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Journal of Biomedical Semantics


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  1. Content type: Research

    The Biomedical Research Integrated Domain Group (BRIDG) model is a formal domain analysis model for protocol-driven biomedical research, and serves as a semantic foundation for application and message developm...

    Authors: Guoqian Jiang, Julie Evans, Cory M. Endle, Harold R. Solbrig and Christopher G. Chute

    Citation: Journal of Biomedical Semantics 2016 7:10

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  2. Content type: Editorial

    The “Vaccine and Drug Ontology Studies” (VDOS) international workshop series focuses on vaccine- and drug-related ontology modeling and applications. Drugs and vaccines have been critical to prevent and treat ...

    Authors: Cui Tao, Yongqun He and Sivaram Arabandi

    Citation: Journal of Biomedical Semantics 2016 7:6

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  3. Content type: Research

    Identifying partial mappings between two terminologies is of special importance when one terminology is finer-grained than the other, as is the case for the Human Phenotype Ontology (HPO), mainly used for rese...

    Authors: Ferdinand Dhombres and Olivier Bodenreider

    Citation: Journal of Biomedical Semantics 2016 7:3

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  4. Content type: Research

    It has been shown that exergames have multiple benefits for physical, mental and cognitive health. Only recently, however, researchers have started considering them as health monitoring tools, through collecti...

    Authors: Giorgos Bamparopoulos, Evdokimos Konstantinidis, Charalampos Bratsas and Panagiotis D. Bamidis

    Citation: Journal of Biomedical Semantics 2016 7:4

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    The Erratum to this article has been published in Journal of Biomedical Semantics 2016 7:31

  5. Content type: Review

    Genotype-phenotype studies aim to identify causative relationships between genes and phenotypes. The International Mouse Phenotyping Consortium is a high throughput phenotyping program whose goal is to collect...

    Authors: Anika Oellrich, Terrence F. Meehan, Helen Parkinson, Sirarat Sarntivijai, Jacqueline K. White and Natasha A. Karp

    Citation: Journal of Biomedical Semantics 2016 7:2

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  6. Content type: Database

    MHC molecules are a highly diverse family of proteins that play a key role in cellular immune recognition. Over time, different techniques and terminologies have been developed to identify the specific type(s)...

    Authors: Randi Vita, James A. Overton, Emily Seymour, John Sidney, Jim Kaufman, Rebecca L. Tallmadge, Shirley Ellis, John Hammond, Geoff W. Butcher, Alessandro Sette and Bjoern Peters

    Citation: Journal of Biomedical Semantics 2016 7:1

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  7. Content type: Research

    The specification of metadata in clinical and epidemiological study projects absorbs significant expense. The validity and quality of the collected data depend heavily on the precise and semantical correct rep...

    Authors: Alexandr Uciteli and Heinrich Herre

    Citation: Journal of Biomedical Semantics 2015 6:41

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  8. Content type: Review

    The bio-ontologies and phenotypes special issue includes eight papers selected from the 11 papers presented at the Bio-Ontologies SIG (Special Interest Group) and the Phenotype Day at ISMB (Intelligent Systems...

    Authors: Larisa N. Soldatova, Nigel Collier, Anika Oellrich, Tudor Groza, Karin Verspoor, Philippe Rocca-Serra, Michel Dumontier and Nigam H. Shah

    Citation: Journal of Biomedical Semantics 2015 6:40

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  9. Content type: Software

    Semantic web technologies have a tremendous potential for the integration of heterogeneous data sets. Therefore, an increasing number of widely used biological resources are becoming available in the RDF data ...

    Authors: Jesse CJ van Dam, Jasper J Koehorst, Peter J Schaap, Vitor AP Martins dos Santos and Maria Suarez-Diez

    Citation: Journal of Biomedical Semantics 2015 6:39

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  10. Content type: Research

    Embryology is a complex morphologic discipline involving a set of entangled mechanisms, sometime difficult to understand and to visualize. Recent computer based techniques ranging from geometrical to physicall...

    Authors: Pierre-Yves Rabattu, Benoit Massé, Federico Ulliana, Marie-Christine Rousset, Damien Rohmer, Jean-Claude Léon and Olivier Palombi

    Citation: Journal of Biomedical Semantics 2015 6:36

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  11. Content type: Software

    The increasing use of ontologies highlights the need for a library for working with ontologies that is efficient, accessible from various programming languages, and compatible with common computational platforms.

    Authors: Mikhail K. Levin and Lindsay G. Cowell

    Citation: Journal of Biomedical Semantics 2015 6:35

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  12. Content type: Research article

    Vaccines are one of the most important public health successes in last century. Besides effectiveness in reducing the morbidity and mortality from many infectious diseases, a successful vaccine program also re...

    Authors: Yuji Zhang, Puqiang Wu, Yi Luo and Cui Tao

    Citation: Journal of Biomedical Semantics 2015 6:33

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  13. Content type: Short Report

    The Genome Variant Format (GVF) uses the Sequence Ontology (SO) to enable detailed annotation of sequence variation. The annotation includes SO terms for the type of sequence alteration, the genomic features t...

    Authors: Fiona Cunningham, Barry Moore, Nicole Ruiz-Schultz, Graham RS Ritchie and Karen Eilbeck

    Citation: Journal of Biomedical Semantics 2015 6:32

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  14. Content type: Research

    Large quantities of biomedical data are being produced at a rapid pace for a variety of organisms. With ontologies proliferating, data is increasingly being stored using the RDF data model and queried using RD...

    Authors: Amir H. Asiaee, Todd Minning, Prashant Doshi and Rick L. Tarleton

    Citation: Journal of Biomedical Semantics 2015 6:31

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  15. Content type: Research Article

    The complexity and scale of the knowledge in the biomedical domain has motivated research work towards mining heterogeneous data from both structured and unstructured knowledge bases. Towards this direction, i...

    Authors: Dirk Weissenborn, Michael Schroeder and George Tsatsaronis

    Citation: Journal of Biomedical Semantics 2015 6:28

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  16. Content type: Research

    In the clinical dentists and periodontal researchers’ community, there is an obvious demand for a systems model capable of linking the clinical presentation of periodontitis to underlying molecular knowledge. ...

    Authors: Asami Suzuki, Takako Takai-Igarashi, Jun Nakaya and Hiroshi Tanaka

    Citation: Journal of Biomedical Semantics 2015 6:30

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  17. Content type: Research article

    There are numerous options available to achieve various tasks in bioinformatics, but until recently, there were no tools that could systematically identify mentions of databases and tools within the literature...

    Authors: Geraint Duck, Aleksandar Kovacevic, David L. Robertson, Robert Stevens and Goran Nenadic

    Citation: Journal of Biomedical Semantics 2015 6:29

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  18. Content type: Research Article

    Phenotypes form the basis for determining the existence of a disease against the given evidence. Much of this evidence though remains locked away in text – scientific articles, clinical trial reports and elect...

    Authors: Nigel Collier, Anika Oellrich and Tudor Groza

    Citation: Journal of Biomedical Semantics 2015 6:24

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  19. Content type: Research article

    Mild traumatic brain injury (mTBI) has high prevalence in the military, among athletes, and in the general population worldwide (largely due to falls). Consequences can include a range of neuropsychological di...

    Authors: Michael J Cairelli, Marcelo Fiszman, Han Zhang and Thomas C Rindflesch

    Citation: Journal of Biomedical Semantics 2015 6:25

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  20. Content type: Research Article

    Discovering gene interactions and their characterizations from biological text collections is a crucial issue in bioinformatics. Indeed, text collections are large and it is very difficult for biologists to fu...

    Authors: Peggy Cellier, Thierry Charnois, Marc Plantevit, Christophe Rigotti, Bruno Crémilleux, Olivier Gandrillon, Jiří Kléma and Jean-Luc Manguin

    Citation: Journal of Biomedical Semantics 2015 6:27

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