The Gene Ontology resource: enriching a GOld mine
Seth Carbon, Eric Douglass, Benjamin M. Good, Deepak Unni, Nomi L. Harris, Chris Mungall, Siddartha Basu, Rex L. Chisholm, Robert J. Dodson, Eric C Hartline, Petra Fey, Paul D. Thomas, Laurent‐Philippe Albou, Dustin Ebert, Michael J Kesling, Huaiyu Mi, Anushya Muruganujan, Xiaosong Huang, Tremayne Mushayahama, Sandra LaBonte, Deborah A. Siegele, Giulia Antonazzo, Helen Attrill, Nick H Brown, Phani Garapati, Steven J Marygold, Vítor Trovisco, Gil dos Santos, Kathleen Falls, Christopher J. Tabone, Pinglei Zhou, Joshua L. Goodman, Victor Strelets, Jim Thurmond, Penelope Garmiri, Rizwan Ishtiaq, M. Rodríguez-López, Márcio Luís Acencio, Martin Kuiper, Astrid Lægreid, Colin Logie, Ruth C. Lovering, Barbara Kramarz, Shirin C C Saverimuttu, Sandra De Miranda Pinheiro, Heather Gunn, Renzhi Su, Kate E. Thurlow, Marcus C. Chibucos, Michelle Giglio, Suvarna Nadendla, James B. Munro, Rebecca Jackson, Margaret Duesbury, Noemí del‐Toro, Birgit Meldal, Kalpana Paneerselvam, Livia Perfetto, Pablo Porras, Sandra Orchard, Anjali Shrivastava, Hsin-Yu Chang, ROBERT FINN, Alex Mitchell, Neil D. Rawlings, Lorna Richardson, Amaia Sangrador‐Vegas, Judith A. Blake, Karen Christie, M. Eileen Dolan, Harold Drabkin, David P. Hill, Li Ni, Dmitry Sitnikov, Midori A. Harris, Stephen G. Oliver, Kim Rutherford, Valerie Wood, Jaqueline Hayles, Jürg Bähler, Elizabeth R. Bolton, Jeffery L De Pons, Melinda R. Dwinell, G. Thomas Hayman, Mary L. Kaldunski, Anne E. Kwitek, Stanley J. F. Laulederkind, Cody Plasterer, Marek Tutaj, Mahima Vedi, Shur‐Jen Wang, Peter D’Eustachio, Lisa Matthews, James P. Balhoff, Suzi Aleksander, Michael J. Alexander, J. Michael Cherry, Stacia R. Engel, Felix Gondwe, Kalpana Karra
Abstract
The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene products. Here, we report the advances of the consortium over the past two years. The new GO-CAM annotation framework was notably improved, and we formalized the model with a computational schema to check and validate the rapidly increasing repository of 2838 GO-CAMs. In addition, we describe the impacts of several collaborations to refine GO and report a 10% increase in the number of GO annotations, a 25% increase in annotated gene products, and over 9,400 new scientific articles annotated. As the project matures, we continue our efforts to review older annotations in light of newer findings, and, to maintain consistency with other ontologies. As a result, 20 000 annotations derived from experimental data were reviewed, corresponding to 2.5% of experimental GO annotations. The website (http://geneontology.org) was redesigned for quick access to documentation, downloads and tools. To maintain an accurate resource and support traceability and reproducibility, we have made available a historical archive covering the past 15 years of GO data with a consistent format and file structure for both the ontology and annotations.