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  1. Content type: Research

    Biomedical ontologies aim at providing the most exhaustive and rigorous representation of reality as described by biomedical sciences. A large part of medical reasoning deals with diagnosis and is essentially ...

    Authors: Adrien Barton, Jean-François Ethier, Régis Duvauferrier and Anita Burgun

    Citation: Journal of Biomedical Semantics 2017 8:1

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  2. Content type: Research

    Semantic relatedness is a measure that quantifies the strength of a semantic link between two concepts. Often, it can be efficiently approximated with methods that operate on words, which represent these conce...

    Authors: Maciej Rybinski and José Francisco Aldana-Montes

    Citation: Journal of Biomedical Semantics 2016 7:67

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  3. Content type: Short Report

    This special issue covers selected papers from the 18th Bio-Ontologies Special Interest Group meeting and Phenotype Day, which took place at the Intelligent Systems for Molecular Biology (ISMB) conference in D...

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

    Citation: Journal of Biomedical Semantics 2016 7:66

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  4. Content type: Research

    Objectives of this work are to (1) present an ontological framework for the TNM classification system, (2) exemplify this framework by an ontology for colon and rectum tumours, and (3) evaluate this ontology b...

    Authors: Martin Boeker, Fábio França, Peter Bronsert and Stefan Schulz

    Citation: Journal of Biomedical Semantics 2016 7:64

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  5. Content type: Research

    The systematic analysis of a large number of comparable plant trait data can support investigations into phylogenetics and ecological adaptation, with broad applications in evolutionary biology, agriculture, c...

    Authors: Robert Hoehndorf, Mona Alshahrani, Georgios V. Gkoutos, George Gosline, Quentin Groom, Thomas Hamann, Jens Kattge, Sylvia Mota de Oliveira, Marco Schmidt, Soraya Sierra, Erik Smets, Rutger A. Vos and Claus Weiland

    Citation: Journal of Biomedical Semantics 2016 7:65

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  6. Content type: Research

    The biomedical community has now developed a significant number of ontologies. The curation of biomedical ontologies is a complex task and biomedical ontologies evolve rapidly, so new versions are regularly an...

    Authors: Astrid Duque-Ramos, Manuel Quesada-Martínez, Miguela Iniesta-Moreno, Jesualdo Tomás Fernández-Breis and Robert Stevens

    Citation: Journal of Biomedical Semantics 2016 7:63

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  7. Content type: Research

    Systematized Nomenclature of Medicine - Clinical Terms (SNOMED CT) has been designed as standard clinical terminology for annotating Electronic Health Records (EHRs). EHRs textual information is used to classi...

    Authors: María del Mar Roldán-García, María Jesús García-Godoy and José F. Aldana-Montes

    Citation: Journal of Biomedical Semantics 2016 7:62

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  8. Content type: Research

    Twitter updates now represent an enormous stream of information originating from a wide variety of formal and informal sources, much of which is relevant to real-world events. They can therefore be highly usef...

    Authors: Nicholas Thapen, Donal Simmie and Chris Hankin

    Citation: Journal of Biomedical Semantics 2016 7:61

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  9. Content type: Research

    One of the current research efforts in the area of biomedicine is the representation of knowledge in a structured way so that reasoning can be performed on it. More precisely, in the field of physiotherapy, in...

    Authors: Idoia Berges, David Antón, Jesús Bermúdez, Alfredo Goñi and Arantza Illarramendi

    Citation: Journal of Biomedical Semantics 2016 7:60

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  10. Content type: Database

    The process of discovering new drugs is a lengthy, time-consuming and expensive process. Modern day drug discovery relies heavily on the rapid identification of novel ‘targets’, usually proteins that can be mo...

    Authors: Prudence Mutowo, A. Patrícia Bento, Nathan Dedman, Anna Gaulton, Anne Hersey, Jane Lomax and John P. Overington

    Citation: Journal of Biomedical Semantics 2016 7:59

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  11. Content type: Research

    Research on medical vocabulary expansion from large corpora has primarily been conducted using text written in English or similar languages, due to a limited availability of large biomedical corpora in most la...

    Authors: Magnus Ahltorp, Maria Skeppstedt, Shiho Kitajima, Aron Henriksson, Rafal Rzepka and Kenji Araki

    Citation: Journal of Biomedical Semantics 2016 7:58

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  12. Content type: Research

    The Environment Ontology (ENVO; http://​www.​environmentontol​ogy.​org/​), first described in 2013, is a resource and research target for the semantically c...

    Authors: Pier Luigi Buttigieg, Evangelos Pafilis, Suzanna E. Lewis, Mark P. Schildhauer, Ramona L. Walls and Christopher J. Mungall

    Citation: Journal of Biomedical Semantics 2016 7:57

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  13. Content type: Research

    In biomedical applications where the size and complexity of SNOMED CT become problematic, using a smaller subset that can act as a reasonable substitute is usually preferred. In a special class of use cases—li...

    Authors: Pablo López-García and Stefan Schulz

    Citation: Journal of Biomedical Semantics 2016 7:56

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  14. Content type: Research

    Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analys...

    Authors: Jie Zheng, Marcelline R. Harris, Anna Maria Masci, Yu Lin, Alfred Hero, Barry Smith and Yongqun He

    Citation: Journal of Biomedical Semantics 2016 7:53

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  15. Content type: Research

    Gene Ontology (GO) terms represent the standard for annotation and representation of molecular functions, biological processes and cellular compartments, but a large gap exists between the way concepts are rep...

    Authors: Christopher S. Funk, K. Bretonnel Cohen, Lawrence E. Hunter and Karin M. Verspoor

    Citation: Journal of Biomedical Semantics 2016 7:52

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  16. Content type: Research

    Ontologies are widely used both in the life sciences and in the management of public and private companies. Typically, the different offices in an organization develop their own models and related ontologies t...

    Authors: Giandomenico Pozza, Stefano Borgo, Alessandro Oltramari, Laura Contalbrigo and Stefano Marangon

    Citation: Journal of Biomedical Semantics 2016 7:51

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  17. Content type: Research

    We developed the Apollo Structured Vocabulary (Apollo-SV)—an OWL2 ontology of phenomena in infectious disease epidemiology and population biology—as part of a project whose goal is to increase the use of epide...

    Authors: William R. Hogan, Michael M. Wagner, Mathias Brochhausen, John Levander, Shawn T. Brown, Nicholas Millett, Jay DePasse and Josh Hanna

    Citation: Journal of Biomedical Semantics 2016 7:50

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  18. Content type: Research

    The increasing number of open-access ontologies and their key role in several applications such as decision-support systems highlight the importance of their validation. Human expertise is crucial for the vali...

    Authors: Asma Ben Abacha, Julio Cesar Dos Reis, Yassine Mrabet, Cédric Pruski and Marcos Da Silveira

    Citation: Journal of Biomedical Semantics 2016 7:48

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  19. Content type: Research

    Reasoning over biomedical ontologies using their OWL semantics has traditionally been a challenging task due to the high theoretical complexity of OWL-based automated reasoning. As a consequence, ontology repo...

    Authors: Luke Slater, Georgios V. Gkoutos, Paul N. Schofield and Robert Hoehndorf

    Citation: Journal of Biomedical Semantics 2016 7:49

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  20. Content type: Research

    The Ontology of Medically Related Social Entities (OMRSE) was initially developed in 2011 to provide a framework for modeling demographic data in Resource Description Framework/Web Ontology Language. It is bui...

    Authors: Amanda Hicks, Josh Hanna, Daniel Welch, Mathias Brochhausen and William R. Hogan

    Citation: Journal of Biomedical Semantics 2016 7:47

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  21. Content type: Research

    Open model repositories provide ready-to-reuse computational models of biological systems. Models within those repositories evolve over time, leading to different model versions. Taken together, the underlying...

    Authors: Martin Scharm, Dagmar Waltemath, Pedro Mendes and Olaf Wolkenhauer

    Citation: Journal of Biomedical Semantics 2016 7:46

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  22. Content type: Research

    Neurodegenerative diseases are incurable and debilitating indications with huge social and economic impact, where much is still to be learnt about the underlying molecular events. Mechanistic disease models co...

    Authors: Anandhi Iyappan, Shweta Bagewadi Kawalia, Tamara Raschka, Martin Hofmann-Apitius and Philipp Senger

    Citation: Journal of Biomedical Semantics 2016 7:45

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