ICBO 2014 Report, Day 1

ICBO has gotten off to a good start with a tutorial and three workshops. I mostly spent the day in the workshops, but the tutorial (OBO Tutorial: Getting Things Done with Open Biological and Biomedical Ontologies) introduces a number of interesting new tools, including Ontofox, Ontodog, and Ontorat. These complement the linked data ontology browsing tool Ontobee. It also included an introduction to RDF and SPARQL that looks like it was very helpful.

The <a href="http://icbo14.com/sessions/drug-drug-interaction-knowledge-representation-workshop/"Drug-Drug Interaction Knowledge Representation Workshop had a really eye-opening keynote about Drug-Drug Interactions (DDIs) by Dan Malone. He showed how there is little agreement among existing DDI authorities, because the standards of evidence are very low. According to him, most major drug interactions are supported by nothing more than case studies.  Many of these interactions persist in these resources mostly because of liability issues – if an interaction is pulled and a patient later suffers (or appears to suffer) from it, then the authorities might be held liable for withholding that information. He also showed some preliminary results that clinicians want to be presented with alternatives to and explanations of the DDIs they are warned about.

I also attended a morning workshop on developing a biobanking ontology using the Ontology for Biomedical Investigations. I think this sort of common vocabulary could have a similar benefit to what schema.org has made it easier to index structured information from web pages. Frank Manion also presented the start of an Informed Consent Ontology, which currently represents informed consent documents. Some notable thoughts and/or quotes:

  • “In data sharing, you’re sharing data with yourself in two years” – Dave Parrish
  • Ontology theory and development would be a really useful undergraduate elective course. – Penn Medicine Biobank team

I’ll check in again tomorrow!


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