Protege seems to be the most ubiquitous one. It can be found at: http://protege.stanford.edu/

Here is a list of biomedical ontology-related repositories and tools I assembled recently for a BIRN information page. It's far from exhaustive - especially given how much ontology-related work & tools takes place outside the biomedical domain - but it's pretty thorough regarding those ontologies and tools being used by bioinformaticists.

Biomedical ontology aggregation sites:
OBO Foundry:
http://www.obofoundry.org/
BioPortal
http://www.bioontology.org/ncbo/faces/in...
EBI Ontology Lookup Service:
http://www.ebi.ac.uk/ontology-lookup/
Berkeley Gene Ontology Download Matrix
http://www.berkeleybop.org/ontologies/
NCBC Scientific Ontology Working Group
http://www.berkeleybop.org/sowg/table.cg...

Though there is considerable overlap across these sites, each provides what I've found to be invaluable non-overlapping content and/or functionality.

Specific Ontologies:
Basic Formal Ontology (BFO)
http://www.ifomis.uni-saarland.de/bfo/ho...

OBO Relations Ontology (OBO-RO)
main:
http://obofoundry.org/ro/
OBO-RO-to-BFO bridge:
http://www.obofoundry.org/cgi-bin/detail...

OBO Phenotypic Quality Ontology (PATO)
main:
http://www.obofoundry.org/cgi-bin/detail...
PATO-to-BFO bridge:
http://obofoundry.org/cgi-bin/detail.cgi...

Ontology of Biomedical Investigation
http://www.obofoundry.org/cgi-bin/detail...

Ontology Tools:
Editing/Browsing/Searching:
Protege-OWL
http://protege.stanford.edu/overview/pro...
Protege-OWL v3.3 (OWL v1.0)
http://protege.stanford.edu/download/reg...
Protege-OWL v4+ (OWL v1.1+)
http://protege.stanford.edu/download/reg...
OBO-Edit
http://oboedit.org/
SWOOP
http://code.google.com/p/swoop/
GrOWL
http://ecoinformatics.uvm.edu/technologi...

Data Annotation with ontologies
Phenote
http://www.phenote.org/

Semantic Search Engines
Swoogle
http://swoogle.umbc.edu/

Community Semantic Web and Ontology Specifications
Resource Description Format (RDF)
http://www.w3.org/TR/rdf-primer/
Web Ontology Language (OWL)
v 1.0:
http://www.w3.org/TR/2004/REC-owl-featur...
v 1.1:
http://www.webont.org/owl/1.1/

Descriptive Logic DIG Reasoners ( reason against OWL ontologies)
Pellet
http://pellet.owldl.com/
FaCT++
http://owl.man.ac.uk/factplusplus/
Racer Pro
http://www.racer-systems.com/

RDF and/or OWL Query Frameworks
SPARQL
http://www.w3.org/TR/rdf-sparql-query/
NOTE: there are a variety of systems supporting queries against RDF or OWL data, in addition to building your own means to do so with the libraries listed below. A few such systems are:

Sesame:
http://sourceforge.net/projects/sesame/
(and the related Simile Project)
http://simile.mit.edu/
KAON:
http://kaon.semanticweb.org/
BOCA:
http://ibm-slrp.sourceforge.net/2006/11/...
Joseki:
http://www.joseki.org/
Kawari:
http://kowari.org/
Oracle+RDF
http://www.oracle.com/technology/tech/se...

Programming Environments/Libraries
RDF
Jena
http://jena.sourceforge.net/
Redland
http://librdf.org/
RDFLib
http://rdflib.net/store/
IBM Integrated Ontology Development Toolkit (IODT)
http://www.alphaworks.ibm.com/tech/seman...
OWL
OWL API
http://owl.man.ac.uk/api.shtml
Pellet
http://pellet.owldl.com/

Academic Journals:
Journal of Web Semantics:
http://www.elsevier.com/wps/find/journal...
Applied Ontology
http://www.iospress.nl/loadtop/load.php?...

Meetings:
ISMB Bioontology Satellite Meeting
http://bio-ontologies.man.ac.uk/
OWLED
http://owl-workshop.man.ac.uk/
Biocurator.org
http://www.biocurator.org/

Excellent listing, Bill! Should this content also migrate to a publicly editable wiki (so that the content can be dynamically updated and commented upon as it evolves)? Is it already listed anywhere else in such a fashion? If not, I would recommend a NITRC wiki. If we choose to cross-list this in a NITRC wiki, tho, I'd recommend waiting a little as I expect (hope!) that the phpwiki-based system will be upgraded shortly to a mediawiki-based product soon.

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

I forgot to mention there is one more ontology community-based Wiki/Forum that has been around for quite some time and does reference a lot of info. That is the Ontolog Wiki started quite a while ago by Peter Yim, now maintained by Peter, Kurt Conrad and Leo Oberst (the latter of MITRE). I find this Wiki quite dense, making it both hard to see the forest for the trees and difficult to find a particular set of trees.

Still - there is a wealth of information here, and an ongoing set of conference calls associate with this forum.

There is also the OntoWorld Wiki (http://ontoworld.org/wiki/Main_Page) associated with the very important annual International Semantic Web Conference (ISWC).

In both cases, these sites both include a breath of coverage that is in no way limited to the biomedical domain, while also tending to be focussed specifically on the project undertaken by the participants of those forums, as opposed to also casting an eye outward to keep track of all the other relevant projects and tools.

Cheers,
Bill