November 17, 2008 by Albert (Compara)

Do you know a bit of Perl? Ensembl hosts an API (Application Programmers Interface) which uses Object-Oriented Perl to extract data from Ensembl databases. This API is public and can be used for people to programmatically access the data in … Continue reading →

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