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BioOntologies SIG

Edited by Karin Verspoor and Anika Oellrich

The BioOntologies SIG provides a a vibrant forum for discussion of the latest and most innovative research in the application of ontologies and more generally the organization, presentation and dissemination of knowledge in biomedicine and the life sciences. BioOntologies has existed as a SIG at ISMB for almost 20 years, making it one of the longest running.

This collection of articles has not been sponsored and articles have undergone the journal’s standard peer-review process. The Guest Editors declare no competing interests.

View all collections published in Journal of Biomedical Semantics.

  1. Research

    Predicting activities of daily living for cancer patients using an ontology-guided machine learning methodology

    Bio-ontologies are becoming increasingly important in knowledge representation and in the machine learning (ML) fields. This paper presents a ML approach that incorporates bio-ontologies and its application to...

    Hua Min, Hedyeh Mobahi, Katherine Irvin, Sanja Avramovic and Janusz Wojtusiak

    Journal of Biomedical Semantics 2017 8:39

    Published on: 16 September 2017

  2. Research

    Ontology-based specification, identification and analysis of perioperative risks

    Medical personnel in hospitals often works under great physical and mental strain. In medical decision-making, errors can never be completely ruled out. Several studies have shown that between 50 and 60% of ad...

    Alexandr Uciteli, Juliane Neumann, Kais Tahar, Kutaiba Saleh, Stephan Stucke, Sebastian Faulbrück-Röhr, André Kaeding, Martin Specht, Tobias Schmidt, Thomas Neumuth, Andreas Besting, Dominik Stegemann, Frank Portheine and Heinrich Herre

    Journal of Biomedical Semantics 2017 8:36

    Published on: 6 September 2017

  3. Research

    Discovering associations between adverse drug events using pattern structures and ontologies

    Patient data, such as electronic health records or adverse event reporting systems, constitute an essential resource for studying Adverse Drug Events (ADEs). We explore an original approach to identify frequen...

    Gabin Personeni, Emmanuel Bresso, Marie-Dominique Devignes, Michel Dumontier, Malika Smaïl-Tabbone and Adrien Coulet

    Journal of Biomedical Semantics 2017 8:29

    Published on: 22 August 2017

  4. Research

    Towards a more molecular taxonomy of disease

    Disease taxonomies have been designed for many applications, but they tend not to fully incorporate the growing amount of molecular-level knowledge of disease processes, inhibiting research efforts. Understand...

    Jisoo Park, Benjamin J. Hescott and Donna K. Slonim

    Journal of Biomedical Semantics 2017 8:25

    Published on: 27 July 2017

  5. Software

    Literature evidence in open targets - a target validation platform

    We present the Europe PMC literature component of Open Targets - a target validation platform that integrates various evidence to aid drug target identification and validation. The component identifies target-...

    Şenay Kafkas, Ian Dunham and Johanna McEntyre

    Journal of Biomedical Semantics 2017 8:20

    Published on: 6 June 2017

  6. Software

    Dead simple OWL design patterns

    Bio-ontologies typically require multiple axes of classification to support the needs of their users. Development of such ontologies can only be made scalable and sustainable by the use of inference to automat...

    David Osumi-Sutherland, Melanie Courtot, James P. Balhoff and Christopher Mungall

    Journal of Biomedical Semantics 2017 8:18

    Published on: 5 June 2017

  7. 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

  8. Research

    Extracting a stroke phenotype risk factor from Veteran Health Administration clinical reports: an information content analysis

    In the United States, 795,000 people suffer strokes each year; 10–15 % of these strokes can be attributed to stenosis caused by plaque in the carotid artery, a major stroke phenotype risk factor. Studies compa...

    Danielle L. Mowery, Brian E. Chapman, Mike Conway, Brett R. South, Erin Madden, Salomeh Keyhani and Wendy W. Chapman

    Journal of Biomedical Semantics 2016 7:26

    Published on: 10 May 2016

  9. Software

    Webulous and the Webulous Google Add-On - a web service and application for ontology building from templates

    Authoring bio-ontologies is a task that has traditionally been undertaken by skilled experts trained in understanding complex languages such as the Web Ontology Language (OWL), in tools designed for such exper...

    Simon Jupp, Tony Burdett, Danielle Welter, Sirarat Sarntivijai, Helen Parkinson and James Malone

    Journal of Biomedical Semantics 2016 7:17

    Published on: 1 April 2016

  10. Research

    Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation

    The Centre for Therapeutic Target Validation (CTTV - https://​www.​targetvalidation​.​org/​) was established to generate therapeutic target evidence from ge...

    Sirarat Sarntivijai, Drashtti Vasant, Simon Jupp, Gary Saunders, A. Patrícia Bento, Daniel Gonzalez, Joanna Betts, Samiul Hasan, Gautier Koscielny, Ian Dunham, Helen Parkinson and James Malone

    Journal of Biomedical Semantics 2016 7:8

    Published on: 23 March 2016

  11. Review

    Reporting phenotypes in mouse models when considering body size as a potential confounder

    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...

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

    Journal of Biomedical Semantics 2016 7:2

    Published on: 9 February 2016

  12. Database

    An ontology for major histocompatibility restriction

    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)...

    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

    Journal of Biomedical Semantics 2016 7:1

    Published on: 11 January 2016

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