Galaxy
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)