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Alan Ruttenberg

Alan Ruttenberg

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: the Ontology for Biomedical Investigations (OBI), the Basic Formal Ontology (BFO) that will form the upper level ontology for the OBO foundry, the Infectious Disease Ontology (IDO), the Program on Ontologies of Neural Structures (PONS), the Information Artifact Ontology (IAO), and BioPAX-OBO for representing molecular and cellular pathways. 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.

Selected publications

  1. Samwald M, Chen H, Ruttenberg A, Lim E, Marenco L, Miller P, Shepherd G, Cheung K. Semantic SenseLab: Implementing the vision of the Semantic Web in neuroscience Artificial Intelligence in Medicine 48 (1) , 21 – 28 (2010)
  2. Ruttenberg A, Rees J, Samwald M, Marshall M. Life sciences on the Semantic Web: the Neurocommons and beyond Briefings in Bioinformatics 10 , 193-204 2009
  3. Courtot M, Bug W, Gibson F, Lister AL, Malone J, Schober D, Brinkman RR, and Ruttenberg A. The OWL of Biomedical Investigations Proceedings of the Fifth OWLED Workshop on OWL: Experiences and Directions. CEUR Workshop Proceedings 432 2009
  4. Ruttenberg A, Clark T, Bug W, Samwald M, Bodenreider O, Chen H, Doherty D, Forsberg K, Gao Y, Kashyap V, Kinoshita J, Luciano J, Scott Marshall M, Ogbuji C, Rees J, Stephens S, Wong GT, Elizabeth Wu, Zaccagnini D, Hongsermeier T, Neumann E, Herman I, Cheung KH. Advancing translational research with the Semantic Web BMC Bioinformatics 8 2007
  5. Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, The OBI Consortium, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone S, Scheuermann RH, Shah N, Whetzel PL & Lewis S. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration Nature Biotechnology 25 , 1251 – 1255 2007
  6. Ruttenberg A, Rees J, Zucker J What BioPAX communicates and how to extend OWL to help it Proceedings of the OWLED*06 Workshop on OWL: Experiences and Directions CEUR-WS 216, 2006
  7. Pradines J, Rudolph-Owen L, Hunter J, Leroy P, Cary M, Coopersmith R, Dancik V, Eltsefon Y, Farutin V, Leroy C, Rees J, Rose D, Rowley S, Ruttenberg A, Wieghardt P, Sander C, Reich C. Detection of activity centers in cellular pathways using transcript profiling Journal of biopharmaceutical statistics Volume 14, Issue 3 December 2004 , pages 701 – 721
  8. Ficenec D, Osborne M, Pradines J, Richards D, Felciano R, Cho RJ, Chen RO, Liefeld T, Owen J, Ruttenberg A, Reich C, Horvath J, Clark T. Computational knowledge integration in biopharmaceutical research Briefings in Bioinformatics 2003 4(3):260-278;