www.plantontology.org plant structure and growth stage ontologies to describe phenotypes and gene...
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www.plantontology.org
Plant structure and growth stage ontologies to describe phenotypes and
gene expression in angiosperms
Pankaj JaiswalCornell University
www.plantontology.org
www.plantontology.org
Different resources try to control their vocabulary.
However there is no standardized format, definition and often no equivalence (cross reference) to another resource.
The vocabularies are organized in a simple tree format….??
Vocabulary examples
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Plant structure
cell root
guard cell trichoblast root hair root cortex
is a i part ofp
is a i is ai
Statement looks like
• Trichome, root hair, root cortex are part of root
• Trichoblast, root hair and guard cell are type of cell
• Root hair develops from trichoblast
• Cell and root are types of plant structure
term to term relationship
Plant Structure +-- cell | +-- guard cell | +-- root hair | +-- trichoblast | +-- root hair +-- root +-- root cortex +-- trichoblast +-- root hair
pp
ii
Di
D
i
i
develops fromD
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Genome Biology 2000, 1:reviews1015.1-1015.4
Plant and Cell Physiology 2005 46(1):69-78
Annual Review of Plant BiologyVol. 53: 399-419
Inflorescence terms were synonymized
Flower terms have children with is_a and sensu
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Temporal aspect
Rice
Arabidopsis
BBCH model
POC
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Temporal
Anatomy
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Use of synonyms to search for species specific stage
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Objectives met
• Ontologies released with an emphasis on rice, maize and Arabidopsis Plant structure Plant growth and plant part developmental stages
• More than 5400 associations to genes and stocks from rice, maize and Arabidopsis.• First publication, Jaiswal et al. Comp. and Funct. Genomics 2006 (in press)
• Users meeting in PAG 2005 and PAG 2006
Future plans
• Extend vocabularies to include terms required by other cereals, legumes (soybean and Medicago), Solanaceae (tomato), tree (Populus) for functional annotation of phenotypes and gene expression
• Resolve the inherent problems faced on multiplicative usage of terms with similar structures under sensu nodes.
• Grant renewal and maintenance
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Funded by NSF
Gramene:
Pankaj Jaiswal, Anuradha Pujar, Shuly Avraham, Doreen Ware, Lincoln Stien [PI]
TAIR:
Katica Ilic, Leonore Reiser, Sue Rhee
UMSL and Missouri Boanical Garden:
Felipe Zapata, Peter Stevens, Toby Kellogg
UMCo and MaizeGDB:
Mary Polacco, Leszek Vincent
Others:
Alice Claire, Quentin Cronk, Victoria Corollo, Naama Menda, Lukas Mueller, and numerous reviewers and experts