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. 2005;6(5):R46.
doi: 10.1186/gb-2005-6-5-r46. Epub 2005 Apr 28.

Relations in biomedical ontologies

Barry Smith  1 , Werner Ceusters, Bert Klagges, Jacob Köhler, Anand Kumar, Jane Lomax, Chris Mungall, Fabian Neuhaus, Alan L Rector, Cornelius Rosse
Affiliations

Relations in biomedical ontologies

Barry Smith et al. Genome Biol. 2005.

Abstract

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. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena.

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Figures

Figure 1
Figure 1
Standard mereotopological relations between spatial regions.
Figure 2
Figure 2
Transformation.
Figure 3
Figure 3
Three simple cases of derivation. (a) Continuation; (b) fusion; (c) fission.
See this image and copyright information in PMC

References

    1. OBO: Open Biomedical Ontologies http://obo.sourceforge.net
    1. Mungall C. OBOL: integrating language and meaning in bio-ontologies. Comp Funct Genomics. 2004;5:509–520. doi: 10.1002/cfg.435. - DOI - PMC - PubMed
    1. Gene Ontology Consortium. Creating the Gene Ontology resource: design and implementation. Genome Res. 2001;11:1425–1433. doi: 10.1101/gr.180801. - DOI - PMC - PubMed
    1. Bada M, Stevens R, Goble C, Gil Y, Ashburner M, Blake JA, Cherry JM, Harris M, Lewis S. A short study on the success of the GeneOntology. J Web Semantics. 2004;1:235–240.
    1. Smith B, Köhler J, Kumar A. On the application of formal principles to life science data: a case study in the Gene Ontology. DILS 2004: Data Integration in the Life Sciences Lecture Notes in Computer Science 2994. 2004. pp. 124–139.

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