www.plantontology.org plant structure and growth stage ontologies to describe phenotypes and gene...

www.plantontology.org

Plant structure and growth stage ontologies to describe phenotypes and

gene expression in angiosperms

Pankaj JaiswalCornell University



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


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


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


Temporal aspect

Rice

Arabidopsis

BBCH model

POC


Temporal

Anatomy


Use of synonyms to search for species specific stage


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


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

www.plantontology.org plant structure and growth stage ontologies to describe phenotypes and gene...

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