Difference between revisions of "Galaxy"

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Erick Antezana, Aravind Venkatesan, C J Mungall, Vladimir Mironov, Martin Kuiper (2010) [http://www.biomedcentral.com/1471-2105/11/S12/S8 ONTO-ToolKit: enabling bio-ontology engineering via Galaxy], ''BMC Bioinformatics 11 (Suppl 12)''
 
Erick Antezana, Aravind Venkatesan, C J Mungall, Vladimir Mironov, Martin Kuiper (2010) [http://www.biomedcentral.com/1471-2105/11/S12/S8 ONTO-ToolKit: enabling bio-ontology engineering via Galaxy], ''BMC Bioinformatics 11 (Suppl 12)''
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[[Category:Galaxy]]

Revision as of 10:02, 27 November 2012

Current URL: http://galaxy.berkeleybop.org

The GO website lists >50 tools for doing GO-based analyses but these are not well integrated. AmiGO/GOOSE offers some functionality such as slimming, enrichment, data extraction but these are difficult to chain together. A simple integrated environment in which tools could be linked in workflows would be beneficial to the community.

The GO Galaxy instance is an environment to do all your analyses in one place

  • term enrichment
  • format conversion (e.g. obo to owl)
  • annotation file munging (e.g. mapping to slim)

Source

We maintain the GO/OBO galaxy tool configurations and helper scripts as a fork off of the main galaxy-dist repo in bitbucket.

Installing locally

1. install mercurial
2. Type:
  hg clone https://bitbucket.org/cmungall/galaxy-obo
3. Follow the instructions in README-galaxy-obo.txt
  more README-galaxy-obo.txt

Term Enrichment Format

See Is there a standard format for TE results?

  • TERF project on googlecode

Publications

Erick Antezana, Aravind Venkatesan, C J Mungall, Vladimir Mironov, Martin Kuiper (2010) ONTO-ToolKit: enabling bio-ontology engineering via Galaxy, BMC Bioinformatics 11 (Suppl 12)