OGG: a Biological Ontology for Representing Genes and Genomes in Specific Organisms.

In this report, we present the development of the Ontology of Genes and Genomes (OGG), a biological ontology in the domain of genes and genomes. To integrate with other ontologies, OGG is aligned with the Basic Formal Ontology (BFO). OGGspecific term IDs and annotations are designed by mapping to NCBI Taxonomy IDs and NCBI Entrez Gene IDs. Each gene in OGG has over 10 annotation items, includes gene-associated Gene Ontology (GO) and PubMed article information. OGG has represented genes in human, two viruses, and four bacteria. Additionally, 7 OGG subsets are developed to represent genes and genomes of 7 model systems including mouse, fruit fly, zebrafish, yeast, A. thaliana, C. elegans, P. falciparum. An ontology URI dereferencing approach was designed and implemented in Ontobee to resolve the issue of dereferencing OGG terms from different OGG subset documents. OGG can be used in different cases, including SPARQL query of gene information within OGG or in combination with other ontologies, and the OGG gene term reuse in other ontologies (e.g., Vaccine Ontology). The OGG project website is: https://code.google.com/p/ogg/. Keywords—ontology; Ontology of Genes and Genomes (OGG); gene; genome; organism; vaccine; Gene Ontology (GO)