Microme Workshop, EBI 7 th October 2013 Programmatic Access to Ensembl Bacteria Dan Staines Ensembl Genomes
Mar 28, 2015
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
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