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United States Department of Agriculture

Agricultural Research Service

Title: The Plant Ontology Consortium and Plant Ontologies

Authors
item Vincent, P - UNIV OF MISSOURI
item Bruskiewich, Richard - INTL RIC RES INST
item Coe Jr, Edward
item Jaiswal, Pankaj - CORNELL UNIVERSITY
item Mccouch, Susan - CORNELL UNIVERSITY
item Schaeffer, Mary
item Stein, Lincoln - COLD SPRING HARBOR LAB
item Ware, Doreen - COLD SPRING HARBOR LAB

Submitted to: Comparative and Functional Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: February 12, 2002
Publication Date: April 1, 2002
Citation: Vincent, P.L., Bruskiewich, R., Coe Jr, E.H., Jaiswal, P., Mccouch, S., Polacco, M.L., Stein, L., Ware, D. 2002. The plant ontology consortium and plant ontologies. Comparative and Functional Genomics. V.3(2):137-142.

Interpretive Summary: Efficient and effective access to data about plant development, anatomy, morphology, and genetics requires that the vocabulary of terms for parts, traits, stages, inheritance, and other features be made readily available to computer analysis. Vocabularies developed with this purpose are termed ontologies. Their design involves establishment of term relationships and concurrence among scientists; clear definitions; and interactions among groups dealing with bioinformatics and with databases. This work is upon the establishment and activities of the Plant Ontology Consortium, an international group that is advancing the work toward the systematic vocabulary purpose. Breeders and biotechnologists can take advantage of the knowledge and tools of this project to access information and diversity for the advancement of maize productivity and efficiency. The present work greatly enhances and facilitates the ability of plant scientists seeking to make crop improvements as well as to understand basic biological systems, to extract current and retrospective data together, and to use them effectively.

Technical Abstract: The goal of the Plant OntologyTM Consortium is to produce structured controlled vocabularies, arranged in ontologies, that can be applied to plant-based database information even as knowledge of the biology of the relevant plant taxa (e.g., development, anatomy, morphology, genomics, proteomics) is accumulating and changing. The collaborators in The Plant OntologyTM Consortium include representatives of a number of core participant database groups. The Plant OntologyTM Consortium is expanding the paradigm of the Gene OntologyTM Consortium (http://www.geneontology.org). Various trait ontologies (agronomic traits, mutant phenotypes, phenotypes, traits, and QTL) and plant ontologies (plant development, anatomy [incl. morphology]) for several taxa (Arabidopsis, maize/corn/Zea mays and rice/Oryza) are under development. The products of the Plant OntologyTM Consortium will be open-source.

Last Modified: 11/27/2014
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