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

Next week, Eric Prud'hommeaux will present an "Overview of the linking open drug data task" at the RDF Symposium of the American Chemical Society on August 22 and 23 in Boston. The RDF Symposium is co-organized by HCLS member Egon Willighagen, who will also present "Linking the Resource Description Framework to Cheminformatics and Proteochemometrics".

A recent article about Data Sharing appeared in the New York Times! The article describes a project that led to biomarker discovery for Alzheimer's Disease, see Sharing of Data Leads to Progress on Alzheimer's. There has been some discussion about it on the HCLS mailing list.

At the Semantic Technology conference in San Francisco in June, in a session organized by Christine Golbreich and M. Scott Marshall, Applications of Biomedical Ontologies and Resources was presented by the trio HCLS/NCBO/NIF. M. Scott Marshall introduced ontologies from both an ontology building perspective (including the Foundational Model of Anatomy and the Translational Medicine Ontology) and an application perspective, while Mark Musen presented on the National Center for Biomedical Ontologies (NCBO) and Jeffrey Grethe presented on the NeuroInformatics Framework (NIF). Together, the presentations provided an overview of the range of general to specific applications of ontologies and Semantic Web. Note also that both NCBO and NIF provide a SPARQL endpoint to their resources: http://sparql.bioontology.org/webui/ and http://neurolex.org/wiki/SparqlEndPoint

Our recent HCLS gatherings went very well in both Boston and Raleigh, with both dinners and discussions. In Boston, we had a fun chat, with a group of people somewhat diminished in size due to the volcano effect. We talked about opportunities presented by the ARRA and increased attention to Electronic Health Records. EHR's have remained a topic of discussion and HCLS is now looking to create a demo that employs EHR scenarios. We are now actively seeking clinical data that could be used build a Semantic Web demo that is realistic to clinical practitioners. Offers of data or help of any kind will be welcomed.

Also, especially since C-SHALS, provenance has become a key theme of research. The BioRDF task force has been working on the best way to model the origins of microarray data (gene lists, experimental conditions, etc.). The Scientific Discourse task has been looking at how to model the origins of both statements made in discussion groups and computational experiments such as those stored at myExperiment.org and Research Objects. BioRDF and SciDisc have recently begun a joint teleconference to discuss provenance overlaps. Translational Medicine Ontology task force has also begun looking at provenance issues.

Great news! NCBO has made it possible for linked data projects to link directly to NCBO hosted ontologies via an *experimental* SPARQL endpoint. Point your browsers at http://sparql.bioontology.org:8080/webui/ and your programs at http://sparql.bioontology.org:8080/sparql/ . This is great news to HCLS because we can build demonstration applications that make direct use of these knowledge resources (includes all of OBO and more)! Although feature requests will be collected, please don't expect too much of this young but valuable resource at this early stage. It's a prototype!

The HCLS IG will be having two informal gatherings in April. The first gathering will be held at the Stata Center, MIT, on April 22, from 5pm. It is expected that many of the people who are attending Bio-IT World in Boston will be able to come along to this gathering. The second gathering will be held in Raleigh, NC, on April 26, from 6pm. It is expected that this meeting will largely be attended by participants at WWW2010. Please add your name to the wiki if you are able to attend either event. I'm looking forward to being able to see many of you in person soon.

The agenda for the WWW2010 workshop on The Future of the Web for Collaborative Science is now available. Due to the large number of high quality submissions some difficult decisions had to be made. In total 9 papers were accepted, covering diverse topics including image annotation, a dashboard for systems chemical biology, a linked data framework, policy mediation, and exchange and reuse of research objects. We look forward to seeing you in April in Raleigh, NC.

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.