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  1. Short Report

    Thematic issue of the Second combined Bio-ontologies and Phenotypes Workshop

    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...

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

    Journal of Biomedical Semantics 2016 7:66

    Published on: 12 December 2016

  2. Research

    The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants

    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...

    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

    Journal of Biomedical Semantics 2016 7:65

    Published on: 14 November 2016

  3. Research

    TNM-O: ontology support for staging of malignant tumours

    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...

    Martin Boeker, Fábio França, Peter Bronsert and Stefan Schulz

    Journal of Biomedical Semantics 2016 7:64

    Published on: 14 November 2016

  4. Research

    Supporting the analysis of ontology evolution processes through the combination of static and dynamic scaling functions in OQuaRE

    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...

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

    Journal of Biomedical Semantics 2016 7:63

    Published on: 17 October 2016

  5. Research

    Dione: An OWL representation of ICD-10-CM for classifying patients’ diseases

    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...

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

    Journal of Biomedical Semantics 2016 7:62

    Published on: 13 October 2016

  6. Research

    TrhOnt: building an ontology to assist rehabilitation processes

    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...

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

    Journal of Biomedical Semantics 2016 7:60

    Published on: 4 October 2016

  7. Database

    A drug target slim: using gene ontology and gene ontology annotations to navigate protein-ligand target space in ChEMBL

    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...

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

    Journal of Biomedical Semantics 2016 7:59

    Published on: 27 September 2016

  8. Research

    The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation

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

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

    Journal of Biomedical Semantics 2016 7:57

    Published on: 23 September 2016

  9. Research

    Can SNOMED CT be squeezed without losing its shape?

    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...

    Pablo López-García and Stefan Schulz

    Journal of Biomedical Semantics 2016 7:56

    Published on: 21 September 2016

  10. Research

    The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis

    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...

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

    Journal of Biomedical Semantics 2016 7:53

    Published on: 14 September 2016

  11. Research

    Information and organization in public health institutes: an ontology-based modeling of the entities in the reception-analysis-report phases

    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...

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

    Journal of Biomedical Semantics 2016 7:51

    Published on: 8 September 2016

  12. Research

    The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation

    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...

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

    Journal of Biomedical Semantics 2016 7:50

    Published on: 18 August 2016

  13. Research

    Using AberOWL for fast and scalable reasoning over BioPortal ontologies

    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...

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

    Journal of Biomedical Semantics 2016 7:49

    Published on: 8 August 2016

  14. Research

    The ontology of medically related social entities: recent developments

    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...

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

    Journal of Biomedical Semantics 2016 7:47

    Published on: 12 July 2016

  15. Research

    NeuroRDF: semantic integration of highly curated data to prioritize biomarker candidates in Alzheimer's disease

    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...

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

    Journal of Biomedical Semantics 2016 7:45

    Published on: 8 July 2016

  16. Database

    The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability

    The Cell Ontology (CL) is an OBO Foundry candidate ontology covering the domain of canonical, natural biological cell types. Since its inception in 2005, the CL has undergone multiple rounds of revision and ex...

    Alexander D. Diehl, Terrence F. Meehan, Yvonne M. Bradford, Matthew H. Brush, Wasila M. Dahdul, David S. Dougall, Yongqun He, David Osumi-Sutherland, Alan Ruttenberg, Sirarat Sarntivijai, Ceri E. Van Slyke, Nicole A. Vasilevsky, Melissa A. Haendel, Judith A. Blake and Christopher J. Mungall

    Journal of Biomedical Semantics 2016 7:44

    Published on: 4 July 2016

  17. Research

    Normalizing acronyms and abbreviations to aid patient understanding of clinical texts: ShARe/CLEF eHealth Challenge 2013, Task 2

    The ShARe/CLEF eHealth challenge lab aims to stimulate development of natural language processing and information retrieval technologies to aid patients in understanding their clinical reports. In clinical tex...

    Danielle L. Mowery, Brett R. South, Lee Christensen, Jianwei Leng, Laura-Maria Peltonen, Sanna Salanterä, Hanna Suominen, David Martinez, Sumithra Velupillai, Noémie Elhadad, Guergana Savova, Sameer Pradhan and Wendy W. Chapman

    Journal of Biomedical Semantics 2016 7:43

    Published on: 1 July 2016

  18. Software

    Knowledge Author: facilitating user-driven, domain content development to support clinical information extraction

    Clinical Natural Language Processing (NLP) systems require a semantic schema comprised of domain-specific concepts, their lexical variants, and associated modifiers to accurately extract information from clini...

    William Scuba, Melissa Tharp, Danielle Mowery, Eugene Tseytlin, Yang Liu, Frank A. Drews and Wendy W. Chapman

    Journal of Biomedical Semantics 2016 7:42

    Published on: 23 June 2016

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