Semantic Web Health Care and Life Sciences (HCLS) Interest Group

The next HCLS F2F meeting is being held on November 2-3, so it's approaching rapidly. We have some excellent talks arranged. Don Doherty (Brainstage) will be giving an introduction to neuroscience, and presenting on informatics requirements. Mark Musen (Stanford) will be providing an overview of BioPortal. Peter Hendler (Kaiser Permanante) will be talking about the use of SNOMED and DL in EHRs. Helena Deus (U Texas MD Anderson Cancer Center) will speak on propagating permissions in biomedicine. We will also have Axel Polleres (DERI) presenting on the SPARQL WG, Yolanda Gil on the Provenance XG, and Eric Prud'hommeaux (W3C) on OWL2 WG, RDF2RDB WG and RIF WG. Scott Marshall (Leiden) will be giving the overview of the HCLS IG. There will also be task breakout sessions, discussions on strategic direction, outreach, collaboration, and funding.

The Semantic Web Health Care and Life Sciences Interest Group is pleased to announce the publishing of three Interest Group notes by the Scientific Discourse Task Force:

• Semantic Web Applications in Neuromedicine (SWAN) Ontology
• SIOC, SIOC Types and Health Care and Life Sciences
• SWAN/SIOC: Alignment Between the SWAN and SIOC Ontologies

These notes describe how one can use the Semantic Web to express and integrate scientific data from different domains and from heterogeneous services. It is hoped that they will inspire further contributions to the ongoing work of the Health Care and Life Sciences Interest Group and its Scientific Discourse Task Force, as well as inspire those in other domains to exploit the Semantic Web. On a related topic, the Interest Group holds a Workshop on Scientific Discourse next monday ISWC 2009

The W3C HCLS Interest Group has now finalized the agenda for the Workshop on Scientific Discourse at ISWC 2009. David Shotton (University of Oxford) has kindly agreed to give a keynote presentation on Enabling Semantic Publication and Integration of Scientific Information. There will be a panel on Scientific Communication in 2010 with panelists including Olivier Bodenreider (NLM), Matt Day (Nature), Anita de Waard (Elsevier), Maryann Martonne (UCSD), and Dietrich Rebholz-Schuhmann (EBI). The workshop has accepted nine peer reviewed papers covering topics such as the analysis of biomedical texts, ontologies for scientific discourse representation, and tools for sharing data, workflows and ontologies.

I'd like to congratulate the Linking Open Drug Data task within W3C's Health Care and Life Sciences Interest Group for winning the Triplification Challenge this year. Anja Jentzsch, Jun Zhao, Oktie Hassanzadeh, Kei-Hoi Cheung, Matthias Samwald and Bo Andersson did a tremendous amount of work to interlink life sciences data relating to traditional Chinese medicine, clinical trials, genes, diseases, drugs, and adverse drug reactions. In total, the data consisted of more than 8.4 million RDF triples and almost 390,000 links to external data sources. Congratulations again to everyone involved in the work!

The Health Care and Life Sciences Interest Group has had a workshop accepted at ISWC 2009 on Semantic Web Applications in Scientific Discourse.

Scientific research is becoming both increasingly interdisciplinary, and dependent for dissemination on the Web. Yet the form of the discourse has remained for the most part, a digital analog of the paper research article. This situation persists despite the emergence of Web 2.0 paradigms (blogs, wikis, online communities), application of Semantic Web technologies to problems in biomedicine, and the introduction of virtual research environments in certain areas. We will bring together experts in semantic technology, scientific informatics, virtual research environments, Web communities and scientific publishing to contribute to the development of new thinking on how scientific research can be communicated, characterized, annotated, searched and shared on the Web.

Details about the workshop including logistics, the deadline for paper submissions, and program committee members are available on the Web site for the workshop.

The W3C Semantic Web for Health Care and Life Sciences Interest Group recently had a very successful Face to Face meeting in Boston, U.S. Although a few of us were meeting F2F for the first time, we had worked together through teleconferences, irc, and e-mail. There were also a number of organizations represented, some of them for the first time, such as caBIG, Bio2RDF, NCBO, Mayo Clinic, and Ontotext, as well as a few organizations invited from BioIT World Expo to join us. Our two day agenda included talks by Maryann Martone and David de Roure, and can be seen here. Our sponsors were myExperiment and Elsevier Labs. All in all, it was good to be among friends and colleagues. The ideas and feedback that we gathered should result in renewed vigor among the task forces. Several other related events seem to show that Semantic Web is gaining mass: Shared Names meeting, Concept Web Alliance inaugural meeting, and the Semantic Web SIG at the PRISM Forum meeting.

Having grown to almost 100 participants and 6 active task forces, the HCLS IG will hold a Face to Face (F2F) meeting in the Stata Center in Boston on April 30 and May 1 (Thu and Fri), directly following the Bio-IT World Expo, as well as a Shared Names meeting that we helped to organize. We are excited to have Karen Skinner (NIH) and David De Roure (Southampton University/myExperiment) as invited speakers. We plan to take a close look at the opportunities for alignment and new activities within the HCLS IG. The latest demonstrations and prototype development have made participants aware of new possibilities for cooperation within the group. Participants are encouraged to add their names to the list of attendees on the F2F wiki page. Prospective members are requested to send e-mail to the co-chairs.

The HCLS IG gave a tutorial at the C-SHALS Conference last week. It was very well attended and consisted of participants from pharma, payers, health care organizations, technology companies, and academia.

The first half of the tutorial began with a primer on the Semantic Web that was delivered by Lee Feigenbaum. He did an excellent job of introducing the technology, and answering a broad range of good questions from the participants.

The second half of the tutorial began with Eric Prud'hommeaux (W3C) introducing HCLS. He highlighted that the mission of the group is to develop, advocate for, and support the use of Semantic Web technologies for biological science, translational medicine, and health care; and described the strong need for interoperability within these domains. He highlighted that almost 100 individuals are now participating in the interest group.

The tutorial then provided an overview of the activities being undertaken by the different tasks within HCLS. Vipul Kashyap (Cigna) described how the Clinical Observations Interoperability task built a demo that enables querying across electronic health records that are in different formats. John Madden (Duke) presented on work within the Terminology task to represent SNOMED within Semantic Web representations, and compared benefits of SKOS to OWL. Susie Stephens (Lilly) presented on making publicly available data sets about drugs available within the Linked Data cloud, which is ongoing work within the Linking Open Drug Data task. She also briefly introduced the new Pharma Ontology task which has the goal of creating a high-level, patient-centric ontology for translational medicine. Tim Clark (Harvard) represented the Scientific Discourse task and described their approach for integrating knowledge relating to hypotheses derived from literature and experiments using SWAN, SIOC, and myExperiment ontologies. The tutorial concluded with Kei Cheung (Yale) providing a description of the accomplishments on aTags and federated query within the BioRDF task.

Slides are available from the tutorial on the HCLS Wiki.