Relations in biomedical ontologies

Relations in biomedical ontologies

28 April 2005 | Barry Smith*,†, Werner Ceusters‡, Bert Klagges§, Jacob Köhler†, Anand Kumar*, Jane Lomax‡, Chris Mungall#, Fabian Neuhaus*, Alan L Rector** and Cornelius Rosse††
The article "Relations in Biomedical Ontologies" by Barry Smith et al. addresses the need for more rigorous and consistent definitions of relational expressions in biomedical ontologies. The authors propose a methodology to provide formal definitions of relational expressions, aiming to enhance interoperability and support automated reasoning about biological and medical phenomena. They identify several shortcomings in existing ontologies, such as informal treatment of relations, lack of clear definitions, and inconsistent usage of terms like "is_a" and "part_of." The paper introduces the Relation Ontology, which includes ten core relations: is_a, part_of, located_in, contained_in, adjacent_to, earlier, transformation_of, derives_from, preceded_by, and has_agent. These relations are defined rigorously and are designed to be easily understandable for both human curators and computer applications. The authors also discuss the logic of biological relations, including inverse and reciprocal relations, and provide examples to illustrate the application of these definitions. The goal is to create a more robust and reliable foundation for life-science knowledge integration.The article "Relations in Biomedical Ontologies" by Barry Smith et al. addresses the need for more rigorous and consistent definitions of relational expressions in biomedical ontologies. The authors propose a methodology to provide formal definitions of relational expressions, aiming to enhance interoperability and support automated reasoning about biological and medical phenomena. They identify several shortcomings in existing ontologies, such as informal treatment of relations, lack of clear definitions, and inconsistent usage of terms like "is_a" and "part_of." The paper introduces the Relation Ontology, which includes ten core relations: is_a, part_of, located_in, contained_in, adjacent_to, earlier, transformation_of, derives_from, preceded_by, and has_agent. These relations are defined rigorously and are designed to be easily understandable for both human curators and computer applications. The authors also discuss the logic of biological relations, including inverse and reciprocal relations, and provide examples to illustrate the application of these definitions. The goal is to create a more robust and reliable foundation for life-science knowledge integration.
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