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Accessing Ensembl Bacteria: Programmatic Interfaces Workshop Overview

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Join us for a comprehensive workshop on Ensembl Bacteria programmatic access. Learn about the Perl API and REST services, which provide a mature interface to genomic data, features, and annotations. Explore tools for finding genomes by name patterns, INSDC accession numbers, and taxonomy IDs. This workshop will cover accessing genomic sequences, features, and cross-references with plenty of examples provided. Gain insights into Ensembl resources and how to efficiently utilize the API for your research projects.

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Accessing Ensembl Bacteria: Programmatic Interfaces Workshop Overview

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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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