The Plant Ontology Consortium website: Contact Information for deliverables Lincoln Stein,

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Presentation transcript:

The Plant Ontology Consortium website: Contact Information for deliverables Lincoln Stein,

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 Project Objectives

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. Example Data Sets

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. Suggested, application of plant ontology helping plant biologist to make useful queries.

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 In order to help in annotation, the project will develop the standardized, controlled vocabulary (ontology) for following aspects of plants.

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.

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

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

Year-1 Q1-Preview and rel 0.1 of Arabidopsis and cereal ontology Q2-Preview rel. 0.2, 1 st POC meeting Q3-Preview rel. 0.3, 2 nd POC meeting Q4-Dicot–monocot integration complete. Rel rd POC and 1 st users meeting at Botany Year-2 Q1-Preview and rel 2.0. legume and solanaceae groups join. Maize associations begin. 4 th POC meeting Q2-Preview rel. 3.0, 5 th POC meeting, 2 nd 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 3 rd users meeting Year-3 Q1-Rel 6.0. Agronomically important crops join. 7 th 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. 8 rd POC and 5 st users Data Release timetable:

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.

Last Name First NameInstitutionRole SteinLincolnCold Spring Harbor Laboratory PI McCouchSusanCornell Univ.co-PI KelloggElizabethUniversity of Missourico-PI RheeSueCarnegie Institution of Washington co-PI JaiswalPankajCornell Universityco-PI WareDoreenCold Spring Harbor Laboratory co-PI ReiserLeonoreCarnegie Institution of Washington Key person StevensPeterMissouri Botanical Garden, University of Missouri Co-PI VincentLeszekUniversity of MissouriKey person DouglasCookUniversity of California Davis Key person TanksleySteveCornell UniversityKey person Medicago truncatula functional genomics Core participants Supporting members