Journal of Biomedical Semantics | Article collections | Semantic technologies in healthcare and life sciences

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Semantic technologies in healthcare and life sciences

Edited by: Prof Jonas Almeida, Dr Albert Burger, Prof Joanne Luciano, Dr Andrea Splendiani

Collection published: 17 December 2012

Last updated: 13 March 2013

This thematic series focuses on the application of web based technologies for knowledge representation and data integration in life sciences, that seek to facilitate biomedical research and healthcare practice. The series originates in research presented at two conferences, SWAT4LS (Semantic Web Application and Tools for Life Sciences) which is held annually in Europe, and CSHALS (Conference on Semantics in Healthcare and Life Sciences), which is held annually in the United States. These two venues foster critical discussions on the limits, challenges, and opportunities in the adoption of semantic web technologies in healthcare and life sciences.

The emergence of the Web as the primary communication medium; the ever increasing amount of biomedical information and the convergence of disciplines in the biomedical spectrum are all phenomena that point at the Web as a promising technology platform to increase the efficiency of biomedical research and healthcare delivery. At the same time, they make evident the need for semantic approaches in order to integrate information that arises from different processes and disciplines in a meaningful way. At this convergence of Web and semantic solutions we are witnessing a front of innovation where various approaches, including Semantic Web and Linked Data solutions, are proposed.

The objective of this thematic series, and of the events that underpin it, is to explore this front of innovation, both in the critical assessment of current technologies and in novel proposals.

The series is open for any submission that fits into these objectives.

		Research Semantic querying of relational data for clinical intelligence: a semantic web services-based approach Alexandre Riazanov, Artjom Klein, Arash Shaban-Nejad, Gregory W Rose, Alan J Forster, David L Buckeridge, Christopher JO Baker Journal of Biomedical Semantics 2013, 4:9 (13 March 2013) Abstract \| Provisional PDF \| PubMed
		Software Deploying and sharing U-Compare workflows as web services Georgios Kontonatsios, Ioannis Korkontzelos, BalaKrishna Kolluru, Paul Thompson, Sophia Ananiadou Journal of Biomedical Semantics 2013, 4:7 (18 February 2013) Abstract \| Full text \| PDF \| PubMed
		Research Dynamic enhancement of drug product labels to support drug safety, efficacy, and effectiveness Richard D Boyce, John R Horn, Oktie Hassanzadeh, Anita de Waard, Jodi Schneider, Joanne S Luciano, Majid Rastegar-Mojarad, Maria Liakata Journal of Biomedical Semantics 2013, 4:5 (26 January 2013) Abstract \| Provisional PDF \| PubMed
		Software OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows Mikel Egaña Aranguren, Jesualdo Tomás Fernández-Breis, Chris Mungall, Erick Antezana, Alejandro Rodríguez González, Mark D Wilkinson Journal of Biomedical Semantics 2013, 4:2 (4 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The Ontology Pre Processor Language (OPPL) combined with the Galaxy framework allows automated ontology manipulations, leading to more advanced biological data analyses.
		Research Semantically enabling a genome-wide association study database Tim Beck, Robert C Free, Gudmundur A Thorisson, Anthony J Brookes Journal of Biomedical Semantics 2012, 3:9 (17 December 2012) Abstract \| Full text \| PDF \| PubMed
		Research Analysing Syntactic Regularities and Irregularities in SNOMED-CT Eleni Mikroyannidi, Robert Stevens, Luigi Iannone, Alan Rector Journal of Biomedical Semantics 2012, 3:8 (17 December 2012) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Editor’s summary The Regularity Inspector of Ontologies (RIO) automatically detects regularities and irregularities in SNOMED-CT, facilitating the quality assurance of semantic resources.
		Software COEUS: “semantic web in a box” for biomedical applications Pedro Lopes, José Luís Oliveira Journal of Biomedical Semantics 2012, 3:11 (17 December 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research Applying semantic web technologies for phenome-wide scan using an electronic health record linked Biobank Jyotishman Pathak, Richard C Kiefer, Suzette J Bielinski, Christopher G Chute Journal of Biomedical Semantics 2012, 3:10 (17 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Resource Description Framework (RDF) can be employed to enable the analysis of genotype to phenotype associations from clinical data, thereby accurately identifying subjects with specific diseases.

		Research Semantic querying of relational data for clinical intelligence: a semantic web services-based approach Alexandre Riazanov, Artjom Klein, Arash Shaban-Nejad, Gregory W Rose, Alan J Forster, David L Buckeridge, Christopher JO Baker Journal of Biomedical Semantics 2013, 4:9 (13 March 2013) Abstract \| Provisional PDF \| PubMed
		Software Deploying and sharing U-Compare workflows as web services Georgios Kontonatsios, Ioannis Korkontzelos, BalaKrishna Kolluru, Paul Thompson, Sophia Ananiadou Journal of Biomedical Semantics 2013, 4:7 (18 February 2013) Abstract \| Full text \| PDF \| PubMed
		Research Dynamic enhancement of drug product labels to support drug safety, efficacy, and effectiveness Richard D Boyce, John R Horn, Oktie Hassanzadeh, Anita de Waard, Jodi Schneider, Joanne S Luciano, Majid Rastegar-Mojarad, Maria Liakata Journal of Biomedical Semantics 2013, 4:5 (26 January 2013) Abstract \| Provisional PDF \| PubMed
		Software OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows Mikel Egaña Aranguren, Jesualdo Tomás Fernández-Breis, Chris Mungall, Erick Antezana, Alejandro Rodríguez González, Mark D Wilkinson Journal of Biomedical Semantics 2013, 4:2 (4 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The Ontology Pre Processor Language (OPPL) combined with the Galaxy framework allows automated ontology manipulations, leading to more advanced biological data analyses.
		Research Semantically enabling a genome-wide association study database Tim Beck, Robert C Free, Gudmundur A Thorisson, Anthony J Brookes Journal of Biomedical Semantics 2012, 3:9 (17 December 2012) Abstract \| Full text \| PDF \| PubMed
		Research Analysing Syntactic Regularities and Irregularities in SNOMED-CT Eleni Mikroyannidi, Robert Stevens, Luigi Iannone, Alan Rector Journal of Biomedical Semantics 2012, 3:8 (17 December 2012) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Editor’s summary The Regularity Inspector of Ontologies (RIO) automatically detects regularities and irregularities in SNOMED-CT, facilitating the quality assurance of semantic resources.
		Software COEUS: “semantic web in a box” for biomedical applications Pedro Lopes, José Luís Oliveira Journal of Biomedical Semantics 2012, 3:11 (17 December 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research Applying semantic web technologies for phenome-wide scan using an electronic health record linked Biobank Jyotishman Pathak, Richard C Kiefer, Suzette J Bielinski, Christopher G Chute Journal of Biomedical Semantics 2012, 3:10 (17 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Resource Description Framework (RDF) can be employed to enable the analysis of genotype to phenotype associations from clinical data, thereby accurately identifying subjects with specific diseases.