Programmatic Access to Ensembl Bacteria

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13 Δεκ 2013 (πριν από 3 χρόνια και 7 μήνες)

73 εμφανίσεις

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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