75 Integrating Membrane Transport with Male Gametophyte ... - TAIR

97 Applications of Plant Ontologies for Describing and Comparing Phenotypes and Gene
Expression in Plant Databases
Katica Ilic 1 , Elizabeth Kellogg 2 , Peter Stevens 3 , Felipe Zapata 3 , Pankaj Jaiswal 4 , Anuradha Pujar 4 , Shulamit
Avraham 5 , Leszek Vincent 6 , Leonore Reiser 1 , Marty Sachs 7 , Susan McCouch 4 , Mary Schaeffer 6 , Doreen Ware 5 , Lincoln
Stein 5 , Seung Rhee 1
1
TAIR, Carnegie Institution, Department of Plant Biology, Stanford, CA, 2 Department of Biology, University
of Missouri-St. Louis, MO, 3 Botanical Garden, University of Missouri - St. Louis, MO, 4 Gramene, Deptartment
of Plant Breeding, Cornell University, Ithaca, NY, 5 Cold Spring Harbor Laboratory, Cold Spring Harbor,
NY, 6 MaizeGDB, University of Missouri - Columbia, MO, 7 Maize Genetics Cooperation - Stock Center &
Department of Crop Sciences, University of Illinois, Urbana, IL
The Plant Ontology Consortium (POC) was established as a collaboration among several plant databases and experts in plant
systematics, botany and genomics. The primary goal of POC was to create a semantic framework for meaningful cross-species
queries across plant databases and to facilitate and accommodate functional annotation efforts in plant databases and by the plant
research community at large. Thus, the POC has created controlled vocabularies (ontologies) which describe 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
10,000 gene annotations and phenotype descriptions from several species-specific databases can now be queried and retrieved using
the Plant Ontology browser. A summary of the organizing principles and rules followed in developing PO will be presented, as
well as the annotation examples from member databases using PO terms. The PO and gene and phenotype associations contributed
from member databases can be obtained at www.plantontology.org.
98 Report on plant resource project in RIKEN BRC
Masatomo Kobayashi, Hiroshi Abe, Satoshi Iuchi, Toshihiro Kobayashi
RIKEN BRC
RIKEN BRC preserves and distribute plant resources such as seeds for Arabidopsis transposon-tagged lines (KOline)
and Arabidopsis full-length cDNA (RAFL) clones that have been developed in Japan. During last year, RIKEN
BRC almost finished the preparation of these important materials for distribution. We are now establishing homozygous
seed stocks of the transposon-tagged lines that will be partially available within the end of this year.
Now approximately 366,000 materials are preserved in RIKEN BRC, and more than 18,000 materials have been
shipped to world research community. Our stock include Arabidopsis transposon-tagged and activation (T-DNA)-
tagged lines, seed lines for natural accessions, RAFL clones and full-length clones of some model plant species such as
Physcomitrella patens (model moss) and Populus nigra (model tree). The detail information is available from our web
site: http://www.brc.riken.jp/lab/epd/Eng/.