Friday, October 10, 2014

ICBO 2014 in Review

We wrapped up ICBO 2014 late yesterday afternoon with an "unconference" session, whereby attendees guided the topics and discussion of the final hour of the program prior to the closing session.

A couple notes:
1. Fred Trotter requests a "10 commandments" of ontology development.
2. Jim Overton says our tools for ontology development and curation are in terrible shape.  He received a round of applause, and it wasn't the applause that came at the end of his two minute spark talk.  It was instead widespread recognition of the problem.

Congratulations to Dr. Werner Ceusters, who won the best paper award for his paper and presentation on Pain Assessment Terminology in the NCBO BioPortal: Evaluation and Recommendations.  The award is sponsored by the National Center for Biomedical Ontology, and Dr. Ceusters will receive a $500 prize for the award.

Thank you once again to our sponsors.  In addition to NCBO, we thank NASA, Apelon, and DiBS (Data is Beautiful Solutions).

Thank you once again to our supporters.  We could not have had such a well-oiled, efficient, smoothly-running conference without Health 2.0 Houston.   We also received support from Houston Technology Center, and the School of Biomedical Informatics at UT Houston Health Science Center.

Sunday, October 5, 2014

The 5th International Conference on Biomedical Ontology kicks off tomorrow

I'm here in Houston with my co-organizer, Sivaram Arabandi, sitting outside on a beautiful day as we put the finishing touch on what promises to be an outstanding program for the 5th International Conference on Biomedical Ontology (ICBO14).

ICBO14 kicks off Monday, Oct 6th with workshops and tutorials.  We have four--yes four--workshops that deal with the ontology of drugs and drug interactions.  There are also workshops on the ontology of biobanking, the OBO Foundry, and definitions in ontologies.  We also have tutorials on the OBO Foundry and mapping relational databases to the Resource Description Framework.

Our keynote speakers are highly distinguished.  Dr. Warren Kibbe--currently the the director of the Center for Biomedical Informatics and Information Technology (CBIIT) at the National Cancer Institute (NCI)--will give a dinner keynote on October 8th entitled Supporting Precision Oncology using Ontologies.

Also giving a keynote address is John Wilbanks--Chief Commons Officer of Sage Bionetworks, who will talk about Ontologies and Open Collaboration.  John has also worked at Harvard’s Berkman Center for Internet & Society, the World Wide Web Consortium, the US House of Representatives, and Creative Commons. John is a past affiliate of MIT’s Project on Mathematics and Computation and also started a bioinformatics company called Incellico, which is now part of Selventa.

We have a great scientific program with full-length and early-career papers, posters, software demonstrations, invited updates, and panels.  We are especially looking forward to a panel on ontology and genomics with Christian Stoeckert, Bjorn Peters, and Jim Zheng of the Center for Computational Biomedicine at the School of Biomedical Informatics here in Houston.

If you are not already registered or planning to come, you're going to miss out on a fantastic program!

Tuesday, June 24, 2014

Age is not a quality

No matter how many times lazy ontologists represent age as a quality of a human, organism, or other material (or immaterial I suppose) entities, it just isn't true.  Age is not a quality.

An age is a measurement of elapsed time since a particular entity came into being.  Typically, it is the measurement of elapsed time in the frame of reference of the entity itself.  For example, muons have a lifetime of 2.2 microseconds as measured from the frame of reference of the muon itself.  However, as measured from the frame of reference of the surface of the Earth, the muons entering the atmosphere have a mean lifetime of approximately 18.5 microseconds.

Therefore, age should be a type of measurement in ontologies.

We also note that age is always with respect to the time the measurement is made.  For example, if John Doe was born on Jan 1, 1970 UTC, then if we measure his age on Jan 2, 1970 UTC, we will obtain that John is 24 hours old.  But if we measure his age on Jan 1, 1971, we will obtain that he is 365*24 =8,760 hours old (1970 not being a leap year).

So an age measurement should always be accompanied by an appropriate measurement date/time.