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Link to PDF of presentation: [[Media:Walls_PO_presentation_IBC11.pdf]]


'''The Plant Ontology: an updated tool for all plant biologists'''

Symposium: Bio-ontologies for Plant Science

Walls, Ramona L., rwalls@nybg.org The New York Botanical Garden, Bronx, NY

Cooper, Laurel D., cooperl@science.oregonstate.edu Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 

Elser, Justin, elserj@science.oregonstate.edu Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR

Preece, Justin, preecej @science.oregonstate.edu Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR

Gandolfo, Maria A., mag4@cornell.edu Department of Plant Biology, Cornell University, Ithaca, NY 

Mungall, Chris, cjm@berkeleybop.org Lawrence Berkeley National Lab, Berkeley, CA

Smith, Barry phismith@buffalo.edu Department of Philosophy, University at Buffalo, NY

Stevenson, Dennis W., dws@nybg.org The New York Botanical Garden, Bronx, NY

Jaiswal, Pankaj, jaiswalp@science.oregonstate.edu Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 



The Plant Ontology (PO: http://plantontology.org) is a structured vocabulary and database resource for plant researchers that links plant anatomy and development to the rapidly expanding field of genomics in the domain of all green plants. The PO contains interrelated concepts or terms, organized in a hierarchical tree, that describe plant anatomy and morphology, as well as plant growth and development stages. Like all ontologies, the PO facilitates data sharing and automated analyses through the consistent use of vocabulary with explicit, logical definitions and defined relationships among terms. Originally designed to span the monocot-dicot divide in flowering plants (based on the model angiosperms Zea mays, Oryza sativa, and Arabidopsis thaliana), the PO has been redesigned to encompass all angiosperm species and to include terms and annotations from non-flowering plants such as gymnosperms, pteridophytes, and bryophytes. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages across such a broad taxonomic range. Over the past 18 months, upper level parent terms have been added, renamed, or revised to ensure applicability to the entire plant kingdom, allowing comparative studies across distantly related taxa. At the same time, many new clade-specific terms have been introduced at lower levels, allowing precise annotation of genomic and genetic datasets for individual species. Throughout the revision process, curators worked to incorporate advances in ontology design and construction. These included the use of logical text and relational definitions and references to external ontologies where appropriate. An essential, powerful feature of the PO is the links through terms to associated structure or growth stage specific genes, proteins, and phenotypes from numerous genomics datasets. One of the main goals of the PO is to facilitate cross-database querying and to foster consistent use of vocabularies in annotation. To this end, the PO is developing annotation tools for the plant science community. Outreach activities include annotation workshops and outreach booths and symposia at international conferences. Currently, the PO includes over 500,000 annotations associated with over 1,100 terms. In this capacity, it is widely applicable to plant genomic and evolutionary developmental studies. In addition, image libraries are being created through PlantSystematics.org and linked to terms to provide reference images for plant structures, along with the definitions. This makes the PO a valuable resource for research and teaching that can be used as a guide to plant structures and the common growth and developmental landmarks in lifecycles of plants across taxa. This presentation will provide an overview of the Plant Ontology and the annotation database, as well as potential applications of the PO. The PO is publicly available and collaboration with diverse user groups is encouraged. Information will be available for research groups that wish to provide annotations or use the PO in novel applications.

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