Exploring the Semantic Web and its relevance to clinical and life sciences - BioMed Central blog

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http://blogs.biomedcentral.com/bmcblog/2013/01/04/exploring-the-semantic-web-and-its-relevance-to-clinical-and-life-sciences/

Exploring the Semantic Web and its relevance to clinical and life sciences

[http://blogs.biomedcentral.com/bmcblog/files/2013/01/JBMS_logo.gif]<http://blogs.biomedcentral.com/bmcblog/files/2013/01/JBMS_logo.gif>Guest blog post from the series editors of the ‘Semantic technologies in healthcare and life sciences’ thematic series<http://www.jbiomedsem.com/series/SWAT4LSCSHALS>, which focuses on the application of web-based technologies for knowledge representation and data integration in clinical and life sciences.

We would like to draw your attention to a new thematic series in Journal of Biomedical Semantics<http://www.jbiomedsem.com/>. The ‘Semantic technologies in healthcare and life sciences’ series<http://www.jbiomedsem.com/series/SWAT4LSCSHALS> focuses on the development and application of web-based technologies for knowledge representation and data integration in clinical and life sciences, with the objective of facilitating biomedical research and healthcare practice.

This thematic series originates from research presented at two conferences; SWAT4LS<http://www.swat4ls.org/> (Semantic Web Application and Tools for Life Sciences) and CSHALS<http://www.iscb.org/cshals2012> (Conference on Semantics in Healthcare and Life Sciences), which are held annually in Europe and in the United States. SWAT4LS’ initial focus was on research on the application of Semantic Web technologies in life sciences, but the growing importance of translational science has resulted in an increasing number of scientific contributions to SWAT4LS that extend across biomedical research. In light of CSHALS focusing on practical applications of semantic technologies to pharmaceutical R&D, healthcare, and life sciences, the creation of this new series was an obvious choice.

We believe this is the right time to focus on semantic technologies in healthcare and life sciences. The Web is a promising technology platform for increasing the efficiency of biomedical research and healthcare delivery: it emerged as the primary communication medium for structured and unstructured information, including the ever increasing amount of biomedical information that is being produced.

[http://blogs.biomedcentral.com/bmcblog/files/2013/01/SWAT4LS-logo-300x244.png]<http://blogs.biomedcentral.com/bmcblog/files/2013/01/SWAT4LS-logo.png>At the same time, semantic approaches are key to integrate information that arises from different processes and disciplines in a meaningful way. At this convergence of Web and semantic solutions, we are now witnessing a front of innovation where various approaches, including Semantic Web<http://en.wikipedia.org/wiki/Semantic_Web> and Linked Data<http://en.wikipedia.org/wiki/Linked_Data> solutions, are being proposed.

These approaches have been attempted in other domains, but clinical and life sciences provide an exemplar milieu for which to apply these technologies, and may advance not only biomedical research but also challenge our understanding of the core semantic technologies and their potential. The objective of this thematic series is therefore to provide a forum to the wider community to explore, showcase and challenge innovative applications of semantic technologies in healthcare and life sciences.

In the inaugural set of papers, Lopes and Oliveira<http://www.jbiomedsem.com/content/3/1/11/abstract> present a “Semantic Web in a box” framework for biomedicine, with the main aim of facilitating easy and rapid development of applications, including advanced data integration and triplification tools, provision of REST services<http://en.wikipedia.org/wiki/Representational_state_transfer>, SPARQL<http://en.wikipedia.org/wiki/SPARQL> endpoints and Linked Data publications. Mikroyannidi and colleagues<http://www.jbiomedsem.com/content/3/1/8/abstract> present a tool that automatically detects regularities and also inspect irregularities in an OWL ontology<http://en.wikipedia.org/wiki/Web_Ontology_Language>, with the aim of facilitating the quality assurance of semantic resources. The tool was used to inspect SNOMED-CT<http://www.ihtsdo.org/snomed-ct/>, and a number of regularity deviations (including some “design defects”) were also identified.

[http://blogs.biomedcentral.com/bmcblog/files/2013/01/CSHALS-logo-150x150.jpg]<http://blogs.biomedcentral.com/bmcblog/files/2013/01/CSHALS-logo.jpg>Furthermore, two papers focus on the application of Semantic Web technologies to genome-wide association studies<http://en.wikipedia.org/wiki/Genome-wide_association_study> (GWAS): Beck and colleagues<http://www.jbiomedsem.com/content/3/1/9/abstract> focus on semantic annotation of GWAS data, cross-species phenotype analysis and publication of genotype-phenotype associations as nanopublications. Pathak and colleagues <http://www.jbiomedsem.com/content/3/1/10/abstract> focus on the use of semantic technologies to enable the analysis of genotype to phenotype associations from clinical data stored in electronic health records<http://en.wikipedia.org/wiki/Electronic_health_record> (EHRs).

We are pleased that in the first week of this thematic series being launched, these papers have already attracted considerable attention and have been acknowledged as highly accessed.

We hope that this series will provide a valuable contribution for the advancement of both Semantic Web and biomedical research, and we welcome any submission that fits into the theme’s objectives.

Joanne S. Luciano, Albert Burger, Jonas Almeida and Andrea Splendiani (series editors for the ‘Semantic technologies in healthcare and life sciences’ thematic series)

Please submit<http://www.jbiomedsem.com/manuscript> your manuscript via our online submission system, and state clearly in your covering letter that it is intended for the ‘Semantic technologies in healthcare and life sciences’ thematic series<http://www.jbiomedsem.com/series/SWAT4LSCSHALS>. For more information, please contact us at editorial@jbiomedsem.com<mailto:editorial@jbiomedsem.com> or visit our instructions for authors<http://www.jbiomedsem.com/authors/instructions>.