OWL2 and Neurocommons @ KONA

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Date: March 18, 2009

Location: KONA

Chapter: New York

Session Type: Concepts - Research - New Standards
Session Level: Intermediate-Advanced

Speaker: Alan Ruttenberg


What OWL2 can and can not do

The second version of the Web Ontology Language, OWL2, is in the last call stage. As such it is a good time to reflect on what OWL and OWL 2 bring to technology of ontology development, as well as clarify what one should not expect from it. This talk will cover two topics: 1) New features of OWL2 and how they enable new computation and expression 2) Some known cases where OWL does not yet meet the needs of projects.

The Neurocommons: Common names and ontologies for open source knowledge integration on the Semantic Web

The Neurocommons prototype is a knowledge base built as a first step towards Web scale integration of scientific knowledge. With it, we are already able to demonstrate how Semantic Web technologies can be applied in biomedical research, for instance by helping scientists more easily answer questions about background science and connections between different research disciplines. The prototype serves as one test bed for exploring the technical, social, and legal processes that will be needed to achieve a future in which the results of research are placed seamlessly into the Web of science. The prototype is based on the Virtuoso open source triple store as an OWL and RDF repository, and comes with open access data. The knowledge base has been released with the express purpose of allowing others to replicate, experiment with, and extend it. We see this prototype as a step towards the Semantic Web for science.


Alan is the chair of the OWL Working Group specifying OWL 2, and a coordinating editor of the OBO Foundry. He is an active participant in W3C Semantic Web activities. In 2006 and 2007 he 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. Prior to joining Science Commons, Alan 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. His graduate work was at the MIT Media Lab in the Music and Cognition Group, and has an undergraduate degree in Physics and Mathematics from Brandeis University. Highlights of previous employment include stints at Thinking Machines and Interval Research.

His 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.

NOTICE The location has a $150 cleaning fee. I am aiming for at least ~15 people. If we don't get 15 registrations KONA will cover the difference. You can get free access to this event if you help me to organize the session. Please contact me directly at marco.neumann AT gmail.com.