Hi David,

I would say pieces of what's here you'll find on various sites, but you aren't likely to find it all gathered together like this - at least, I haven't.

It would be wonderful to have this on a Wiki, where others could contribute. In particular, I know there are other journals and meetings that have a specific biomedical ontology focus. AMIA, for instance, has had a very significant ontology contingent over the last decade. Mark Musen SMI group and the UK groups that have worked on clinical ontologies (e.g., GALEN) frequently participate in the AMIA meetings.

There are also a select few sites around the web where you'll find some of these resources aggregated together - along with others.

So - yes - I think that's an excellent suggestion. If you feel the NITRC Wiki - despite NITRC's neuroimaging focus - would be an appropriate place for this, that works for me. Possibly a more appropriate place for such a Wiki to reside would be either the NCBO Resources page (http://www.bioontology.org/resources.htm...) or the NCBC Scientific Ontology WG Wiki (http://na-mic.org/Wiki/index.php/SDIWG:_...).

The NCBC SOWG page is currently focussed on provided a listing of "gold standard" NCBC-approved ontologies to promote data sharing and systems interoperability across NCBCs.

Right now, NCBO almost exclusively focuses on tools they are being funded to create, distribute, and support (http://www.bioontology.org/tools.html), but I believe it would be helpful for them (the experts) to host a list with a wider scope than that, since there is so much more out there and in fairly widespread use.

Having said that, you were right to pick out Protege. It is THE most widespread ontology curation tool in use today. It's quite a remarkable feat they (in collaboration with the U. Manchester OWL group) were able to take a tool based on the highly complex Protege-Frames (OKBC) formalism and adapt it to OWL. Unfortunately, that did not come without a price, and as we've all learned the hard way, there are some "gotchas" one needs to be aware of when working with Protege-OWL. Protege v4 (built on OWL v1.1 from the ground up) is a completely re-engineered tool that eliminates many of these issues, but its still relatively new (about 1 year old) and doesn't have all the functionality of its bigger brother (Protege v3 - currently at v3.3.1).

One of the reasons I assembled this list is because I tend to use > 1 tool at a time when curating/developing ontologies. Frequently, I'll be running ontology generation/processing code in Netbeans coding against the Jena libraries, while also checking the results both in Protege and SWOOP, using an XML editor such as oXygen to check for certain anomologies in the RDF/XML representation, and running QA tests on the structure using the Pellet DIG reasoner.

Cheers,
Bill