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As I am working on ontology support in Bioclipse, I am increasingly interested in locally providing ontologies and linking them to namespaces. There are increasingly many ontologies around, and I want to support (at least recognize) as many life science related ontologies as possible.

Now, the XML world has the concept of an XML catalog linking SYSTEM and PUBLIC identifiers to schema. Similarly, I'd like to use something like that for linking namespaces to ontology specifications (TBOX), so that Bioclipse can use reasoning to validate ABOX input. Additionally, I'd very much like to annotate ontologies by category (e.g. http://dbpedia.org/page/Chemistry).

I'd can come up with something myself, but much rather use something existing. Is there an (OWL) ontology around that allows me to categorize ontologies into something like an catalog, which allows me to annotate entries too?

flag	asked Nov 10 at 12:01 Egon Willighagen 488●1●9

fgibson · Accepted Answer · 2009-11-10 17:23:24Z UTC

An ontology of ontologies has been mentioned for some time. Phil Lord made an attempt at Ontology Ontology[1] but I dont think this got further than this. As far as integrating and re-useing ontologies within your system. Have a look as ISA-creator [2] which makes calls to the Ontology Lookup Service [3] and BioPortal [4] in real time.

The current way users identify ontologies is at the term level. So they ask the question, " I need this term, what ontology is it in?", rather than, "what is the ontology that my term I need, might appear in", which I am assuming is the question you would ask if you had a category list of ontologies. The other reason it doesnt exist, is that many of the bio-ontologies are poor at defining their scope and often have feature creep, which would cause any classification of ontologies difficult to maintain.

My recommendation would be to try and re-use the OLS and BIO-Portal mechanisms for obtaining terms rather than to try and buidl a classification of them.

dullhunk · Answer 2 · 2009-11-10 23:24:30Z UTC

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Egon http://bioportal.bioontology.org/ ?

answered Nov 10 at 23:24

dullhunk
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Hi Duncan, I had a look around on the website, and it sure lists many bio-oriented ontologies, but I do not seem able to find the ontology they use for the database of ontologies... that's what I am really after: an ontology to make such a list. – Egon Willighagen Nov 11 at 6:25

Jiří Procházka · Answer 3 · 2009-11-10 13:16:56Z UTC

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Best would be to cook something up yourself, reusing what there already is.

Maybe you could use SKOS/

answered Nov 10 at 13:16

Jiří Procházka
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Is there an ontology to link to and annotate (OWL) ontologies?

3 Answers