W3C has announced a call for participation in a public W3C Workshop on Semantic Web for Life Sciences, to be held October 27-28, 2004 in Cambridge, Massachusetts, USA.
Position papers published in advance of the Workshop will form the basis of the discussion. Workshop attendees will discuss "how Semantic Web technologies such as RDF, OWL and the Life Sciences Identifier (LSID) help to manage modern life sciences research, enable disease understanding, and accelerate the development of therapies."
The workshop is free and open to the public, but will be limited to 100 participants; companies, government agencies, or individuals wishing to participate must submit a position paper by September 6, 2004.
The scope of the workshop includes technology considerations and application use cases including new features or applications of Resource Description Framework (RDF), the Web Ontology Language (OWL), or OMG Life Sciences Identifiers Specification (LSID). Workshop papers may also address technical implementation problems with RDF/OWL/LSID, or requirements unmet by these specifications, including Semantic Web Advanced Development questions that have arisen as a result of SW-LS implementation. Proposals regarding intellectual property issues arising from SW-LS (Semantic Web and Life Sciences) adoption will also be considered.
Technology papers are expected to "propose a new application of RDF/OWL/LSID in Life Sciences or identify a technical problem, explaining 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."
Motivation for the workshop is found in the "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."
The W3C Workshop hosts believe that "Semantic Web technologies such as RDF, OWL and 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... there is a very real need to reduce the barriers and costs associated with effective data integration, analysis and collaboration to improve health care."
The Workshop is being organized by the W3C Technology and Society Domain under the direction of Workshop Chairs are Andy Palmer and Daniel Weitzner. Program Chairs include Eric Miller (W3C Semantic Web Activity Lead), Eric Neumann (Aventis Pharmaceuticals), and John Wilbanks (W3C/I3C).
Goals of the W3C Life Sciences Workshop
"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 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...
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 Semantic Web technologies within the Life Sciences may include:
- Mapping biological networks — connecting genes, proteins, metabolites, pathways and functional activity
- Decision support systems — targets, leads, biomarkers
- Hypothesis description, capture, storage and tracking
- Hypothesis stratification and ranking through automated inference
- Web Services and the Three A's: Authentication, Access and Audit
- Lightweight, evolvable knowledge aggregation and management
- Distributed annotation systems
- Managing complexity across distributed data sources and e-collaboration among geographically distributed teams..." [from the CFP]
Expected Workshop Audience
"We expect several communities to contribute to the Life Sciences Workshop:
- Organizations that represent industry sectors on pharmaceutical development and discovery
- Organizations that represent industry sectors related to pharmaceutical development — such as software vendors and developers of content databases
- Organizations that represent industry sectors related to genomics, proteomics, metabolomics, and other emerging biotechnology platforms for data generation
- Technologists from academia and industry who are experimenting with Semantic Web, Web Services and related technologies
- Organizations that are developing standards that may use Semantic Web or Web Services technologies in Life Sciences applications
- Academic scholars and organizations that are actively publishing Life Sciences data and ontologies on the Web
- Organizations that represent industry sectors publishing peer-reviewed scientific articles
- Government regulators and policy makers and members of their staff from around the world [from the CFP]
About the W3C Forum on Application of Semantic Web to Life Sciences Informatics
W3C maintains a public list 'public-semweb-lifesci' to support discussions about the application of Semantic Web to life sciences informatics. The list "provides an open forum for scientists and informaticists to discuss issues and initiatives relevant to the exploration and use of the Semantic Web for the life sciences.
The forum is intended to identify opportunities for applying semantic-based approaches to life sciences, as well as advance the rapid design and development of reference models in several areas of life sciences informatics and knowledge exchange.
The 'public-semweb-lifesci' discussion list is a forum for detailed domain-related and technical discussions of all approaches to the use of classical logic and ontologies within the Life Science community for the representation of data, ontologies, intepretations, knowledge, biological systems, mechanisms of action, and inference rules..."
About the W3C Technology and Society Domain
The October 2004 W3C Workshop on Semantic Web for Life Sciences is being organized by the W3C Technology and Society Domain.
W3C's Technology and Society Domain aims to provide "technical building blocks that help address critical public policy issues on the Web. Working at the intersection of Web technology and public policy, the Technology and Society Domain's goal is to augment existing Web infrastructure with building blocks that assist in addressing critical public policy issues affecting the Web.
Technical building blocks available across the Web are a necessary, though not by themselves sufficient to ensure that the Web is able to respond to fundamental public policy challenges such as privacy, security, and intellectual property questions. Policy-aware Web technology is essential in order to help users preserve control over complex policy choices in the global, trans-jurisdictional legal environment of the Web. At the same time, technology design alone cannot and should not be offered as substitutes for basic public policy decisions that must be made in the relevant political fora around the world..."
Domain Activities include the Semantic Web, Privacy (Platform for Privacy Preferences — P3P), Security (XML Signature, XML Encryption, XML Key Management), Patent Policy and Standards, and Digital Rights Management.
- W3C Life Sciences Workshop Home Page
- W3C Life Sciences Workshop Call For Participation
- Web Links: Bio-Ontology Resources, Biotechnology Organizations, Biotechnology News, Biotechnology Resources, And Bioinformatics Databases, Meetings of Interest.
- Mail Archives for W3C public list 'email@example.com'
- Contact: Andy Palmer and Daniel Weitzner (Workshop Chairs).
- W3C news item
- W3C Semantic Web Interest Group. See also the RDF Interest Group 1999-2004
- W3C Technology and Society Domain
- W3C Workshops
- W3C Semantic Web resources
- W3C Semantic Web Activity Statement
- Resource Description Framework (RDF)
- Web Ontology Language (OWL)
- "OMG Life Sciences Identifiers Specification (LSID)" - Main reference page.
- Related (some items with dated references):
- Molecular Dynamics [Markup] Language (MoDL)
- NCBI Molecular Biology Data Model
- StarDOM - Transforming Scientific Data into XML
- Bioinformatic Sequence Markup Language (BSML)
- BIOpolymer Markup Language (BIOML)
- Gene Expression Markup Language (GEML)
- GeneX Gene Expression Markup Language (GeneXML)
- Genome Annotation Markup Elements (GAME)
- "OMG Life Sciences Identifiers Specification
- MicroArray and Gene Expression Markup Language (MAGE-ML)
- Microarray Markup Language (MAML)
- XML for Multiple Sequence Alignments (MSAML)
- Systems Biology Markup Language (SBML)
- OMG Gene Expression RFP
- Protein Extensible Markup Language (PROXIML)
- Taxonomic Markup Language
- XDELTA: XML Format for Taxonomic Information
- The Species Analyst Project
- Structured Product Labeling (SPL)