Using bio-ontologies as data annotation, integration & analytical tools at the Mouse Genome Informatics resource

The mouse genome informatics (MGI) resource, an in-depth resource for the genetics, genomics and biology of the laboratory mouse, provides free access to integrated data on diverse biological attributes, ranging from sequence to phenotype and disease model representation. MGI advances translational research through an integrated data platform that facilitates acquisition, explicit representation, and semantic querying and interpretation of multi-parametric genome-scale datasets, and fosters interoperability across different model organism systems and disparate data sources. To this end, MGI employs a set of logically rigorous, dynamic, and cross-referenceable ontologies to unambiguously describe current biological knowledge, expedite manual curation, and advance the informatics capacity to execute complex data mining tasks relevant to comparative and functional genomics. Major bio-ontologies developed and implemented at MGI include the gene ontology (GO), Mammalian Phenotype (MP) ontology, and adult mouse anatomical (MA) Dictionary, reviewed in this paper. All these share a common generic vocabulary infrastructure, and utilize identical annotation tools and web-based browsers to reinforce ontology-centric curation and support ontology-driven querying of the vocabularies and the associated knowledgebase.