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Each organism has a genetic blueprint consisting of the linear strings of DNA bases and, as a result of the successes of the genome project, we now have available this blueprint for a large number of organisms. Every organism is perfectly capable of taking that one-dimensional string of information and converting it into a dynamic, living three-dimensional being. Unfortunately, we do not understand fundamentally how this is done. We cannot predict by simply examining the strings of DNA comprising a new organism what that organism would look like and we certainly can't take an existing blueprint and understand how changes in that blueprint affect an organism in the course of evolution or, on a shorter time-scale, in the course of a disease. - Lewis-Sigler Institute for Integrative Genomics, Princeton University
The World Wide Web Consortium is sponsoring a workshop to discuss emerging and future applications of Semantic Web for Life Sciences (SW-LS), and get feedback on what additional specification or coordination efforts might be necessary to support this area. Specifically, how can Semantic Web technologies such as the Resource Description Framework (RDF), Web Ontology Language (OWL) and domain-specific standards such as the Life Sciences Identifier (LSID) help to manage the inherent complexity of modern life sciences research, enable disease understanding, and accelerate the development of new therapies for disease?
We are inviting position papers that discuss technology and/or policy considerations for the future of SW-LS. The results of this workshop will inform W3C's decision making on future SW-LS-related efforts, stimulate discussions of new applications of Semantic Web that are possible based on the current RDF and OWL specifications, explore the Life Sciences Identifier (LSID) technology (an accepted OMG standard developed through the Interoperable Informatics Infrastructure Consortium) and facilitate coordination with organizations engaged in related efforts.
There is a growing realization that the complexity of life sciences research requires new approaches to understanding disease and developing new drugs. With pharmaceutical companies stretched across time zones and countries, data sources emerging from unconnected groups and a growing need to map all knowledge into molecular networks, the reductionist approach to scientific discovery increasingly strains to serve human health. The growing acceptance of a network biology perspective can be seen in recent actions by the U.S. government. The United States' National Institutes of Health (NIH) have named biological networks as an essential issue in making the translation from mapping the one-dimensional DNA to understanding multi-dimensional organisms and their diseases. Elias Zerhouni, Director of the NIH, stated in a recent interview, "Life self-assembled. We don't even know the degrees of complexity, the dimensions of the system. The problem is quite daunting...I don't think the data quality we have is necessarily sufficient [or that] the way we pose the questions is necessarily sufficient."
Semantic Web technologies such as RDF and OWL, with domain-specific standards like LSID, represent an evolvable, interoperable and fundamentally network-driven approach to information and knowledge aggregation. As such, they appear to represent an opportunity for developing solutions to some of the difficult technology issues in life sciences: disparate, constantly evolving data sources and ontologies (in both public and private settings) and above all the need to aggregate the data and ontologies into a resource that can be queried, securely, with a single authencation and result in an audit trail. Simply put, there is a very real need to reduce the barriers and costs associated with effective data integration, analysis and collaboration to improve health care.
Semantic Web technologies enable the rapid creation of semantically rich information networks that can represent underlying biological networks and assist the generation of hypotheses across the massive data sets being generated in both public life sciences efforts and pharmaceutical companies. There is an emerging and growing community of life sciences data resources and ontologies exposed in RDF and OWL, and a variety of RDF-enabled applications have been proposed. The Life Sciences Identifier (LSID) is an I3C and OMG Life Sciences Research (LSR) Uniform Resource Name (URN) specification. The LSID concept introduces a straightforward approach to naming and identifying data resources stored in multiple, distributed data stores in a manner that overcomes the limitations of naming schemes in use today. By defining a simple, common way to identify and access biologically significant data, whether that data is stored in files, relational databases, in applications, or in internal or public data sources, LSID provides a naming standard underpinning for wide-area science and interoperability.
Several ontologies for biology and chemistry, such as GeneOntology, BioPAX, and the National Library of Medicine's UMLS, offer the possibility to develop RDF models and strategies that can best support scientific discovery across both heterogenous databases and peer-reviewed literature. The use of these ontologies in conjunction with other Semantic Web approaches could greatly accelerate the practical use of web-based technologies throughout the science community. Applications of RDF, OWL, LSID and other such technologies within the Life Sciences may include:
The workshop will discuss technology considerations and application use cases including new features or applications of RDF/OWL and LSID, technical problems with RDF/OWL and LSID implementation, requirements unmet by RDF/OWL and LSID, and Semantic Web Advanced Development questions that have arisen as a result of SW-LS implementation. The Program Committee will also consider proposals regarding intellectual property issues arising from broad SW-LS adoption, though policy will not be the primary focus of the workshop.
To help prepare for discussions at the workshop and to continue discussions following the workshop, we invite discussions on the public-semweb-lifesci forum. To subscribe, send mail to public-semweb-lifesci-request@w3.org and put the word "subscribe" in the subject line.
W3C provides the public-semweb-lifesci forum as a home for detailed domain-related and technical discussions of all approaches to the use of classical logic, unique naming methods, and ontologies within the Life Science community. Specific topics include the representation and utilization of data, ontologies, interpretations, knowledge, biological systems, mechanisms of action, and inference rules. The life science list, through association with the Semantic Web Interest Group, also serves as a mechanism to provide input into W3C's Semantic Web activities, in particular relating the needs of the life sciences community to future Semantic Web standards
The workshop is expected to result in the following deliverables:
These will be published on the workshop home page.
We expect several communities to contribute to the workshop:
Position papers are the basis for the discussion at the workshop. These papers will also be made available to the public from the W3C Web site. We are inviting position papers that discuss either technology or application considerations (or both) for the future of SW-LS.
Technology papers should propose a new application of RDF/OWL or LSID in Life Sciences or identify a technical problem with RDF, RDF-S, OWL or LSID. They should explain how the new feature or application might be achieved technically, or how the technical problem might be addressed. New features proposed may enable RDF/OWL/LSID to function better in new application contexts such as knowledge aggregation, scientifically relevant search or pharmaceutical decision support. Papers may also propose features be added to further integrate RDF/OWL or LSID with other W3C standards under development (such as Web Services) and with technologies under development in other organizations.
Papers proposing new features or applications should also discuss the following: Can this new feature or application be implemented within the existing RDF/OWL and LSID framework? If so, is there any need to coordinate this? Would this new feature or application benefit from additions or changes to the RDF/OWL and LSID specifications?
All papers should be 1 to 5 pages, although they may link to longer versions or appendixes. Papers should indicate what, if any, work has already been done towards developing a new feature or application, and any companies or organizations tat are willing to commit resources towards this effort.
Position papers will be published on the public Web pages of the workshop, so position papers and slides of presentations must be available for public dissemination. Submitting a position paper comprises a default recognition of these terms for publication. Allowed formats are HTML/XHTML, PDF, or ASCII. Papers in any other formats will be returned with a request for correct formatting. Good examples of position papers can be seen in the QL'98 workshop.
The Program Committee may ask the authors of particularly salient position papers to explicitly present their position at the workshop to foster discussion. Presenters will also make the slides of the presentation available on the workshop Web home page.
Position papers must be submitted via email to public-swls-ws@w3.org no later than 15 September 2004.
Atul Butte (Children's Hospital Boston), Melissa Cline (Affymetrix), Brian Gilman (Panther Informatics), Carol Goble (Manchester/myGRID), Mike Jones (Novartis), Joanne Luciano (BioPathways), Sean Martin (IBM), Martin Merry (Hewlett-Packard), Forbes Dewey (CSBI/MIT), Jeff Pollock (Network Inference), Otto Ritter (Astra Zeneca), David States (University of Michigan), Susie Stephens (Oracle), Greg Tucker-Kellogg (Millenium Pharmaceuticals)
The workshop program will to run from 9 am to 6 pm on both days and features Tim Berners-Lee (Director, W3C) and Ken Buetow, Director of the National Cancer Institute's Center for Bioinformatics, as keynote speakers.
Infinity Pharmaceuticals, Inc. is an innovative cancer drug discovery company focused on discovering and developing therapeutics that target cancer cell survival utilizing Infinity’s novel small molecule chemistry platform.
Network Inference is the leading provider of standards-based, enterprise-ready, semantic technologies. Network Inference enterprise solutions offer Global 2000 organizations short-term payback through lower maintenance costs and project risk, and new integration and application capabilities, while providing a standards-driven pragmatic roadmap towards the model-driven Adaptive Enterprise. Network Inference’s flagship Cerebra Server™ and Construct™ visual modeler provide an enterprise-strength integration and business application environment on an SOA ready platform based on the W3C's OWL, RDF, XML, SOAP, and WSDL standards. Network Inference’s corporate offices include Carlsbad CA, Menlo Park CA, Boston MA, and Manchester UK. For more information, see http://www.networkinference.com.
The Workshop will be held at the Radisson Hotel on Memorial Drive in Cambridge, MA USA.
Radisson Cambridge
777 Memorial Drive
Cambridge MA 02139
(on the Charles River)
Telephone: 617-492-7777
Fax: 617-492-6038
Toll Free: 800-333-3333
The Radisson listed above is the featured hotel for the Workshop - please ask for the Semantic Web for Life Sciences room rate.
If you cannot get a room at the Radisson, trythe MIT Hotel Page for other accommodations in the area.
| Date | Event |
|---|---|
| 15 September 2004 | Deadline for position papers (1 to 5 pages in HTML format - send to public-swls-ws@w3.org) |
| 11 October 2004 | Program released |
| 15 October 2004 | Deadline for registration . |
| 27-28 October 2004 | W3C Workshop on Semantic Web for Life Sciences |
Over the period of ten weeks, this work will consume 30% of the time of W3C Team staff for committee work, 20% of the time of W3C Team staff to handle local organization, and 10% of the time of W3C Team staff for managing the workshop Web pages.
This effort is part of the W3C Technology and Society Domain.
Author:
John Wilbanks, W3C Fellow - I3CLast update $Date: 2005/11/28 16:16:32 $