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
mailing list
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