Explorer Integrating partonomic hierarchies in anatomy ontologies

Background: Anatomy ontologies play an increasingly important role in developing integrated bioinformatics applications. One of the primary relationships between anatomical tissues represented in such ontologies is part-of. As there are a number of ways to divide up the anatomical structure of an organism, each may be represented by more than one valid partonomic (part-of) hierarchy. This raises the issue of how to represent and integrate multiple such hierarchies. Results: In this paper we describe a solution that is based on our work on an anatomy ontology for mouse embryo development, which is part of the Edinburgh Mouse Atlas Project (EMAP). The paper describes the basic conceptual aspects of our approach and discusses strengths and limitations of the proposed solution. A prototype was implemented in Prolog for evaluation purposes. Conclusion: With the proposed name set approach, rather than having to standardise hierarchies, it is sufficient to agree on a suitable set of basic tissue terms and their meaning in order to facilitate the integration of multiple partonomic hierarchies. Background Introduction As the bioinformatics emphasis has shifted from gene sequence analysis to functional genomics and proteomics, the need to describe gene function in the context of specific tissues of an organism has increased. Hence, in addition to anatomy ontologies built for medical purposes, e.g. GALEN [1], descriptions of anatomies are now often used to annotate a variety of genetic data, such as geneexpression. (A list of such ontologies for human as well as model organisms, e.g. mouse, Drosophila, zebrafish and C elegans, can be found on the Open Biological Ontologies web site [2]. An ontology model typically consists of concepts and relationships between these concepts. One of the key relationships in anatomy is part-of. It is possible to distinguish between different kinds of part-of, e.g. structural part-of and functional part-of. Each anatomy ontology may define one or more such part-of relationships. Even for a single type of part-of, there may be more than one correct way to devide the anatomy of an organism into parts and subparts. Hence, multiple valid partonomic (part-of) hierarchies may exist for any organism. This raises the issue of interoperability across such hierarchies: when is a tissue in one hierarchy equivalent to a tissue in another hierarchy, and what are the part-of relationships across these hierarchies? Published: 26 November 2004 BMC Bioinformatics 2004, 5:184 doi:10.1186/1471-2105-5-184 Received: 12 December 2003 Accepted: 26 November 2004 This article is available from: http://www.biomedcentral.com/1471-2105/5/184 © 2004 Burger et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. BMC Bioinformatics 2004, 5:184 http://www.biomedcentral.com/1471-2105/5/184