Ontologies - October 2008

Major work proceeded on the Ontology Registry and Repository, inspired by collaboration with the Stanford BioPortal team.

The MMI team met twice with Stanford University's Biomedical Informatics team, led by Dr. Mark Musen, and finalized an agreement to base the MMI Ontology Registry and Repository on the Stanford team's BioPortal. This product has undergone extensive development over multiple years under grants from the National Institute of Health, and is in use serving nearly a hundred ontologies for the biomedical community.

As part of this activity, the MMI team has had to analyze and select numerous strategies for dealing with ontologies and URIs. Challenges addressed included:

  • how to respond to both ontology inference engines (which want terms to dereference as RDF 'code') and browsers (which want terms to be resolved as HTML code)
  • whether to maintain URLs, URNs, or both as the primary unique identifer(s) for term resources
  • what metadata fields to collect, how to capture them from ontology providers, and where to maintain them
  • how to represent terms that do not change over multiple vocabulary versions
  • how to specify the most recent ontology or term, as opposed to an unversioned form of the ontology
  • under what circumstances one term should be called the sameAs another term
Many of these challenges have been settled, but some were not; it turns out most had not previously been addressed in this context.

Work continued on the Device Ontology; the team continues to identify and resolve challenges in approach and understanding. The ability of the MMI leads to keep this activity moving smoothly along is limited due to the effort preparing the Ontology Registry.

Posted November 7th, 2008 by graybeal
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