Submitted to: Comparative and Functional Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/7/2005
Publication Date: 12/15/2005
Citation: Jaiswal, P., Avraham, S., Ilic, K., Kellogg, E.A., Mccouch, S., Pujar, A., Reiser, L., Rhee, S.Y., Sachs, M.M., Schaeffer, M.L., Stein, L., Stevens, P., Vincent, L., Ware, D., Zapata, F. 2005. Plant ontology (po): a controlled vocabulary of plant structures and growth stages. Comparative and Functional Genomics. 6:388-397. Interpretive Summary: Because plant genome databases use diverse vocabularies to describe anatomy, morphology and growth stages, it is difficult to query multiple databases for all genome information about a particular topic, for example root growth. We have integrated these diverse vocabularies into a networked hierarchy or ontology for several plant species, which include a model plant, thale cress and the cereal grains: corn, rice, wheat, barley, oats, and rye. A browser installed at www.plantontology.org accesses 3500 gene annotations in three different plant genome databases. An immediate result of the work is to leverage gene function information gained in any of the plant species using the ontology to the understanding of similar genes in other plants, in particular the crop plants. In the long term, maximizing gene function knowledge will enhance productivity and reduce costs to the consumers for food and other plant-based products.
Technical Abstract: The Plant Ontology Consortium (POC) (www.plantontology.org) is a collaborative effort among several plant databases and experts in plant systematics, botany and genomics. A primary goal of the POC is to develop simple, yet robust and extensible controlled vocabularies that accurately reflect the biology of plant structures and developmental stages. These provide a network of vocabularies linked by relationships (ontology) to facilitate queries that cut across datasets within a database or between multiple databases. The current version of the ontology integrates diverse vocabularies used to describe Arabidopsis, maize and rice (Orysa sp.) anatomy, morphology and growth stages. Using the ontology browser, over 3500 gene annotations from three species-specific databases, The Arabidopsis Information Resource (TAIR) for Arabidopsis, Gramene for rice and Maize GDB for maize can now be queried and retrieved.