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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. Content type: Database

    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 ...

    Authors: 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…

    Citation: Journal of Biomedical Semantics 2014 5:14

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  2. Content type: Review

    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...

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

    Citation: Journal of Biomedical Semantics 2014 5:15

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  3. Content type: Research

    The Zebrafish Anatomy Ontology (ZFA) is an OBO Foundry ontology that is used in conjunction with the Zebrafish Stage Ontology (ZFS) to describe the gross and cellular anatomy and development of the zebrafish, Dan...

    Authors: Ceri E Van Slyke, Yvonne M Bradford, Monte Westerfield and Melissa A Haendel

    Citation: Journal of Biomedical Semantics 2014 5:12

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  4. Content type: Research

    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...

    Authors: 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

    Citation: Journal of Biomedical Semantics 2014 5:7

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  5. Content type: Research

    Epidemiology is a data-intensive and multi-disciplinary subject, where data integration, curation and sharing are becoming increasingly relevant, given its global context and time constraints. The semantic ann...

    Authors: Catia Pesquita, João D Ferreira, Francisco M Couto and Mário J Silva

    Citation: Journal of Biomedical Semantics 2014 5:4

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  6. Content type: Research

    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...

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

    Citation: Journal of Biomedical Semantics 2013 4:43

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  7. Content type: Research

    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...

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

    Citation: Journal of Biomedical Semantics 2013 4:37

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  8. Content type: Database

    The Rat Genome Database (RGD) (http://​rgd.​mcw.​edu/​) is the premier site for comprehensive data on the different strains of the laboratory rat (Rattus n...

    Authors: Rajni Nigam, Diane H Munzenmaier, Elizabeth A Worthey, Melinda R Dwinell, Mary Shimoyama and Howard J Jacob

    Citation: Journal of Biomedical Semantics 2013 4:36

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  9. Content type: Database

    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, ...

    Authors: 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

    Citation: Journal of Biomedical Semantics 2013 4:34

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  10. Content type: Research

    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...

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

    Citation: Journal of Biomedical Semantics 2013 4:31

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  11. Content type: Research

    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...

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

    Citation: Journal of Biomedical Semantics 2013 4:32

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  12. Content type: Research

    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...

    Authors: 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

    Citation: Journal of Biomedical Semantics 2013 4:30

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  13. Content type: Research

    Large-scale mutagenesis projects are ongoing to improve our understanding about the pathology and subsequently the treatment of diseases. Such projects do not only record the genotype but also report phenotype...

    Authors: Anika Oellrich, Christoph Grabmüller and Dietrich Rebholz-Schuhmann

    Citation: Journal of Biomedical Semantics 2013 4:29

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  14. Content type: Research

    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...

    Authors: 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

    Citation: Journal of Biomedical Semantics 2013 4:23

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  15. Content type: Research

    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.

    Authors: Catia M Machado, Ana T Freitas and Francisco M Couto

    Citation: Journal of Biomedical Semantics 2013 4:21

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  16. Content type: Research

    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 ...

    Authors: 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

    Citation: Journal of Biomedical Semantics 2013 4:26

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  17. Content type: Research

    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...

    Authors: Georg Fuellen, Ludger Jansen, Ulf Leser and Andreas Kurtz

    Citation: Journal of Biomedical Semantics 2013 4:25

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  18. Content type: Database

    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...

    Authors: 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

    Citation: Journal of Biomedical Semantics 2013 4:20

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  19. Content type: Short Report

    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...

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

    Citation: Journal of Biomedical Semantics 2013 4:16

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  20. Content type: Short Report

    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 ...

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

    Citation: Journal of Biomedical Semantics 2013 4:15

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  21. Content type: Database

    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 ...

    Authors: 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

    Citation: Journal of Biomedical Semantics 2013 4:13

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