1. The Plant Ontology Consortium Lincoln Stein 1, Susan McCouch 2, Elizabeth Kellogg 3, Seung Rhee 4, Pankaj Jaiswal 2, Doreen Ware 1, Peter Stevens 5 1 Cold Spring Harbor Laboratory, Cold Spring harbor, NY; 2 Cornell University, Ithaca, NY; 3 University of Missouri, St. Lois, MO; 4 Carnegie Institution of Washington, Stanford University, San Francisco, CA; 5 Missouri Botanical Garden, University of Missouri, St. Lois, MO website: http://www.plantontology.org 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 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. 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. The PO Consortium adopted a simple data structure called the Directed Acyclic Graph (DAG), keeping it consistent with its use by the Gene Ontology Consortium (www.geneontology.org). This structure is a type of hierarchy where the biological concepts are organized as a network tree structure in which the nodes at the top (“root”) of the tree are more general cases of specific terms at the bottom (“leaves”) of the structure. Like a simple hierarchy, children are not allowed to be their own ancestors; hence cycles are forbidden. The different term-term relationships described are: instance-of: This relationship is used in both the developmental and anatomy ontologies to indicate the relationship between a specific term to a more general one. For example achenium is an instance-of a dry indeshiscent fruit, which in turn is an instance-of fruit. part-of: This relationship is used in the anatomy ontology to indicate a subpart/part relationship within a tissue or organ. Ectocarp is part-of pericarp, which in turn is part-of fruit derived-from: This relationship is used in the anatomy and developmental stage ontologies to indicate the temporal relationship between a tissue or organ and its developmental predecessor. Ectocarp is derived- from ovary outer. Unlike a simple hierarchy, child nodes are allowed to have more than one parent node, thus allowing multiple child to parent relationships. The broader impact of this project is that it will provide a framework of plant development to allow researchers to make meaningful cross-database queries across the various species-specific resources in order to discover patterns of similarities and dissimilarities involved in plant development. For example, researchers will be able to obtain a definitive list of genes whose action affects plant stem development. The interaction between research communities will be facilitated by a “rosetta stone” that bridges their historical differences in terminology. This will allow the fruits of research in one plant species to be more easily used in the study of other species, leading to a greater understanding of plant biology. Medicago truncatula functional genomics Last NameFirst NameInstitutionRoleE-Mail SteinLincolnCold Spring Harbor LaboratoryPIlstein@cshl.org McCouchSusanCornell Univ.co-PIsrm4@cornell.edu KelloggElizabethUniversity of Missourico-PIkellogge@msx.umsl.edu RheeSueCarnegie Institution of Washingtonco-PIrhee@acoma.stanford.edu JaiswalPankajCornell Universityco-PIpj37@cornell.edu WareDoreenCold Spring Harbor Laboratoryco-PIware@cshl.org ReiserLeonoreCarnegie Institution of WashingtonKey personlreiser@acoma.stanford.edu StevensPeterMissouri Botanical Garden, University of Missouri Key personpeter.stevens@mobot.org VincentLeszekUniversity of MissouriKey personLeszek@missouri.edu DouglasCookUniversity of California DavisKey persondrcook@ucdavis.edu TanksleySteveCornell UniversityKey personsdt4@cornell.edu Plant anatomy ontology: Anatomic terms and relationships. Plant development ontology: Developmental terms and relationships. Plant Ontology definitions: Definitions of anatomy and developmental terms The Plant Ontology Consortium website. A CVS repository and FTP site for distribution of the consortium’s resources Contact Information for deliverables Lincoln Stein, lstein@cshl.org 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 NSF Award - #0321666 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 the one to one relationships. An example displaying how “endosperm” will be defined in the anatomy tree. An example displaying the organization of growth and developmental stages in rice plant. An example displaying the organization of fruits in an anatomy ontology tree and their relationship to each other. An example displaying annotation of Arabidopsis gene PHR1 using the Ontology term. 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 Example Data Sets Project Objectives Information/Materials to be Generated: Broader Impact