GOMMA: a component-based infrastructure for managing and analyzing life science ontologies and their evolution

We present GOMMA, a generic infrastructure for managing and analyzing life science ontologies and their evolution. GOMMA utilizes a generic repository to uniformly and efficiently manage ontology versions and different kinds of mappings. Furthermore, it provides components for ontology matching, and determining evolutionary ontology changes. These components are used by analysis tools, such as the Ontology Evolution Explorer (OnEX) and the detection of unstable ontology regions. We introduce the component-based infrastructure and show analysis results for selected components and life science applications. GOMMA is available at http://dbs.uni-leipzig.de/GOMMA webcite.GOMMA provides a comprehensive and scalable infrastructure to manage large life science ontologies and analyze their evolution. Key functions include a generic storage of ontology versions and mappings, support for ontology matching and determining ontology changes. The supported features for analyzing ontology changes are helpful to assess their impact on ontology-dependent applications such as for term enrichment. GOMMA complements OnEX by providing functionalities to manage various versions of mappings between two ontologies and allows combining different match approaches.Ontologies and taxonomies have become increasingly important especially in the life sciences [1,2]. They are predominantly utilized to structure and uniformly describe the entities of a domain of interest such as molecular functions or the anatomy of species [3,4]. Ontologies consist of a set of concepts that are usually interrelated by "is-a", "part-of" or other semantically meaningful relationships (e.g., "regulated-by") [5]. Ontologies enable a consistent annotation of biological objects, experiments, publications or clinical documents by describing their properties. For instance, the Molecular Function ontology of the Gene Ontology [6] is used to specify the functions of genes and proteins on the molecular level. Biomedical ontol