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)

Using GO Galaxy

Basic Term Enrichment

First upload your gene set. Select "Get data > upload file".
Bring in the latest version of GO into your instance. Select "OBO/OWL Tools" and "fetch ontology". Type "GO" in the box.
1. TIP: when the ontology come in click on "attributes" (the pen symbol) and rename this "GO"
Bring in the latest version of GO into your instance. Select "Annotation > Fetch associations"
Select "Term enrichment / GO termfinder"
1. Enter the number of background genes in the genome, or an estimate
2. Make sure your uploaded genes go into the "genes" selection
3. Make sure GO and your GAF go into the respective fields
4. Execute

the results here is a human-readable report file

Term Enrichment using Ontologizer

Follow the steps above, with the additional steps or modification

Upload a population gene set.
1. If you wish to consider all annotated genes, use "Text manipulation / cut" to select col3 from your GAF
Select "Term enrichment / ontologizer"
1. There are a variety of methods - consult the ontologizer site for details. try Parent-Child and Bonferoni as default
2. Execute

Note that this produces two outputs - a tabular file that can be processed further and a visual display with enriched terms highlighted

Map2Slim

Mapping an annotation file to a slim (ontology subset) is a common operation

Load an ontology (e.g. GO) and a GAF file - follow the steps above
Select "Annotation > map2slim"
Enter the name of your slim. This must be declared in the ontology file.
Execute

The header of the processed GAF states that this is a mapped GAF, and tells you how many terms were mapped.

Note that the result is a valid GAF file and can be used anywhere a GAF can be used, including Term Enrichment, above

Map2Slim, custom

This is similar to the above step, except instead of a pre-defined slim in the GO, we will generate our own set of IDs and use that

Open "GOtools > AmiGO"
Select the "Ontology" tab
Open "source" and select "biological_process"
Type "metabolic process" in the filter box to start your search
Open isa/partof/regulates and click "+" next to "metabolic process" (should be ranked around 2nd)
In "found entires" click "download to galaxy" (if not present, click to download to hard drive, save, and upload in galaxy)
In galaxy, select "Annotation > map2slim, idlist"
1. Select the file you uploaded
2. Follow the steps for map2slim above

The result will be a GAF that is mapped to your terms

Converting between OBO and OWL

Bring in the latest version of the ontology into your instance. Select "OBO/OWL Tools" and "fetch ontology". Type the ontology ID space (e.g. MP) in the box.
Select "OBO/OWL Tools > obo2owl"
Execute

You can perform the reverse translation easily using owl2obo

Mapping identifiers

Load in a set of identifiers. E.g UniProt ACCs
Select "Annotation > ID map"

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)