Plant structure and growth stage ontologies to describe phenotypes and gene expression in angiosperms
Pankaj Jaiswal (A), Shulamit Avraham (B), Katica Ilic (C), Elizabeth A Kellogg (D), Susan R
McCouch (A), Mary Polacco (G, E), Anuradha Pujar (A), Leonore Reiser (C), Seung Y Rhee
(C), Marty Sachs (F), Lincoln Stein (B), Peter Stevens (D), Leszek Vincent, Doreen Ware (B, E),
Felipe Zapata (D)
(A) Cornell University, Ithaca, NY 14853; (B) Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; (C) Carnegie Institution of Washington, Stanford, CA 94305; (D) University of Missouri at St. Louis, St. Louis MO 63121;(E) University of Missouri - Columbia, Columbia, MO 65211; (F) Maize Genetic Cooperation - Stock Center, Department of Crop Sciences - University of Illinois, Urbana, IL 61801.(G) USDA-ARS
ABSTRACT
Plant Ontology Consortium (POC) (www.plantontology.org)
is a collaborative effort of 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 to facilitate meaningful cross-species queries across datasets
from various species or from plant databases. The current
ontology release integrates the diverse vocabularies in use
to describe Arabidopsis, maize, rice and Triticeae anatomy,
morphology and growth stages. This integration spans two
major flowering plant taxonomic divisions namely, the monocots and eudicots. Using the ontology browser, over 3500
gene annotations from three species-specific databases,
TAIR, Gramene and MaizeGDB, can now be queried and
retrieved. In the presentation, with the help of examples from
member databases, we will demonstrate how the PO supports gene discovery, phenotype prediction, and gene product functions, as well as the organizing principles and rules
followed in developing the Plant Ontologies. The project is
supported by National Science Foundation grant No.
0321666.
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