Hi,
I currently work at Millennium Pharmaceuticals as a senior scientist in the computational biology group. For the last several years my groups focus has been on building pathway databases and tools that use these to analyze experimental data, particularly transcriptional profiling data. Our pathway database combines a mixture of licensed databases, such as Ingenuity Pathway Knowledge Base (http:// www.ingenuity.com/products/pathways_knowledge.html) and HPRD (http:// www.hprd.org/), public databases such as KEGG's LIGAND (http:// www.genome.jp/ligand/), as well some information our group has curated from the literature. A powerpoint touching on the sorts of things we do is available at http://www.massbio.org/attachments/ Pathways_Seminar-Ruttenberg_MBC_Oct_05.pdf
I've also built a number of specialized information resources, enabled by access to this structured knowledge, and write specialized queries in response to requests from our scientists.
My interest in the Semantic Web started with involvement developing BioPAX (http://biopaxwiki.org/) a pathway interchange format described as an OWL ontology. I've since learned a bunch about OWL and written some lisp tools (http://svn.mumble.net:8080/svn/lsw/) to work with OWL and SPARQL using the Pellet (http://www.mindswap.org/ 2003/pellet/) reasoner, and participate in a new series of workshops called OWL: Experiences and Directions. Last year's contribution was: Experience Using OWL DL for the Exchange of Biological Pathway Information (http://www.mindswap.org/2005/OWLWorkshop/sub37.pdf).
Before I working in biotech, I worked in a variety of areas of computation including knowledge representation, supercomputing, and multimedia authoring.
I'm participating in the BioRDF and Ontology task forces. -Alan
