Microme Workshop, EBI

7th October 2013

Programmatic Access to Ensembl Bacteria

Dan Staines

Ensembl Genomes

Programmatic Interfaces

• Ensembl Perl API

• http://bacteria.ensembl.org/info/docs/api/index.html

• http://bacteria.ensembl.org/info/data/accessing_ensembl_bacteria.html

• Ensembl Genomes REST service

• http://beta.rest.ensemblgenomes.org/

Ensembl Perl API

• Ensembl API

• Mature, fully featured Perl API for Ensembl resources

• Provides access to:

• Genomic sequence

• Genome features e.g. genes, translations

• Annotation e.g. cross-references

• http://bacteria.ensembl.org/info/docs/api/index.html

Ensembl Genomes Perl API

• Ensembl Genomes Perl API

• Supplementary to Ensembl API

• Provides additional tools for finding Ensembl Bacteria genomes:

• Find genomes by name pattern

• Find genomes by INSDC accession

• Find genomes by taxonomy ID

• http://bacteria.ensembl.org/info/data/accessing_ensembl_bacteria.html

Ensembl Genomes REST API

• Language independent programmatic interface to Ensembl resources

• http://beta.rest.ensemblgenomes.org

• Endpoints provide access to wide variety of data e.g.

• Sequences

• Features

• Cross-references

Ensembl Genomes REST API

• Endpoints provide data in different formats e.g.

• JSON

• XML

• FASTA

• GFF3

• Fully documented including examples in different languages

Resources

• http://beta.rest.ensemblgenomes.org

• http://bacteria.ensembl.org/info/docs/api/index.html

• http://bacteria.ensembl.org/info/data/accessing_ensembl_bacteria.html

• dev@ensembl.org mailing list