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Introduction: Alan Ruttenberg

From: Alan Ruttenberg <alanruttenberg@gmail.com>
Date: Sun, 19 Mar 2006 15:13:22 -0500
Message-Id: <5F3E7241-CE1C-4705-B806-EB6ACB48952A@gmail.com>
To: public-semweb-lifesci@w3.org


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/ 

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.

Received on Sunday, 19 March 2006 20:13:33 UTC

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