Ensembl website refactoring James Smith [email protected] Ensembl Web Team Project Leader
Microme Workshop, EBI 7 th October 2013 Programmatic Access to Ensembl Bacteria Dan Staines Ensembl...
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Transcript of Microme Workshop, EBI 7 th October 2013 Programmatic Access to Ensembl Bacteria Dan Staines Ensembl...
![Page 1: Microme Workshop, EBI 7 th October 2013 Programmatic Access to Ensembl Bacteria Dan Staines Ensembl Genomes.](https://reader036.fdocuments.in/reader036/viewer/2022081602/5516c2f4550346a25b8b6168/html5/thumbnails/1.jpg)
Microme Workshop, EBI
7th October 2013
Programmatic Access to Ensembl Bacteria
Dan Staines
Ensembl Genomes
![Page 2: Microme Workshop, EBI 7 th October 2013 Programmatic Access to Ensembl Bacteria Dan Staines Ensembl Genomes.](https://reader036.fdocuments.in/reader036/viewer/2022081602/5516c2f4550346a25b8b6168/html5/thumbnails/2.jpg)
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/
![Page 3: Microme Workshop, EBI 7 th October 2013 Programmatic Access to Ensembl Bacteria Dan Staines Ensembl Genomes.](https://reader036.fdocuments.in/reader036/viewer/2022081602/5516c2f4550346a25b8b6168/html5/thumbnails/3.jpg)
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
![Page 4: Microme Workshop, EBI 7 th October 2013 Programmatic Access to Ensembl Bacteria Dan Staines Ensembl Genomes.](https://reader036.fdocuments.in/reader036/viewer/2022081602/5516c2f4550346a25b8b6168/html5/thumbnails/4.jpg)
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
![Page 5: Microme Workshop, EBI 7 th October 2013 Programmatic Access to Ensembl Bacteria Dan Staines Ensembl Genomes.](https://reader036.fdocuments.in/reader036/viewer/2022081602/5516c2f4550346a25b8b6168/html5/thumbnails/5.jpg)
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
![Page 6: Microme Workshop, EBI 7 th October 2013 Programmatic Access to Ensembl Bacteria Dan Staines Ensembl Genomes.](https://reader036.fdocuments.in/reader036/viewer/2022081602/5516c2f4550346a25b8b6168/html5/thumbnails/6.jpg)
Ensembl Genomes REST API
• Endpoints provide data in different formats e.g.
• JSON
• XML
• FASTA
• GFF3
• Fully documented including examples in different languages
![Page 7: Microme Workshop, EBI 7 th October 2013 Programmatic Access to Ensembl Bacteria Dan Staines Ensembl Genomes.](https://reader036.fdocuments.in/reader036/viewer/2022081602/5516c2f4550346a25b8b6168/html5/thumbnails/7.jpg)
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
• [email protected] mailing list