The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data

An important role for biological databases is the integration of different types of data. Ontologies aim to overcome the semantic differences encountered in data collection and representation, providing common terminology in order to facilitate this integration. An anatomy ontology is a structured vocabulary of anatomical entities in which the terms have unique identities and relate to each other in meaningful ways. For many biological applications, anatomy ontologies are essential for standardized description of data directly related to anatomy, such as gene expression patterns and phenotype information.The Gene Expression Database (GXD) is a resource for gene expression information from the mouse [1]. GXD has been designed as an open-ended system able to store and integrate primary data from many types of expression assays, each of which describe gene expression at different levels of spatial resolution. Currently, both GXD and the Edinburgh Mouse Atlas Gene Expression (EMAGE) database [2] use terms from the Mouse Embryo Anatomy Nomenclature Database [3] developed by the Edinburgh Mouse Atlas Project (EMAP) to describe patterns of gene expression in the developing mouse. However, since GXD also collects gene expression data from mice at postnatal stages, including adult, it became apparent that extension of GXD to fully annotate expression data for adult structures would require the development of a controlled vocabulary beyond the scope of the embryonic mouse anatomy ontology. Therefore, we developed an anatomy ontology for the postnatal mouse.Critical to this effort was the realization that existing sources of controlled vocabularies for anatomy were not sufficient for use with the adult mouse, for several reasons. First, none conforms well to the structure of the embryonic mouse anatomy ontology created by our Edinburgh collaborators, an important factor in enabling planned integration between these ontologies (see below). Human-oriented anatomical ontologies h