HCLSIG/Products

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Revision as of 16:55, 13 February 2013

Semantic Web for Health Care and Life Sciences Interest Group

Home | Outreach | Documents | Demonstrations | Translational Medicine perspective | High-level Use Cases

This list of HCLSIG products serves as an index for the community and attests to the productivity and impact of the group. Presentations are on their own page.

Summary of Deliverables

We would like to acknowledge the health care and life sciences community for meeting the goals of the last charter. Over the course of the charter, the IG has developed a set of data and demonstrators enabling life science and health care practitioners to consume and reason over domain data. Here are some highlights:

• Linked Open Drug Data (LODD) and winning the iTriplification Challenge 2009
• Light-weight CDISC – HL7 bridge for patient eligibility studies
• SPARQL Federation and RDF to SQL through SWObjects
• Semantic integration of LODD, patient data via the Translational Medicine Ontology (TMO)
• non-proliferation of ontologies and interoperability with other standards and conventions
• HCLS Knowledge Base

More follow in the sections below.

Recent/Upcoming Outreach Activities

• Open PHACTS/GEN2PHEN Workshop: Solving Bottlenecks in Data Sharing in the Life Sciences, Trish Whetzel, Michel Dumontier, M. Scott Marshall invited, Volendam, NL, Sept. 19-20, 2011
• Biohackathon 2011 Trish Whetzel, Michel Dumontier, Mark Wilkinson, M. Scott Marshall invited, Kyoto, Aug. 21-26, 2011
• Biomedical Informatics without Borders, Joint NCRI / NCI Conference Joanne Luciano, Charlie Mead, Vijay Bulusu, Eric Prud'hommeaux, Trish Whetzel, Michel Dumontier, M. Scott Marshall invited, London, June 13 -14, 2011
• EBI Semantic Web Industry Workshop Michel Dumontier, Matthias Samwald, and M. Scott Marshall invited to speak, May 16 - 18, 2011
• PRISME meeting M. Scott Marshall invited to present W3C perspective, Wellcome Trust, Hinxton, UK May 2011
• Japanese Semantic Web conference M. Scott Marshall gave HCLS Keynote, March 2011
• Best Practices in Personalized Medicine Workshop HCLS Presentation, March 2011
• Vancouver Bioinformatics Users Group M. Scott Marshall, HCLS presentation, March 2011
• C-SHALS 2011 HCLS members gave tutorials and presentations
• Semantic Web Applications and Tools for the Life Sciences (SWAT4LS) in Berlin Dec 2010
• Pharmaceutical Technology IT Summit M. Scott Marshall invited speaker, London, Sept 2010
• Semantic Technology Conference M. Scott Marshall co-organized HCLS session with Christine Golbreich June 2010
• The Future of the Web for Collaborative Science 2010
• HCLS Tutorial at CSHALS 2010
• Meeting Archive

HCLS Documents

• Health Care and Life Science (HCLS) Linked Data Guide W3C Note 2013
• Emerging practices for mapping and linking life sciences data using RDF — A case series, Journal of Web Semantics: Science, Services and Agents on the World Wide Web, 2012, Draft
• Translating standards into practice - One Semantic Web API for Gene Expression, Journal of Biomedical Informatics 2012 Mar 24
• Semantically enabling pharmacogenomic data for the realization of personalized medicine, Pharmacogenomics (2012) 13(2):201-12
• Ontology of Rhetorical Blocks (ORB) W3C Note 2011
• The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside
• Linked open drug data for pharmaceutical research and development Journal of Cheminformatics Thematic Series around the "ACS RDF 2010" meeting 2011
• Tutorial: Query Federation with SWObjects at SWAT4LS 2010
• Provenance of Microarray Experiments for a Better Understanding of Experiment Results
• Integrating findings of traditional medicine with modern pharmaceutical research: the potential role of linked open data Chinese Medicine Journal 2010
• Semantic Web Applications in Neuromedicine (SWAN) Ontology - W3C Note 2009
• SIOC, SIOC Types and Health Care and Life Sciences - W3C Note 2009
• SWAN/SIOC: Alignment Between the SWAN and SIOC Ontologies - W3C Note 2009
• A journey to Semantic Web query federation in the life sciences - BMC Bioinformatics Special Issue: "Semantic Web Applications and Tools for Life Sciences" 2009
• Linking Open Drug Data - iTriplification Challenge 2009
• Linked Data for Connecting Traditional Chinese Medicine and Western Medicine - Abstract for poster at DILS 2009
• Pharma Ontology: Creating a Patient-centric Ontology for Translational Medicine - Abstract for poster at ICBO 2009
• Enabling Tailored Therapeutics with Linked Data - LDOW Workshop, WWW 2009
• A Prototype Knowledge Base for the Life Sciences - W3C Note 2008
• Experiences with the Conversion of SenseLab Databases to RDF/OWL - W3C Note 2008

HCLS Demonstrations

• BioRDF Microarray RDF Demo
• Clinical Observations Interoperability Demonstration 2008 - 2012 (looking for new host)
• 7 Translational Membrane federated query
• HCLS Knowledge Base 2007 - 2012 (looking for new host)