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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. To improve the outcomes of biological pathway analysis, a better way of integrating pathway data is needed. Ontologies can be used to organize data from disparate sources, and we leverage the Pathway Ontology ...

    Authors: Lucy Lu Wang, G. Thomas Hayman, Jennifer R. Smith, Monika Tutaj, Mary E. Shimoyama and John H. Gennari
    Citation: Journal of Biomedical Semantics 2019 10:11
  2. One of the most successful approaches to develop new small molecule therapeutics has been to start from a validated druggable protein target. However, only a small subset of potentially druggable targets has a...

    Authors: Yu Lin, Saurabh Mehta, Hande Küçük-McGinty, John Paul Turner, Dusica Vidovic, Michele Forlin, Amar Koleti, Dac-Trung Nguyen, Lars Juhl Jensen, Rajarshi Guha, Stephen L. Mathias, Oleg Ursu, Vasileios Stathias, Jianbin Duan, Nooshin Nabizadeh, Caty Chung…
    Citation: Journal of Biomedical Semantics 2017 8:50
  3. 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...

    Authors: Hua Min, Hedyeh Mobahi, Katherine Irvin, Sanja Avramovic and Janusz Wojtusiak
    Citation: Journal of Biomedical Semantics 2017 8:39
  4. 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...

    Authors: 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
    Citation: Journal of Biomedical Semantics 2017 8:36
  5. 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...

    Authors: Gabin Personeni, Emmanuel Bresso, Marie-Dominique Devignes, Michel Dumontier, Malika Smaïl-Tabbone and Adrien Coulet
    Citation: Journal of Biomedical Semantics 2017 8:29
  6. 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...

    Authors: Jisoo Park, Benjamin J. Hescott and Donna K. Slonim
    Citation: Journal of Biomedical Semantics 2017 8:25
  7. 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-...

    Authors: Şenay Kafkas, Ian Dunham and Johanna McEntyre
    Citation: Journal of Biomedical Semantics 2017 8:20
  8. 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...

    Authors: David Osumi-Sutherland, Melanie Courtot, James P. Balhoff and Christopher Mungall
    Citation: Journal of Biomedical Semantics 2017 8:18
  9. Clinical practice guidelines (CPGs) recommend pharmacologic treatments for clinical conditions, and drug structured product labels (SPLs) summarize approved treatment indications. Both resources are intended t...

    Authors: Tiffany I. Leung and Michel Dumontier
    Citation: Journal of Biomedical Semantics 2016 7:37
  10. 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...

    Authors: Solomon Adebayo, Kenneth McLeod, Ilinca Tudose, David Osumi-Sutherland, Tony Burdett, Richard Baldock, Albert Burger and Helen Parkinson
    Citation: Journal of Biomedical Semantics 2016 7:35
  11. 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...

    Authors: Danielle L. Mowery, Brian E. Chapman, Mike Conway, Brett R. South, Erin Madden, Salomeh Keyhani and Wendy W. Chapman
    Citation: Journal of Biomedical Semantics 2016 7:26
  12. 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...

    Authors: Simon Jupp, Tony Burdett, Danielle Welter, Sirarat Sarntivijai, Helen Parkinson and James Malone
    Citation: Journal of Biomedical Semantics 2016 7:17
  13. The Centre for Therapeutic Target Validation (CTTV - https://​www.​targetvalidation​.​org/​) was established to generate therapeutic target evidence from ge...

    Authors: 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
    Citation: Journal of Biomedical Semantics 2016 7:8
  14. Identifying partial mappings between two terminologies is of special importance when one terminology is finer-grained than the other, as is the case for the Human Phenotype Ontology (HPO), mainly used for rese...

    Authors: Ferdinand Dhombres and Olivier Bodenreider
    Citation: Journal of Biomedical Semantics 2016 7:3
  15. 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...

    Authors: Anika Oellrich, Terrence F. Meehan, Helen Parkinson, Sirarat Sarntivijai, Jacqueline K. White and Natasha A. Karp
    Citation: Journal of Biomedical Semantics 2016 7:2
  16. 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)...

    Authors: 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
    Citation: Journal of Biomedical Semantics 2016 7:1

Annual Journal Metrics

  • 2022 Citation Impact
    1.9 - 2-year Impact Factor
    2.6 - 5-year Impact Factor
    0.870 - SNIP (Source Normalized Impact per Paper)
    0.697 - SJR (SCImago Journal Rank)

    2023 Speed
    23 days submission to first editorial decision for all manuscripts (Median)
    265 days submission to accept (Median)

    2023 Usage 
    206 Altmetric mentions