Are There Any Tools For Ontology Enrichment Analysis That Work With Any Ontology? (Not Just Gene Ontology)

Question

[Pablacious]

Hi!

I'm looking for tools that would allow me to do enrichment analysis not just over the Gene Ontology, but on any ontology that you can provide on .obo (or owl, or any standard) format. I have used BiNGO in the past and done some adaptations on it to use it with ChEBI, but now I need to deal with more ontologies I was wondering whether there is something that just works with obo stored ontologies.

Does anyone know if the R package topGO could be used with other ontologies for instance?

Thanks!

[Larry_Parnell]

Good question. It would be interesting to try such on a disease ontology or MeSH headings, for example, as well as GO terms.

Answer 1

[Andrew Su]

From this previous question, someone suggests Ontologizer as a tool that will take arbitrary OBO files... The BiNGO Cytoscape plugin also says it will accept OBO files.

EDIT: Also, the folks at NCBO have also created an enrichment tool called RANSUM that is based on arbitrary ontologies (ref).

[Pablacious]

Thanks Andrew, this looks promising.

[Khader Shameer]

+1 Ontologizer.

Answer 2

[Leo Meerman]

Why not use Protege (Stanford Univ Open Source) ? RDF (RDF/XML) and OWL editions. Don't know obo environment. Succes

[Khader Shameer]

AFAIK, Protege is for creating ontologies not specifically for biological enrichment analysis.