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.
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)