Genomic ontology

The MAGE has built within it a controlled vocabulary that is used to standardize communication between data providers. However, MAGE can also be extended to encode other types of omic data beyond genomics, such as proteomic data, so long as a reference to the ontology or controlled vocabulary is provided. Although a description of the extension mechanism is beyond scope of this book, practitioners must become familiar with it in order to ensure their software products and applications will be able to accept any and all annotation data that may be submitted with the genomic data. 

J. Bard, S. Y. Rhee, and M. Ashbumer. 2005. An ontology for cell types, Genome Biology 6 R21. 

K. Eilbeck, S. E. Lewis, C. J. Mungall, M. Yandell, L. Stein, R. Durbin, and M. Ashbumer. 2005. The Sequence Ontology a tool for the unification of genome annotations, Genome Biology, 6 R44. 

B. Smith, W. Ceusters, B. Klagges, J. Kohler, A. Kumar, J. Lomax, C. Mungall, F. Neuhaus, A. L. Rector, C. Rosse. 2005. Relations in biomedical ontologies, Genome Biol., 6 R46. 

Dwight, S.S., Harris, M.A., Dolinski, K., Bell, C.A., Binkley, G., Christie, K.R., Fisk, D.G., Issel-Tarver, L., Schroeder, M., Sherlock, G., Sethuraman, A., Weng, S., et al. 2002. Saccharomyces genome database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 30, 69-72. 

Stanley, S., Bailey, T., and Mattick, J. (2006) GONOME measuring correlations between gene ontology terms and genomic positions. BMC Bioinformatics 7, 94. 

Milward, D., M. Bjareland, W. Hayes, M. Maxwell, L. Oberg, N. Tilford, J. Thomas, et al. 2005. Ontology-based interactive information extraction from scientific abstracts. Comp Fund Genomics 6 67-71. 

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