FINAL AGENDA

27 October

9:00-9:15AM Introductions and Welcome - Danny Weitzner

9:15-10:00AM Keynote Address

Semantic Web for Life Sciences

Tim Berners-Lee - Director, World Wide Web Consortium

10:00-10:15AM Q&A

10:15-11:45AM Session I: Industry Perspectives On Semantic Web For Life Sciences

SPEAKERS:

Pharmaceutical R&D and the Role of Semantics in Information Management and Decision-Making, Otto Ritter - Associate Director, Bioinformatics, Astra Zeneca R&D

SCRIBE:

John Wilbanks

11:45-12:00PM Break

12:00-1:00PM Working Lunch (provided)

Luncheon Speakers:

Exploring Semantic Web Infrastructure for Life Science Knowledge-bases, Ian Wilson - University of Colorado

GoPubMed and Beyond: Rules and Reasoning for Ontology-Based Literature Search, Michael Schroeder - European Network of Excellence REWERSE

The Protege Ontology Editor, Natasha Noy - Stanford Medical Informatics

A KnowledgeBase Project for Alzheimer Disease Research, Tim Clark - Massachusetts General Hospital

1:00-2:30PM Session II: Scientific Publishing and Semantic Web

• What would a standard approach to mapping between multiple vocabularies look like?
• Where should Semantic Web intersect with text mining, annotations and literature distribution?
• What is the potential impact of distributed annotation?

MODERATOR:

Alan Aronson - Semantic Knowledge Representation Group, National Library of Medicine

SPEAKERS:

Urchin RSS / The Urchin/Kowari Project, Ben Lund - Nature Publishing Group / David Wood - Tucana Technologies

Semantic Web and Elsevier (no URI), Marc Krellenstein - Vice President, Search & Discovery Technology, Elsevier

Semantic Web for Data Interpretation & Integration: Lessons Learned from Scientific Publishing and the Distributed Annotation System, Steve Chervitz - Bioinformatics Engineer, Affymetrix

SCRIBE

Nada Hashmi

2:30-2:45PM Break

2:45-4:15 PM Session III: Triples and Ontologies

• What will it take to convert major public life sciences databases and ontologies into RDF/OWL?
• What mechanisms are required to connect terms in standard vocabularies to objects in experimental databases?
• What are the implications of evolving an existing ontology standard?

MODERATOR:

David States - Professor of Human Genetics, Director of Bioinformatics, University of Michigan School of Medicine

SPEAKERS:

UniProt in RDF Format: Use Cases and Open Issues, Eric Jain - Swiss Institute of Bioinformatics / UniProt

Data Integration, Gene Ontology, and the Mouse, Joel Richardson - Jackson Laboratories

The MGED Ontology, Liju Fan - KEVRIC (on behalf of the Microarray Gene Expression Data Society)

SCRIBE

Joanne Luciano

4:15-4:30PM Break

4:30-6:00 PM Session IV: Web Services and Semantic Web

• How do ontologies impact the utility of Web Services?
• How do Web Services imact the utility of ontologies?
• How does the combination of Web Services and ontologies impact the availability of resources to a wide life sciences community?

MODERATOR:

Arumani Marisanduram - Lead Architect, National Cancer Institute's caBIG

SPEAKERS:

The Semantic Web: Service Discovery and Provenance in myGrid, Chris Wroe/Phil Lord - University of Manchester

Accessing and Manipulating Ontologies Using Web Services, Oliver Dameron - Stanford Medical Informatics

Semantic MOBY, Gary Schiltz - National Center for Genome Resources

SCRIBE

John Wilbanks

28 October

9:00-9:15AM Introductions and Welcome - Danny Weitzner

9:15-10:00AM Keynote Address

The Cancer Bioinformatics Grid

Ken Buetow - Director, National Cancer Institute Center for Bioinformatics

10:00-10:15AM Q&A

10:15-11:45AM Session V: Life Science Identifiers - Use Cases, Future Directions

• What does it actually mean to identify a biological object such as "a gene"?
• How does LSID address structural elements of biological and chemical objects?
• What are the lessons learned from early implementations of LSID?

MODERATOR:

Ted Liefeld - Senior Software Architect, Cancer Genomics, Broad Institute (MIT)

SPEAKERS:

Object Identity and Life Science Research, Robert Robbins - VP Information Technology, Fred Hutchison Cancer Research Center

Fine-grained References into Binary Data and Data Virtualization Services, Jim Myers - Computational Sciences and Mathematics Division, Pacific Northwest National Laboratory

Semantic Layered Research Platform, Sean Martin - IBM

SCRIBE

Nada Hashmi

11:45-12:00PM Break

12:00-1:00PM Working Lunch (provided)

Luncheon Speakers

Semantic Web Technology in Support of Bioinformatics for Glycan Expression, Amit Sheth - University of Georgia and Semagix, Inc.

ExperiBase, C. Forbes Dewey - Professor of Mechanical Engineering / Bioengineering, MIT/CSBi

A Framework for Annotating High-Throughput Genome-wide Screens, Josh Moore

Semantic Web Technologies for Analysis of Transcriptome, Rose Dieng-Kuntz -INRIA, UR Sophia Antipolis Project ACACIA

1:00-2:30PM Session VI: Cheminformatics and the Semantic Web

• How can Semantic Web impact the problem of integrating and normalizing data from diverse assays of cheminformatic entities?
• What is the business impact of non-standard semantics in compound collection management?
• How will cheminformatic markup languages intersect with Semantic Web?

MODERATOR:

Susie Stephens - Prinicpal Product Manager, Oracle Life Sciences

SPEAKERS:

Chemical Annotations Using Semantic Web, Eric Neumann - Global Head of Knowledge Management, Aventis Pharmaceuticals

Babel-fish in Cheminformatics, Richard Scott - Technology Development Director, De Novo Pharmaceuticals

Inchl LSID, Henry Rzepa, Peter Murray-Rust

SCRIBE

Joanne Luciano

2:30-2:45PM Break

2:45-4:15PM Session VII: Semantic Aggregation, Integration and Inference

• What are the challenges for deploying very large datasets in Semantic Web formats?
• How do existing, widely deployed database technologies intersect with Semantic Web?
• How does Semantic Web enable rule-based inference?

MODERATOR:

Joanne Luciano - Harvard Medical School / BioPAX / Biopathways Consortium

SPEAKERS:

Data Integration: Some Enabling Steps, Andy Seaborne - Semantic Web Group/Bristol, Hewlett Packard

RDF in Oracle Network Data Model, Nicole Alexander - Oracle

Lab-to-Lab Connectivity and Semantics in the Life Sciences, Greg Meredith - Djinnisys

SCRIBE

Nada Hashmi

4:15-4:30PM Break

4:30-6:00PM Session VIII: Semantic Web For Life Sciences and W3C: Current Work, Next Steps

• How are current W3C efforts are being used in life sciences outside the W3C?
• What is W3C doing internally in life sciences?
• What would a charter for activity in the life sciences look like?

SPEAKERS:

TBD

SCRIBE

John Wilbanks