Transcript Programmatic Access to Ensembl Bacteria

Programmatic Access to Ensembl
Bacteria
Microme Workshop, EBI
7th October 2013
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_ba
cteria.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_ba
cteria.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
• [email protected] mailing list