Summary
The Edinburgh Mouse Atlas Project (EMAP) Anatomy Ontology is a hierarchically organised list of histologically distinguishable tissues visible at each Theiler stage of development. The ontology is held in the EMAP Anatomy Database freely available from http://genex.hgu.mrc.ac.uk/. The ontology was developed to be both a standard reference for describing normal and mutant tissue anatomy, and a mechanism to allow textual descriptions of gene expression patterns submitted to the Edinburgh Mouse Atlas of Gene Expression (EMAGE) database. It has also been adopted by the Mouse Genome Informatics (MGI) Group for use in their GXD gene expression database. The ontology uses ‘part-of’ relationships and is based primarily on anatomical structure rather than function. Presentation of the ontology as a hierarchy (tree) for each developmental stage displays the structural relationships between the anatomical entities within each stage as well as during the process of development. This part-of hierarchy defines how the ontology is used in the annotation of gene expression patterns, specifically how logic relating to annotated regions is propagated up and down the tree.
The anatomy ontology is an integral part of the EMAP Mouse Atlas. The Atlas also includes three-dimensional models of mouse embryos, one or more for each developmental stage. Selected anatomical terms are represented by domains in the corresponding model. These domains link anatomical concepts with space in the embryo and thus give a structural definition to the corresponding terms in the ontology. Current developments include the provision of additional parent anatomical terms that can be envisioned as standing above the basic tree to provide alternative groupings of the underlying tissues. The ontology is also being expanded to include tissue derivation relationships. The anatomy hierarchy for each stage represents instances of stage-independent concepts. Future versions of the ontology will provide this stage-independent view of the entire mouse anatomy.
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© 2008 Albert Burger, Duncan Davidson, Richard Baldock
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Baldock, R., Davidson, D. (2008). The Edinburgh Mouse Atlas. In: Burger, A., Davidson, D., Baldock, R. (eds) Anatomy Ontologies for Bioinformatics. Computational Biology, vol 6. Springer, London. https://doi.org/10.1007/978-1-84628-885-2_12
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