Wednesday, April 2, 2008

Tick Tock

I've just returned from watching my second PhD defense in as many weeks. The first one was my younger sister's, and this one was a good friend of mine who started at UBC at the same time as me. I'm reminded of the time in my mid twenties when friends started getting married and disappearing, one by one. The obvious response is to wonder, "when will I be next?". Well it looks like it will be some time yet for me; however, I think I had a little bit of a conceptual breakthrough the other day that may help straighten my path a bit.

I've spent a bit more than half of the past year working with a professor from the library and information sciences on ways to generate useful comparisons of different "types" of information organization system. Throughout this collaboration we've struggled to both communicate with one another and write collaboratively because of the vastly different training and work practices of the social sciences versus the biological sciences.  The realization I had was that his concern is completely to do with information systems at the level of the Type - social tagging, semantic web, subject indexing, and so on, while my concern should really be with information systems at the level of the Instance - Connotea, the Gene Ontology, MEDLINE..   I think this is really the mark that distinguishes bioinformatics from information science,  at its heart it is a completely applied science.  I hope that keeping that up front in my mind will help me keep on track going forward.

For this particular project, now 4 months overdue, I'm now planning to change from building a general purpose framework for defining axes of similarity of semantic indexing systems to conducting a straighforward comparison of Pubmed and Connotea.  This comparison will be specifically designed only to identify ways that the data from Connotea might be used to enhance user's experiences with Pubmed.  I think this will make for more definable goals and easier justifications for the work though I will be using some of the more generic code and concepts we came up with along the way.  
In any case, well done Obi and Erin!