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Biomedical Ontologies

Edited by Robert Hoehndorf, Melissa Haendel, Robert Stevens and Dietrich Rebholz-Schumann

Collection published: 27 August 2013
Last updated: 16 September 2015

  1. Review

    Thematic series on biomedical ontologies in JBMS: challenges and new directions

    Over the past 15 years, the biomedical research community has increased its efforts to produce ontologies encoding biomedical knowledge, and to provide the corresponding infrastructure to maintain them. As ont...

    Robert Hoehndorf, Melissa Haendel, Robert Stevens and Dietrich Rebholz-Schuhmann

    Journal of Biomedical Semantics 2014 5:15

    Published on: 6 March 2014

  2. Database

    The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery

    The Semanticscience Integrated Ontology (SIO) is an ontology to facilitate biomedical knowledge discovery. SIO features a simple upper level comprised of essential types and relations for the rich description ...

    Michel Dumontier, Christopher JO Baker, Joachim Baran, Alison Callahan, Leonid Chepelev, José Cruz-Toledo, Nicholas R Del Rio, Geraint Duck, Laura I Furlong, Nichealla Keath, Dana Klassen, James P McCusker, Núria Queralt-Rosinach, Matthias Samwald, Natalia Villanueva-Rosales, Mark D Wilkinson…

    Journal of Biomedical Semantics 2014 5:14

    Published on: 6 March 2014

  3. Research

    The pathway ontology – updates and applications

    The Pathway Ontology (PW) developed at the Rat Genome Database (RGD), covers all types of biological pathways, including altered and disease pathways and captures the relationships between them within the hier...

    Victoria Petri, Pushkala Jayaraman, Marek Tutaj, G Thomas Hayman, Jennifer R Smith, Jeff De Pons, Stanley JF Laulederkind, Timothy F Lowry, Rajni Nigam, Shur-Jen Wang, Mary Shimoyama, Melinda R Dwinell, Diane H Munzenmaier, Elizabeth A Worthey and Howard J Jacob

    Journal of Biomedical Semantics 2014 5:7

    Published on: 5 February 2014

  4. Research

    The environment ontology: contextualising biological and biomedical entities

    As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growi...

    Pier Luigi Buttigieg, Norman Morrison, Barry Smith, Christopher J Mungall and Suzanna E Lewis

    Journal of Biomedical Semantics 2013 4:43

    Published on: 11 December 2013

  5. Database

    The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes

    A hierarchical taxonomy of organisms is a prerequisite for semantic integration of biodiversity data. Ideally, there would be a single, expansive, authoritative taxonomy that includes extinct and extant taxa, ...

    Peter E Midford, Thomas Alex Dececchi, James P Balhoff, Wasila M Dahdul, Nizar Ibrahim, Hilmar Lapp, John G Lundberg, Paula M Mabee, Paul C Sereno, Monte Westerfield, Todd J Vision and David C Blackburn

    Journal of Biomedical Semantics 2013 4:34

    Published on: 22 November 2013

  6. Research

    PAV ontology: provenance, authoring and versioning

    Provenance is a critical ingredient for establishing trust of published scientific content. This is true whether we are considering a data set, a computational workflow, a peer-reviewed publication or a simple...

    Paolo Ciccarese, Stian Soiland-Reyes, Khalid Belhajjame, Alasdair JG Gray, Carole Goble and Tim Clark

    Journal of Biomedical Semantics 2013 4:37

    Published on: 22 November 2013

  7. Research

    The Drosophila phenotype ontology

    Phenotype ontologies are queryable classifications of phenotypes. They provide a widely-used means for annotating phenotypes in a form that is human-readable, programatically accessible and that can be used to...

    David Osumi-Sutherland, Steven J Marygold, Gillian H Millburn, Peter A McQuilton, Laura Ponting, Raymund Stefancsik, Kathleen Falls, Nicholas H Brown and Georgios V Gkoutos

    Journal of Biomedical Semantics 2013 4:30

    Published on: 18 October 2013

  8. Research

    The Drosophila anatomy ontology

    Anatomy ontologies are query-able classifications of anatomical structures. They provide a widely-used means for standardising the annotation of phenotypes and expression in both human-readable and programmati...

    Marta Costa, Simon Reeve, Gary Grumbling and David Osumi-Sutherland

    Journal of Biomedical Semantics 2013 4:32

    Published on: 18 October 2013

  9. Research

    Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase

    The African clawed frogs Xenopus laevis and Xenopus tropicalis are prominent animal model organisms. Xenopus research contributes to the understanding of genetic, developmental and molecular mechanisms underlying...

    Erik Segerdell, Virgilio G Ponferrada, Christina James-Zorn, Kevin A Burns, Joshua D Fortriede, Wasila M Dahdul, Peter D Vize and Aaron M Zorn

    Journal of Biomedical Semantics 2013 4:31

    Published on: 18 October 2013

  10. Research

    Using ontologies to study cell transitions

    Understanding, modelling and influencing the transition between different states of cells, be it reprogramming of somatic cells to pluripotency or trans-differentiation between cells, is a hot topic in current...

    Georg Fuellen, Ludger Jansen, Ulf Leser and Andreas Kurtz

    Journal of Biomedical Semantics 2013 4:25

    Published on: 8 October 2013

  11. Research

    The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications

    The Clinical Measurement Ontology (CMO), Measurement Method Ontology (MMO), and Experimental Condition Ontology (XCO) were originally developed at the Rat Genome Database (RGD) to standardize quantitative rat ...

    Jennifer R Smith, Carissa A Park, Rajni Nigam, Stanley JF Laulederkind, G Thomas Hayman, Shur-Jen Wang, Timothy F Lowry, Victoria Petri, Jeff De Pons, Marek Tutaj, Weisong Liu, Elizabeth A Worthey, Mary Shimoyama and Melinda R Dwinell

    Journal of Biomedical Semantics 2013 4:26

    Published on: 8 October 2013

  12. Research

    Enrichment analysis applied to disease prognosis

    Enrichment analysis is well established in the field of transcriptomics, where it is used to identify relevant biological features that characterize a set of genes obtained in an experiment.

    Catia M Machado, Ana T Freitas and Francisco M Couto

    Journal of Biomedical Semantics 2013 4:21

    Published on: 8 October 2013

  13. Research

    Developing a semantically rich ontology for the biobank-administration domain

    Biobanks are a critical resource for translational science. Recently, semantic web technologies such as ontologies have been found useful in retrieving research data from biobanks. However, recent research has...

    Mathias Brochhausen, Martin N Fransson, Nitin V Kanaskar, Mikael Eriksson, Roxana Merino-Martinez, Roger A Hall, Loreana Norlin, Sanela Kjellqvist, Maria Hortlund, Umit Topaloglu, William R Hogan and Jan-Eric Litton

    Journal of Biomedical Semantics 2013 4:23

    Published on: 8 October 2013

  14. Database

    The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments

    The Gene Ontology (GO) (http://​www.​geneontology.​org/​) contains a set of terms for describing the activity and actions of gene products across all kingd...

    Paola Roncaglia, Maryann E Martone, David P Hill, Tanya Z Berardini, Rebecca E Foulger, Fahim T Imam, Harold Drabkin, Christopher J Mungall and Jane Lomax

    Journal of Biomedical Semantics 2013 4:20

    Published on: 7 October 2013

  15. Short Report

    IDOMAL: the malaria ontology revisited

    With about half a billion cases, of which nearly one million fatal ones, malaria constitutes one of the major infectious diseases worldwide. A recently revived effort to eliminate the disease also focuses on I...

    Pantelis Topalis, Elvira Mitraka, Vicky Dritsou, Emmanuel Dialynas and Christos Louis

    Journal of Biomedical Semantics 2013 4:16

    Published on: 13 September 2013

  16. Short Report

    EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update

    The Edinburgh Mouse Atlas Project (EMAP) ontology of mouse developmental anatomy provides a standard nomenclature for describing normal and mutant mouse embryo anatomy. The ontology forms the core of the EMAP ...

    Terry F Hayamizu, Michael N Wicks, Duncan R Davidson, Albert Burger, Martin Ringwald and Richard A Baldock

    Journal of Biomedical Semantics 2013 4:15

    Published on: 26 August 2013

  17. Database

    The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species

    The use of ontologies to standardize biological data and facilitate comparisons among datasets has steadily grown as the complexity and amount of available data have increased. Despite the numerous ontologies ...

    Carissa A Park, Susan M Bello, Cynthia L Smith, Zhi-Liang Hu, Diane H Munzenmaier, Rajni Nigam, Jennifer R Smith, Mary Shimoyama, Janan T Eppig and James M Reecy

    Journal of Biomedical Semantics 2013 4:13

    Published on: 9 August 2013

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