Www.plantontology.org Plant structure and growth stage ontologies to describe phenotypes and gene...
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![Page 1: Www.plantontology.org Plant structure and growth stage ontologies to describe phenotypes and gene expression in angiosperms Pankaj Jaiswal Cornell University.](https://reader035.fdocuments.us/reader035/viewer/2022062520/5697c0271a28abf838cd6434/html5/thumbnails/1.jpg)
www.plantontology.org
Plant structure and growth stage ontologies to describe phenotypes and
gene expression in angiosperms
Pankaj JaiswalCornell University
www.plantontology.org
![Page 2: Www.plantontology.org Plant structure and growth stage ontologies to describe phenotypes and gene expression in angiosperms Pankaj Jaiswal Cornell University.](https://reader035.fdocuments.us/reader035/viewer/2022062520/5697c0271a28abf838cd6434/html5/thumbnails/2.jpg)
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
![Page 3: Www.plantontology.org Plant structure and growth stage ontologies to describe phenotypes and gene expression in angiosperms Pankaj Jaiswal Cornell University.](https://reader035.fdocuments.us/reader035/viewer/2022062520/5697c0271a28abf838cd6434/html5/thumbnails/3.jpg)
www.plantontology.org
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
![Page 4: Www.plantontology.org Plant structure and growth stage ontologies to describe phenotypes and gene expression in angiosperms Pankaj Jaiswal Cornell University.](https://reader035.fdocuments.us/reader035/viewer/2022062520/5697c0271a28abf838cd6434/html5/thumbnails/4.jpg)
www.plantontology.org
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
![Page 5: Www.plantontology.org Plant structure and growth stage ontologies to describe phenotypes and gene expression in angiosperms Pankaj Jaiswal Cornell University.](https://reader035.fdocuments.us/reader035/viewer/2022062520/5697c0271a28abf838cd6434/html5/thumbnails/5.jpg)
www.plantontology.org
Temporal aspect
Rice
Arabidopsis
BBCH model
POC
![Page 6: Www.plantontology.org Plant structure and growth stage ontologies to describe phenotypes and gene expression in angiosperms Pankaj Jaiswal Cornell University.](https://reader035.fdocuments.us/reader035/viewer/2022062520/5697c0271a28abf838cd6434/html5/thumbnails/6.jpg)
www.plantontology.org
Temporal
Anatomy
![Page 7: Www.plantontology.org Plant structure and growth stage ontologies to describe phenotypes and gene expression in angiosperms Pankaj Jaiswal Cornell University.](https://reader035.fdocuments.us/reader035/viewer/2022062520/5697c0271a28abf838cd6434/html5/thumbnails/7.jpg)
www.plantontology.org
![Page 8: Www.plantontology.org Plant structure and growth stage ontologies to describe phenotypes and gene expression in angiosperms Pankaj Jaiswal Cornell University.](https://reader035.fdocuments.us/reader035/viewer/2022062520/5697c0271a28abf838cd6434/html5/thumbnails/8.jpg)
www.plantontology.org
Use of synonyms to search for species specific stage
![Page 9: Www.plantontology.org Plant structure and growth stage ontologies to describe phenotypes and gene expression in angiosperms Pankaj Jaiswal Cornell University.](https://reader035.fdocuments.us/reader035/viewer/2022062520/5697c0271a28abf838cd6434/html5/thumbnails/9.jpg)
www.plantontology.org
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
![Page 10: Www.plantontology.org Plant structure and growth stage ontologies to describe phenotypes and gene expression in angiosperms Pankaj Jaiswal Cornell University.](https://reader035.fdocuments.us/reader035/viewer/2022062520/5697c0271a28abf838cd6434/html5/thumbnails/10.jpg)
www.plantontology.org
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