UStanford’s Protégé, Webprotege and NCBO BioPortal sites and applications for creating and posting new ontologies. (12/1/2010)

Protégé is an open source application that lets you read in your flat file excel ontology and converts it to an owl file. Once created, the owl file can then be uploaded into the NCBO BioPortal site (non-proprietary) to be viewed and used by others (public). Subsequently the created ontology can then be linked through openMDR to the i2b2 workbench.

Webprotege is an online ontology builder (convenient if you don’t already have a specified ontology). It is a private space for permissioned group members to view, edit and comment on an ontology in progress. Generally Webprotege would be used if the ontology is proprietary (e.g. disposition codes from clinical systems). If an existing ontology in flat file format is proprietary then it is best to use Protégé to create the owl file and then have the Stanford staff upload the file to your Webprotege space for further annotation.

There are plans for the Stanford crew to create a private BioPortal space, so that proprietary Protégé created owl files can be uploaded there and be used in i2b2 test cases (as mentioned above).