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Nucleic Acids Research 2008 36(Database issue):D449-D454; doi:10.1093/nar/gkm908
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Nucleic Acids Research, 2008, Vol. 36, Database issue D449-D454
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations

Shulamit Avraham1, Chih-Wei Tung2, Katica Ilic3, Pankaj Jaiswal2, Elizabeth A. Kellogg4, Susan McCouch2, Anuradha Pujar2, Leonore Reiser5, Seung Y Rhee3, Martin M Sachs6,7, Mary Schaeffer7,8, Lincoln Stein1, Peter Stevens4,9, Leszek Vincent8, Felipe Zapata4,9 and Doreen Ware1,7,*

1Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, 2Department of Plant Breeding and Genetics, 240 Emerson Hall, Cornell University, Ithaca, NY 14853, 3Department of Plant Biology, Carnegie Institution of Washington, 260 Panama Street, Stanford, CA 94305, 4Department of Biology, University of Missouri at St. Louis, St Louis, MO 63121, 5Molecular Sciences Institute, 2168 Shattuck Ave., Berkeley, CA 94704, 6Maize Genetics Cooperation, Stock Center, Department of Crop Sciences, University of Illinois, Urbana, IL 61801, 7Agricultural Research Service, United States Department of Agriculture-Agricultural Research Service, Washington, DC 20250, 8Curtis Hall, University of Missouri at Columbia, Columbia, MO 65211 and 9Missouri Botanical Garden, 4344-Shaw Boulevard, St Louis, MO 63110, USA

*To whom correspondence should be addressed. Tel: +1 516 367 6979; Fax: +1 516 367 6851; Email: ware{at}cshl.edu

Received September 12, 2007. Revised October 5, 2007. Accepted October 6, 2007.

The Plant Ontology Consortium (POC, http://www.plantontology.org) is a collaborative effort among model plant genome databases and plant researchers that aims to create, maintain and facilitate the use of a controlled vocabulary (ontology) for plants. The ontology allows users to ascribe attributes of plant structure (anatomy and morphology) and developmental stages to data types, such as genes and phenotypes, to provide a semantic framework to make meaningful cross-species and database comparisons. The POC builds upon groundbreaking work by the Gene Ontology Consortium (GOC) by adopting and extending the GOC's principles, existing software and database structure. Over the past year, POC has added hundreds of ontology terms to associate with thousands of genes and gene products from Arabidopsis, rice and maize, which are available through a newly updated web-based browser (http://www.plantontology.org/amigo/go.cgi) for viewing, searching and querying. The Consortium has also implemented new functionalities to facilitate the application of PO in genomic research and updated the website to keep the contents current. In this report, we present a brief description of resources available from the website, changes to the interfaces, data updates, community activities and future enhancement.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.


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