1. www.plantontology.org Plant structure and growth stage ontologies to describe phenotypes and gene expression in angiosperms Pankaj Jaiswal Cornell University www.plantontology.org

2. 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

3. www.plantontology.org Plant structure cell root guard cell trichoblast root hair root cortex is a i part of p is a i i 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 p p i i D i D i i develops from D

4. www.plantontology.org Genome Biology 2000, 1:reviews1015.1-1015.4 Plant and Cell Physiology 2005 46(1):69-78 Annual Review of Plant Biology Vol. 53: 399-419 Inflorescence terms were synonymized Flower terms have children with is_a and sensu

5. www.plantontology.org Temporal aspect Rice Arabidopsis BBCH model POC

6. www.plantontology.org Temporal Anatomy

7. www.plantontology.org

8. Use of synonyms to search for species specific stage

9. 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

10. 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