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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.

Collection published: 14 January 2005

Last updated: 29 April 2005

		Method The Sequence Ontology: a tool for the unification of genome annotations Karen Eilbeck, Suzanna E Lewis, Christopher J Mungall, Mark Yandell, Lincoln Stein, Richard Durbin, Michael Ashburner Genome Biology 2005, 6:R44 (29 April 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The goal of the Sequence Ontology (SO) project is to produce a structured controlled vocabulary with a common set of terms and definitions for parts of a genomic annotation, and to describe the relationships among them. Details of SO construction, design and use, particularly with regard to part-whole relationships are discussed and the practical utility of SO is demonstrated for a set of genome annotations from Drosophila melanogaster.
		Method Relations in biomedical ontologies Barry Smith, Werner Ceusters, Bert Klagges, Jacob Köhler, Anand Kumar, Jane Lomax, Chris Mungall, Fabian Neuhaus, Alan L Rector, Cornelius Rosse Genome Biology 2005, 6:R46 (28 April 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary 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 way designed to assist developers and users in avoiding errors in coding and annotation.
		Software The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data Terry F Hayamizu, Mary Mangan, John P Corradi, James A Kadin, Martin Ringwald Genome Biology 2005, 6:R29 (15 February 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary The Adult Mouse Anatomical Dictionary was developed to provide an ontology for standardized nomenclature for anatomical terms in the postnatal mouse. The ontology will be used to annotate and integrate different types of data pertinent to anatomy.
		Method An ontology for cell types Jonathan Bard, Seung Y Rhee, Michael Ashburner Genome Biology 2005, 6:R21 (14 January 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An ontology for cell types that covers the prokaryotic, fungal, animal and plant worlds is described. It includes over 680 cell types. These cell types are classified under several generic categories and are organized as a directed acyclic graph.
		Method Using ontologies to describe mouse phenotypes Georgios V Gkoutos, Eain CJ Green, Ann-Marie Mallon, John M Hancock, Duncan Davidson Genome Biology 2004, 6:R8 (20 December 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary By combining ontologies from different sources the authors developed a novel approach to describing phenotypes of mutant mice in a standard, structured manner.
		Method The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information Cynthia L Smith, Carroll-Ann W Goldsmith, Janan T Eppig Genome Biology 2004, 6:R7 (15 December 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Mammalian Phenotype (MP) Ontology enables robust annotation of mammalian phenotypes in the context of mutations, quantitative trait loci and strains that are used as models of human biology and disease.

		Method The Sequence Ontology: a tool for the unification of genome annotations Karen Eilbeck, Suzanna E Lewis, Christopher J Mungall, Mark Yandell, Lincoln Stein, Richard Durbin, Michael Ashburner Genome Biology 2005, 6:R44 (29 April 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The goal of the Sequence Ontology (SO) project is to produce a structured controlled vocabulary with a common set of terms and definitions for parts of a genomic annotation, and to describe the relationships among them. Details of SO construction, design and use, particularly with regard to part-whole relationships are discussed and the practical utility of SO is demonstrated for a set of genome annotations from Drosophila melanogaster.
		Method Relations in biomedical ontologies Barry Smith, Werner Ceusters, Bert Klagges, Jacob Köhler, Anand Kumar, Jane Lomax, Chris Mungall, Fabian Neuhaus, Alan L Rector, Cornelius Rosse Genome Biology 2005, 6:R46 (28 April 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary 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 way designed to assist developers and users in avoiding errors in coding and annotation.
		Software The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data Terry F Hayamizu, Mary Mangan, John P Corradi, James A Kadin, Martin Ringwald Genome Biology 2005, 6:R29 (15 February 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary The Adult Mouse Anatomical Dictionary was developed to provide an ontology for standardized nomenclature for anatomical terms in the postnatal mouse. The ontology will be used to annotate and integrate different types of data pertinent to anatomy.
		Method An ontology for cell types Jonathan Bard, Seung Y Rhee, Michael Ashburner Genome Biology 2005, 6:R21 (14 January 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An ontology for cell types that covers the prokaryotic, fungal, animal and plant worlds is described. It includes over 680 cell types. These cell types are classified under several generic categories and are organized as a directed acyclic graph.
		Method Using ontologies to describe mouse phenotypes Georgios V Gkoutos, Eain CJ Green, Ann-Marie Mallon, John M Hancock, Duncan Davidson Genome Biology 2004, 6:R8 (20 December 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary By combining ontologies from different sources the authors developed a novel approach to describing phenotypes of mutant mice in a standard, structured manner.
		Method The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information Cynthia L Smith, Carroll-Ann W Goldsmith, Janan T Eppig Genome Biology 2004, 6:R7 (15 December 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Mammalian Phenotype (MP) Ontology enables robust annotation of mammalian phenotypes in the context of mutations, quantitative trait loci and strains that are used as models of human biology and disease.