Programmatic Access to Ensembl Bacteria

Microme

Workshop, EBI

7
th

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_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

•
dev@ensembl.org

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