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Programmatic Access to Ensembl Bacteria

Programmatic Access to Ensembl Bacteria. Microme Workshop, EBI 7 th 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_bacteria.html

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Programmatic Access to Ensembl Bacteria

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  1. Programmatic Access to Ensembl Bacteria Microme Workshop, EBI 7th October 2013 Dan Staines Ensembl Genomes

  2. 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/

  3. 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

  4. 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

  5. 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

  6. Ensembl Genomes REST API • Endpoints provide data in different formats e.g. • JSON • XML • FASTA • GFF3 • Fully documented including examples in different languages

  7. 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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