| Abstract Detail
Tuesday Morning Contributed Talks Ilic, Katica [1]. Applications of Plant Ontologies for Describing and Comparing Phenotypes and Gene Expression in Angiosperms. THE Plant Ontology Consortium (POC) is a collaborative effort of several plant databases and experts in plant systematics, botany and genomics, sharing a goal of developing controlled vocabularies that accurately reflect morphology, anatomy, growth and developmental stages of a flowering plant. Plant Ontology (PO) has two aspects: 1) Plant Structure Ontology, with terms describing organs, organ systems, tissues, and cell types; and 2) Plant Growth and Developmental Stage Ontology, with terms describing spatial-temporal growth stages of a whole plant and developmental stages of organs and organ systems. The initial releases of Plant Ontology included integration of existing ontologies for Arabidopsis, maize and rice, thus spanning the eudicot-monocot divide. Recently, we have expanded PO to encompass Fabaceae, Solanaceae and other cereal crops. Consistent use of these ontologies potentially reduces the problem of heterogeneity of terminology used to describe comparable object types in plant databases - an obvious obstacle for conducting queries for multiple species across plant genomic databases. As a part of ongoing functional annotation efforts, participating databases, such as TAIR, NASC, Gramene, MaizeGDB and SOL Genomics Network, have been using PO to describe expression patterns of genes and phenotypes of mutants and natural variants. Close to 9,000 gene annotations and phenotype descriptions from several species-specific databases can now be queried and retrieved using the Plant Ontology browser. We will present a summary of the organizing principles and rules followed in developing PO. Standards and methods for using PO to annotate gene expression patterns and to describe phenotypes of mutants and natural variants will be addressed with examples from member databases, demonstrating how the PO supports searching and retrieval of genetic and genomic information as well as mutant stocks and germplasm data. The PO as well as gene and phenotype associations contributed from member databases can be obtained at www.plantontology.org.
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Related Links:
Plant Ontology Consortium (POC) web site
1 - Carnegie Institution, Department of Plant Biology, 260 Panama St., Stanford, CA, 94305, USA
Keywords:
ontology
Bioinformatics
.
Session: SOL04-7
Location: Ballroom AB/Monona Terrace
Date: Tuesday, July 25th, 2006
Time: 10:30 AM
Abstract ID:284 |
