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

W3C's HCLS group is going to be giving a tutorial at the upcoming Conference on Semantics in Healthcare and Life Sciences (CSHALS), which is being held on February 24-26, in Cambridge, MA. Lee Feigenbaum (Cambridge Semantics) is going to start off the tutorial by giving background information on all of the key Semantic Web standards. Scott Marshall (University of Amsterdam) is then going to give an introduction to the HCLS IG. This will be followed by Elgar Pichler (AstraZeneca), Vipul Kashyap (Cigna), and Tim Clark (Harvard) describing applications of the Semantic Web that they have developed within pharma, healthcare, and scientific publishing respectively. The tutorial will conclude with John Madden (Duke) and Kei Cheung (Yale) describing some of the most cutting edge uses of the technology within terminology and federated query. I'm looking forward to catching up with many people at the conference.

The HCLS IG had a good year in 2009, with lots of interaction, demonstration, and outreach. HCLS was involved in: C-SHALS Tutorial, Shared Names, Bio-IT World (in Boston and Hannover), Concept Web Alliance (CWA), PRISM Forum SIG, AMIA conferences, 7th Annual Pharma Technology IT Summit, the Data Integration for the Life Sciences (DILS) Workshop, and SWAT4LS.

We held two Face2Face meetings (Boston,MA and Santa Clara,CA), organized the Workshop on Scientific Discourse at ISWC2009, and helped organize the Semantic Web Applications and Tools for the Life Sciences (SWAT4LS) in Amsterdam - all well-received. HCLS produced some deliverables such as a Translational Medicine Ontology, articles in journals and proceedings, lots of Linked Open Drug Data, three W3C Interest Group notes, an approach to query federation, and presented a new version of the Clinical Observations Interoperability demo. We also helped initiate Shared Names, participated in the development of the Concept Web Alliance demo, and won the Triplification Challenge of 2009. In 2009, several of our members have joined together to write grant proposals in both Europe and the U.S. which could provide more support for some HCLS activities. BTW, another way to support those activities is to join us (see top of page for instructions)!

A development that I am excited about is the collaborative effort involving HCLS and CWA and the Swiss Institute of Bioinformatics (SIB) to create a SPARQL endpoint for Uniprot. Such an endpoint could make it possible to perform essential bioinformatics information retrieval without ever leaving the comfort of your SPARQL query interface.

I'm writing to you from Stanford, California where I am visiting the Musen Lab, home of the National Center for Biomedical Computing (NCBO), and the creators of BioPortal and Protégé. NCBO just put in for a renewal grant so keep your fingers crossed! In HCLS, we hope to see continued support for the very valuable knowledge resources that have been made available to biomedical researchers by NCBO. HCLS is looking at how to incorporate BioPortal services into our demonstrations.

Good news! The Translational Medicine Ontology task has had a poster accepted for presentation at the 2010 AMIA Summit on Translational Bioinformatics. The conference is being held in San Francisco, on March 10-12, 2010. Please come along to learn more about our work.

The HCLS IG is going to be having a workshop at WWW2010 on The Future of the Web for Collaborative Science. More details about the workshop, including information related to submitting a paper, is available on the group's wiki site.

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!