Question: Are There Any Tools For Ontology Enrichment Analysis That Work With Any Ontology? (Not Just Gene Ontology)
9
gravatar for Pablacious
8.4 years ago by
Pablacious610
Cambridge, UK
Pablacious610 wrote:

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!

enrichment ontology R • 4.2k views
ADD COMMENTlink modified 7.0 years ago by Biostar ♦♦ 20 • written 8.4 years ago by Pablacious610

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

ADD REPLYlink written 8.4 years ago by Larry_Parnell16k
6
gravatar for Andrew Su
8.4 years ago by
Andrew Su4.8k
San Diego, CA
Andrew Su4.8k wrote:

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).

ADD COMMENTlink modified 9 months ago by RamRS27k • written 8.4 years ago by Andrew Su4.8k

Thanks Andrew, this looks promising.

ADD REPLYlink written 8.4 years ago by Pablacious610

+1 Ontologizer.

ADD REPLYlink written 8.4 years ago by Khader Shameer18k
0
gravatar for Leo Meerman
8.4 years ago by
Leo Meerman0 wrote:

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

ADD COMMENTlink written 8.4 years ago by Leo Meerman0

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

ADD REPLYlink written 8.4 years ago by Khader Shameer18k
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