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  1. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. Content type: Research article

    While the association between a drug and an adverse event (ADE) is generally detected at the level of individual drugs, ADEs are often discussed at the class level, i.e., at the level of pharmacologic classes ...

    Authors: Rainer Winnenburg, Alfred Sorbello and Olivier Bodenreider

    Citation: Journal of Biomedical Semantics 2015 6:18

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  8. Content type: Research Article

    Lately, ontologies have become a fundamental building block in the process of formalising and storing complex biomedical information. The community-driven ontology curation process, however, ignores the possib...

    Authors: Tudor Groza, Tania Tudorache, Peter N Robinson and Andreas Zankl

    Citation: Journal of Biomedical Semantics 2015 6:21

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  9. Content type: Research Article

    Model repositories such as BioModels Database provide computational models of biological systems for the scientific community. These models contain rich semantic annotations that link model entities to concept...

    Authors: Rebekka Alm, Dagmar Waltemath, Markus Wolfien, Olaf Wolkenhauer and Ron Henkel

    Citation: Journal of Biomedical Semantics 2015 6:20

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  10. Content type: Review

    Establishing robust links among gene expression, pathways and phenotypes is critical for understanding diseases and developing treatments. In recent years there have been many efforts to develop the computatio...

    Authors: Irene Papatheodorou, Anika Oellrich and Damian Smedley

    Citation: Journal of Biomedical Semantics 2015 6:17

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  11. Content type: Research Article

    There is an increasing recognition of the need for the data capture phase of clinical studies to be improved and for more effective sharing of clinical data. The Health Care and Life Sciences community has emb...

    Authors: Hugo Leroux and Laurent Lefort

    Citation: Journal of Biomedical Semantics 2015 6:16

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  12. Content type: Research article

    Electronic Health Records (EHRs) contain a wealth of information useful for studying clinical phenotype-genotype relationships. Severity is important for distinguishing among phenotypes; however other severity...

    Authors: Mary Regina Boland, Nicholas P Tatonetti and George Hripcsak

    Citation: Journal of Biomedical Semantics 2015 6:14

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  13. Content type: Research Article

    Ontologies play a major role in life sciences, enabling a number of applications, from new data integration to knowledge verification. SNOMED CT is a large medical ontology that is formally defined so that it ...

    Authors: Alina Petrova, Yue Ma, George Tsatsaronis, Maria Kissa, Felix Distel, Franz Baader and Michael Schroeder

    Citation: Journal of Biomedical Semantics 2015 6:22

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  14. Content type: Software

    We develop medical-specialty specific ontologies that contain the settled science and common term usage. We leverage current practices in information and relationship extraction to streamline the ontology deve...

    Authors: Kristina Doing-Harris, Yarden Livnat and Stephane Meystre

    Citation: Journal of Biomedical Semantics 2015 6:15

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  15. Content type: Research Article

    With the increasing presence of biomedical data sources on the Internet more and more research effort is put into finding possible ways for integrating and searching such often heterogeneous sources. Ontologie...

    Authors: Patrick Lambrix, Fang Wei-Kleiner and Zlatan Dragisic

    Citation: Journal of Biomedical Semantics 2015 6:12

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  16. Content type: Research

    The NDF-RT (National Drug File Reference Terminology) is an ontology, which describes drugs and their properties and supports computerized physician order entry systems. NDF-RT’s classes are mostly specified u...

    Authors: Rainer Winnenburg, Jonathan M Mortensen and Olivier Bodenreider

    Citation: Journal of Biomedical Semantics 2015 6:13

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  17. Content type: Research article

    A vast array of data is about to emerge from the large scale high-throughput mouse knockout phenotyping projects worldwide. It is critical that this information is captured in a standardized manner, made acces...

    Authors: Cynthia L Smith and Janan T Eppig

    Citation: Journal of Biomedical Semantics 2015 6:11

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  18. Content type: Research

    Engineered nanomaterials (ENMs) are being developed to meet specific application needs in diverse domains across the engineering and biomedical sciences (e.g. drug delivery). However, accompanying the exciting...

    Authors: Janna Hastings, Nina Jeliazkova, Gareth Owen, Georgia Tsiliki, Cristian R Munteanu, Christoph Steinbeck and Egon Willighagen

    Citation: Journal of Biomedical Semantics 2015 6:10

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  19. Content type: Research

    Most computational methods that predict protein function do not take advantage of the large amount of information contained in the biomedical literature. In this work we evaluate both ontology term co-mention ...

    Authors: Christopher S Funk, Indika Kahanda, Asa Ben-Hur and Karin M Verspoor

    Citation: Journal of Biomedical Semantics 2015 6:9

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  20. Content type: Research article

    Chronic obstructive pulmonary disease (COPD) is a life-threatening lung disorder whose recent prevalence has led to an increasing burden on public healthcare. Phenotypic information in electronic clinical reco...

    Authors: Xiao Fu, Riza Batista-Navarro, Rafal Rak and Sophia Ananiadou

    Citation: Journal of Biomedical Semantics 2015 6:8

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  21. Content type: Software

    As the availability of open access full text research articles increases, so does the need for sophisticated search services that make the most of this new content. Here, we present a new feature available in ...

    Authors: Şenay Kafkas, Xingjun Pi, Nikos Marinos, Francesco Talo’, Andrew Morrison and Johanna R McEntyre

    Citation: Journal of Biomedical Semantics 2015 6:7

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  22. Content type: Software

    Semantic similarity measures over phenotype ontologies have been demonstrated to provide a powerful approach for the analysis of model organism phenotypes, the discovery of animal models of human disease, nove...

    Authors: Robert Hoehndorf, Michael Gruenberger, Georgios V Gkoutos and Paul N Schofield

    Citation: Journal of Biomedical Semantics 2015 6:6

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