Semantic Web Applications and Tools for Life Sciences (SWAT4LS Workshop in Edinburgh 2013)

5 Jan 2014
Semantic Web Applications and Tools for Life Sciences  (SWAT4LS Workshop in Edinburgh 2013)

On December 9-12, 2013, the 6th International Workshop on Semantic Web Applications and Tools for Life Sciences (SWAT4LS 2013) took place in Edinburgh at the Edinburgh University Informatics Forum (Tutorials and Hackathon) and the Royal Society of Edinburgh (Workshop).

SWAT4LS is an international workshop series set up to meet and to present high-quality research results and relevant demonstrations, applications and tutorials from all fields of Semantic Web technologies in the Life Sciences.

The objective of the SWAT4LS workshop is to provide a forum dedicated to the dissemination of original research, the discussion of practical insights, and the reporting of relevant experience relating to the adoption of Web-based information systems and Semantic technologies in biomedical informatics and computational biology.

The workshop is also aimed at providing a forum to exchange ideas, for example, through poster papers and demo papers.

The topics covered by SWAT4LS are relevant to a number of European projects including: EURECA, INTEGRATE, p-medicine, EHR4CR, Linked2Safety, Euregional Computer Assisted Theragnostics project (EuroCAT), eTRIKS, PhUSE, SALUS, OpenPHACTS, Granatum – think tank for biomedical progress, SemanticHealthNet, IT Future of Medicine, as well as U.S. initiatives such as the NCBO (Nation Center for Biomedical Ontologies), Neuroscience Information Framework (NIF), Indivo, Dossia, CTS2, I2B2, SHRINE, Health Ontology Mapper, and SMART.

More information on such related projects is available on the Clinical Observations Interoperability wiki page of the W3C Semantic Web Health Care and Life Sciences (HCLS) Interest Group. EURECA held a Technical Meeting following the SWAT4LS Workshop, which was hosted by Heriot-Watt University.

The call for papers solicited research contributions in eHealth, biomedical and clinical informatics, systems biology, computational biology, drug discovery, bioinformatics and biocomputing. The call for contributions attracted 47 submissions from around the globe. The technical program shows a carefully selected presentation of research and development in 13 full papers, 1 short paper, 6 demos and 11 posters. These were complemented by 5 tutorials and 3 keynote talks provided by:

• David A. Kerr, Director, Watson for Healthcare, IBM Corporation
IBM Watson: Improving care for complex diseases
• Kerstin Forsberg, Astra Zeneca, Sweden
"Pushing back" — standards and standard organizations in a Semantic Web enabled world
• Frank Van Harmelen, VU University, Amsterdam
SWAT4CC: Semantic Web Applications and Tools for Clinical Care

• Alasdair J G Gray and Andrea Splendiani
The (Hitch-)hackers Guide to the Semantic Web
• James Malone, Simon Jupp, Marco Brandizi, Sarala Wimalaratne
RDF linked data and at the European Bioinformatics Institute
• Charlie Mead and Eric Prud’hommeaux
Applying Semantic Web Technologies in Clinical Care and Clinical Research: A SWOT (Strength, Weaknesses, Opportunities, and Threats) Perspective
• Pedro Lopes
The COEUS Platform
• Trish Whetzel
The Neuroscience Information Framework (NIF)

The speakers, a few tutorial givers, and a professor specialized in medical applications of Semantic Web were interviewed by ecancer. The interviews can be viewed at the ecancer Conferences web page for the SWAT4LS Workshop.

To place emphasis on the practical use of Semantic Web technologies in Life Sciences, SWAT4LS 2013 included a two day Hackathon. Data sets provided and experimented with during the Hackathon included artificial patient data for breast cancer clinical trials, de-identified patient data from the VATE project, adverse event data, pathways from Wikipathways, the linked data API from Open PHACTS and data from the EBI (European Bioinformatics Institute) RDF Platform. EBI also announced the RDFApp Challenge during the Hackathon. Institutes and projects providing data and SPARQL access to triple stores included EBI, VU Amsterdam, MAASTRO Clinic, University of Maastricht, Data2Semantics (COMMIT project), DisGeNET project, Mayo Clinic, and Open PHACTS (EU IMI project). The results of several activities were presented at the end of the first day and most are documented at Activities included creating dataset descriptions in RDF based on a W3C Note from the HCLS interest group, validators for RDF data, dynamic translation from one data schema to another, access control for SPARQL endpoints, EBI-WikiPathways-Disgenet integration, and an exploration of cancer therapy drugs extracted from NCI Thesaurus, and molecular targets, interactions, and pathways contained in EBI RDF resources. 

The workshop was a great success with more than 30 people attending the tutorials and hackathon, and over 70 attendees at the workshop. Proceedings of the workshop have been made available on