Prior to joining Science Commons, I worked at Millennium Pharmaceuticals as a senior scientist in the computational biology group for about 9 years. For the latter several years my group’s focus was on building a pathway database and tools, including PARIS, that use it to analyze experimental data, particularly transcriptional profiling data. Our pathway database combined a mixture of licensed databases, such as Ingenuity Pathway Knowledge Base and HPRD, public databases such as KEGG’s LIGAND, as well some information our group has curated from the literature. A powerpoint touching on the sorts of things we worked on is available here.
My graduate work was at the MIT Media Lab in the Music and Cognition Group, and I’ve an undergraduate degree in Physics and Mathematics from Brandeis University. Highlights of previous employment include stints at Thinking Machines and Interval Research.
My interest lies in structuring and using biological and clinical knowledge to answer questions and computationally interpret experimental data. I’m currently involved in a number of open biomedical ontology efforts, including: BioPAX-OBO for representing molecular and cellular pathways, the Ontology for Biomedical Investigations (OBI), and the Basic Formal Ontology (BFO) that will form the upper level ontology for the OBO foundry. These interests and efforts come together in my project at Science Commons - the Neurocommons, a large scale Semantic Web knowledge base of biological information aimed at supporting, initially, the neurosciences.
I’m an active participant in W3C Semantic Web activities. In 2006 and 2007 I was a member of the Health Care Life Sciences Interest Group, and early work on the Neurocommons became the core of the prototype life sciences knowledge base that the group has documented. I’m a chair of the OWL Working Group specifying OWL 2, and a coordinating editor of the OBO Foundry. For more information about what I’m up to, google me, or drop me a note.
