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Ontologies

A series of Open Access refereed research articles describing new research with ontologies are freely available online. The articles describe mouse and mammalian phenotype ontologies, an ontology for cell types, an ontology for annotating different types of data pertinent to anatomy, a sequence ontology for annotating genomes, and a relation ontology that can promote interoperability of ontologies.

  1. Method

    The Sequence Ontology: a tool for the unification of genome annotations

    The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. SO provides a common set of terms and definitions that will facilitate the exchange, analysis and managem...

    Karen Eilbeck, Suzanna E Lewis, Christopher J Mungall, Mark Yandell, Lincoln Stein, Richard Durbin and Michael Ashburner

    Genome Biology 2005 6:R44

    Published on: 29 April 2005

  2. Method

    Relations in biomedical ontologies

    To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a wa...

    Barry Smith, Werner Ceusters, Bert Klagges, Jacob Köhler, Anand Kumar, Jane Lomax, Chris Mungall, Fabian Neuhaus, Alan L Rector and Cornelius Rosse

    Genome Biology 2005 6:R46

    Published on: 28 April 2005

  4. Method

    An ontology for cell types

    We describe an ontology for cell types that covers the prokaryotic, fungal, animal and plant worlds. It includes over 680 cell types. These cell types are classified under several generic categories and are or...

    Jonathan Bard, Seung Y Rhee and Michael Ashburner

    Genome Biology 2005 6:R21

    Published on: 14 January 2005

  5. Method

    Using ontologies to describe mouse phenotypes

    The mouse is an important model of human genetic disease. Describing phenotypes of mutant mice in a standard, structured manner that will facilitate data mining is a major challenge for bioinformatics. Here we...

    Georgios V Gkoutos, Eain CJ Green, Ann-Marie Mallon, John M Hancock and Duncan Davidson

    Genome Biology 2004 6:R8

    Published on: 20 December 2004

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