Journal of Biomedical Semantics addresses issues of semantic enrichment and semantic processing in the biomedical domain. The scope of the journal covers two main areas:

Infrastructure for biomedical semantics: focusing on semantic resources and repositories, meta-data management and resource description, knowledge representation and semantic frameworks, the Biomedical Semantic Web, and semantic interoperability.

Semantic mining, annotation, and analysis: focusing on approaches and applications of semantic resources; and tools for investigation, reasoning, prediction, and discoveries in biomedicine.

Editors-in-Chief

  • Dietrich Rebholz-Schuhmann, University of Zurich
  • Goran Nenadic, University of Manchester

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Articles

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  • BioHackathon: Life sciences and the Semantic Web

    This meeting report from the 3rd DBCLS BioHackathon examines how Semantic Web technologies can improve the quality and accessibility of life science research data on the Web.

    Journal of Biomedical Semantics 2013, 4:6

  • Standardized guidelines for annotated corpora

    Pooling annotated corpora does not improve concept extraction, prompting the authors to recommend standardized guidelines to facilitate pooling corpora across institutions.

    Journal of Biomedical Semantics 2013, 4:3

  • OPPL-Galaxy tool enriches biomedical ontologies

    The Ontology Pre Processor Language (OPPL) combined with the Galaxy framework allows automated ontology manipulations, leading to more advanced biological data analyses.

    Journal of Biomedical Semantics 2013, 4:2

  • Enhanced analysis of vaccine adverse events

    An ontology-based representation of the Vaccine Adverse Event Reporting System (VAERS) allows the analysis of both structured and narrative data, culminating in improved vaccine safety studies.

    Journal of Biomedical Semantics 2012, 3:13

  • RDF improves mining of Biobank data

    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.

    Journal of Biomedical Semantics 2012, 3:10
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Author profiles

Ulf Leser

Ulf Leser Ulf Leser is a professor of Knowledge Management in Bioinformatics at Humboldt-Universität in Berlin, Germany, working on semantic issues in biomedical data including database integration and text mining.

"With the ever increasing amount and heterogeneity of data that forms the ground for modern molecular biology, issues concerning the meaning of different data sets are more and more important. Therefore, it is very timely to have a journal that specifically focuses on this topic. I think that Journal of Biomedical Semantics has the potential to become the premier place to publish results in this area."

Mark A. Musen

Mark A. Musen
Mark A. Musen is Director of the Stanford University Center for Biomedical Informatics Research, where he is Professor of Medicine and Computer Science.

"Journal of Biomedical Semantics provides a unique opportunity for scientific exploration at the intersection of semantic systems and biomedicine. The complexities of health, healthcare, and the life sciences often demand computational approaches that make knowledge about the domain and about problem-solving strategies explicit and declarative. Indeed, because computational solutions in biomedicine so often require detailed semantic modeling for their success, important advances in semantic systems seem to spring naturally from the pragmatics of work in this area."

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Call for papers

Journal of Biomedical Semantics and BMC Bioinformatics are currently accepting submissions to an exciting new article series entitled 'Annotation, Interpretation and Management of Mutations'. Please see the call for papers for more details and how to submit.

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Latest supplements

Volume 4 Suppl 1 (15 April 2013)

Proceedings of the Bio-Ontologies Special Interest Group 2012

Proceedings
Long Beach, CA, USA. 13-14 July 2012

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  • PubMed
  • PubMed Central

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ISSN: 2041-1480