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The Plant Ontology Consortium

The Plant Ontology Consortium aims to develop a common vocabulary for describing anatomy and developmental stages in rice, maize, and Arabidopsis plants. This ontology will be used to annotate gene expression, phenotypes, and mutants in these plants, enabling comparative genomics and facilitating plant research and breeding. The consortium also provides training and outreach to involve plant researchers, breeders, and systematists.

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The Plant Ontology Consortium

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  1. The Plant Ontology Consortium website: http://www.plantontology.org Contact Information for deliverables  Lincoln Stein, lstein@cshl.org

  2. Project Objectives • Pilot project to develop a common set of standardized and controlled vocabulary (Ontology) terms to describe anatomy and developmental stages for rice, maize and Arabidopsis. • Apply the vocabulary to the task of describing the localized expression of the genes and phenotypes of mutants in experimental and agronomically important plants, such as Arabidopsis, rice and maize • Develop an infrastructure to support plant comparative genomics to discover patterns of similarities and dissimilarities involved in plant development. • Impart training to collaborators from other model organism databases. • Community outreach to involve plant researchers, breeders, and systematists

  3. Example Data Sets Some example datasets displaying transcript or protein expression, localization and Mutant phenotypes in cereals and Arabidopsis which needs annotation with a standardized anatomy and growth stage vocabulary terms.

  4. Suggested, application of plant ontology helping plant biologist to make useful queries. • Find all rice mutants associated with dwarfism (Trait-Plant Height/culm or stem length). • What genes are predicted to be involved in association to a particular phenotype ? • Find orthologs between rice / maize / Arabidopsis that may lead to similar phenotypes. • Show all the genes that are induced by growth hormone which are also expressed in the plant’s internode.

  5. In order to help in annotation, the project will develop the standardized, controlled vocabulary (ontology) for following aspects of plants. Plant Ontology (PO) Plant anatomy Describes the location in a plant where the gene is expressed, a gene product is localized and its associated phenotype is observed Plant growth stage Describes the developmental stage at which the gene and /or phenotype expression is observed and assayed

  6. Classically various models of plant glossaries were established over a period of time, by numerous researchers, namely, Katherine Esau, A. Fahn, Elizabeth Cutter and those who defined the growth stages in different plants. These glossaries were primarily organized by simple hierarchy addressing only one to one relationships.

  7. Anatomy instance_of Term-1 Term-7 Term-6 instance_of instance_of Term-2 Term-3 part_of Term-4 derived_from Term-5 Instance_of

  8. An example displaying annotation of Arabidopsis gene PHR1 using the Ontology term.

  9. Data Release timetable: Year-1 Q1-Preview and rel 0.1 of Arabidopsis and cereal ontology Q2-Preview rel. 0.2, 1st POC meeting Q3-Preview rel. 0.3, 2nd POC meeting Q4-Dicot–monocot integration complete. Rel 1.0. 3rd POC and 1st users meeting at Botany 2004. Year-2 Q1-Preview and rel 2.0. legume and solanaceae groups join. Maize associations begin. 4th POC meeting Q2-Preview rel. 3.0, 5th POC meeting, 2nd users meeting Q3-Preview rel. 4.0, with preliminary legume and solanaceae ontology Q4-Preview rel. 5.0 with legume and solanaceae integration complete and begin association activities. 6th POC and 3rd users meeting Year-3 Q1-Rel 6.0. Agronomically important crops join. 7th POC meeting Q2-Rel. 7.0, 8th POC meeting, 4th users meeting Q3-Rel 8.0, with prelim. Ontology contains prelim term from new members Q4-Rel 9.0 new members integrated. 8rd POC and 5st users

  10. Discussion points • What mechanisms should be introduced so that all the groups annotating rice gene products share the same annotation tools, guidelines/standards and Ontology association files.

  11. Last Name First Name Institution Role Stein Lincoln Cold Spring Harbor Laboratory PI McCouch Susan Cornell Univ. co-PI Kellogg Elizabeth University of Missouri co-PI Rhee Sue Carnegie Institution of Washington co-PI Jaiswal Pankaj Cornell University co-PI Ware Doreen Cold Spring Harbor Laboratory co-PI Reiser Leonore Carnegie Institution of Washington Key person Stevens Peter Missouri Botanical Garden, University of Missouri Co-PI Vincent Leszek University of Missouri Key person Douglas Cook University of California Davis Key person Tanksley Steve Cornell University Key person Core participants Supporting members Medicago truncatula functional genomics

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