Galaxy

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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. Galaxy provides an environment for doing this

The GO Galaxy instance is a place 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)