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  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. Research

    Functional coherence metrics in protein families

    Biological sequences, such as proteins, have been provided with annotations that assign functional information. These functional annotations are associations of proteins (or other biological sequences) with de...

    Hugo P. Bastos, Lisete Sousa, Luka A. Clarke and Francisco M. Couto

    Journal of Biomedical Semantics 2016 7:41

    Published on: 23 June 2016

  14. Research

    FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation

    Nucleotide and protein sequence feature annotations are essential to understand biology on the genomic, transcriptomic, and proteomic level. Using Semantic Web technologies to query biological annotations, the...

    Jerven T. Bolleman, Christopher J. Mungall, Francesco Strozzi, Joachim Baran, Michel Dumontier, Raoul J. P. Bonnal, Robert Buels, Robert Hoehndorf, Takatomo Fujisawa, Toshiaki Katayama and Peter J. A. Cock

    Journal of Biomedical Semantics 2016 7:39

    Published on: 13 June 2016

  15. Research

    DermO; an ontology for the description of dermatologic disease

    There have been repeated initiatives to produce standard nosologies and terminologies for cutaneous disease, some dedicated to the domain and some part of bigger terminologies such as ICD-10. Recently, formall...

    Hannah M. Fisher, Robert Hoehndorf, Bruno S. Bazelato, Soheil S. Dadras, Lloyd E. King, Georgios V. Gkoutos, John P. Sundberg and Paul N. Schofield

    Journal of Biomedical Semantics 2016 7:38

    Published on: 13 June 2016

  16. Software

    PhenoImageShare: an image annotation and query infrastructure

    High throughput imaging is now available to many groups and it is possible to generate a large quantity of high quality images quickly. Managing this data, consistently annotating it, or making it available to...

    Solomon Adebayo, Kenneth McLeod, Ilinca Tudose, David Osumi-Sutherland, Tony Burdett, Richard Baldock, Albert Burger and Helen Parkinson

    Journal of Biomedical Semantics 2016 7:35

    Published on: 7 June 2016

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