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Plant Ontology database


NAR Molecular Biology Database Collection entry number 926
Jaiswal P.1, Avraham S.2, Ilic K.3, Kellogg E.A.4, McCouch S.1, Pujar A.1, Reiser L.3, Rhee S.Y.3, Sachs M.M.5,6, Schaeffer M.6,7, Stein L.2, Stevens P. 4,8, Vincent L.7, Ware D.2,6, Zapata F.4,8
1Department of Department of Plant Breeding, 240 Emerson Hall, Cornell University, Ithaca, NY, 14853, USA
2Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA 3Carnegie Institution of Washington, Stanford, CA 94305, USA
4Department of Biology, University of Missouri at St. Louis, St. Louis MO 63121, USA
5Maize Genetics Cooperation - Stock Center, Department of Crop Sciences - University of Illinois, Urbana, IL 61801, USA
6Agricultural Research Service, United States Department of Agriculture, USA
7Curtis Hall University of Missouri-Columbia, Columbia, MO 65211, USA
8Missouri Botanical Garden, 4344-Shaw Boulevard, St. Louis, MO 63110

Database Description

The Plant Ontology (PO, http://www.plantontology.org) is a collaborative effort among several plant databases and experts in plant systematics, botany and genomics. The goal of the PO is to develop simple yet robust and extensible controlled vocabularies that accurately reflect the biology of plant structures (morphology and anatomy) and developmental stages. Once implemented, these provide a network of vocabularies linked by relationships (ontology) to facilitate queries that cut across data sets within a database or between multiple databases. Using the ontology browser (http://www.plantontology.org/amigo/go.cgi), over 5000 gene annotations from Arabidopsis, maize and rice can be searched. Using the same browser a user can also search the plant structure (e.g. root hair) and growth stage (e.g. reproductive stage) terms. Learn how to browse and use the ontologies by visiting http://www.plantontology.org/docs/otherdocs/tutorials.html. The vocabularies, annotations, mappings and the database can be downloaded by following the instructions provided at http://www.plantontology.org/download/download.html. Learn more about the ontologies, design and development aspects by visiting http://www.plantontology.org/docs/docs.html

Recent Developments

The current version of the ontology integrates diverse vocabularies used to describe Arabidopsis, maize, rice, Triticeae, legumes and tomato plant anatomy, morphology, growth and developmental stages. Using the ontology browser (http://www.plantontology.org/amigo/go.cgi), over 5000 gene annotations from three species specific databases, The Arabidopsis Information Resource (TAIR, http://www.arabiidopsis.org) for Arabidopsis, Gramene (http://www.gramene.org) for rice and MaizeGDB (http://www.maizegdb.org) for maize, can now be queried and retrieved.

Acknowledgements

We gratefully acknowledge the Gene Ontology Consortium for making the ontology browser (AmiGO), editor (DAG-Edit), Obol tool and database software available and for help with modifications and implementation. We are grateful to many researchers, reviewers, database groups and curators for help in reviewing, adding new terms to the ontology and using them in their annotation work. This work is supported by the National Science Foundation award (Grant No. 0321666) to the Plant Ontology Consortium and USDA-ARS, USA.

References

1. The Plant Ontology Consortium. (2002) The Plant Ontology Consortium and Plant Ontologies. Comparative and Functional Genomics, 3: 137-142.
2. P. Jaiswal, S. Avraham, K. Ilic, E.A. Kellogg, A. Pujar, L. Reiser, R.Y. Seung, M.M. Sachs, M. Schaeffer, L. Stein et al. (2005) Plant Ontology (PO): a controlled vocabulary of plant structures and growth stages. Comparative and Functional Genomics, 6: 388-397.

Category: Plant databases

Go to the abstract in the NAR 2008 Database Issue.
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