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

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!

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.