Difference between revisions of "Mini-symposium presentation"
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As data is generated from the various plant genome and comparative genomics projects, the working vocabulary from group to group and species to species can be disparate. To enable researchers across species to draw conclusions from known or predicted experiments, we are developing controlled vocabularies (ontologies) to describe plant morphologies, anatomical structures, and growth and developmental stages. Since the inception of the Plant Ontology (PO) database in 2003, plant biologists have been able to annotate and describe tissue and/or growth stage specific expression of proteins, genes, and phenotypes that were observed in experiments by utilizing PO terms in the database. There are currently over 1,100 terms documented in the PO, with over 500,000 associations, of which over 85% have been added within the last year. Currently, we are in the process of expanding the coverage of PO to non-angiosperm plants to include mosses (<i>Physcomitrella</i>), Lycopods (<i>Selaginella</i>), pteridophytes (ferns) and gymnosperms (conifers and cycads). We are also adding additional species-specific terms to accommodate annotations from Vitaceae (grape), Rosaceae (apple, cherry), Fabaceae (<i>Medicago</i> and soybean), Compositeae (sunflower), Solanaceae (potato, tomato), Poaceae (wheat, barley, oat, <i>Sorghum</i> and <i>Brachypodium</i>), Salicaceae (poplar) and Malvaceae (cotton). The development of the PO is coordinated with the development of the Gene Ontology (GO), and together these resources can be used to provide a comprehensive picture of the function, location and phenotypic effects of genes and gene products. The Plant Ontology project is funded by the National Science Foundation, USA and includes collaborations with groups from around the world. | As data is generated from the various plant genome and comparative genomics projects, the working vocabulary from group to group and species to species can be disparate. To enable researchers across species to draw conclusions from known or predicted experiments, we are developing controlled vocabularies (ontologies) to describe plant morphologies, anatomical structures, and growth and developmental stages. Since the inception of the Plant Ontology (PO) database in 2003, plant biologists have been able to annotate and describe tissue and/or growth stage specific expression of proteins, genes, and phenotypes that were observed in experiments by utilizing PO terms in the database. There are currently over 1,100 terms documented in the PO, with over 500,000 associations, of which over 85% have been added within the last year. Currently, we are in the process of expanding the coverage of PO to non-angiosperm plants to include mosses (<i>Physcomitrella</i>), Lycopods (<i>Selaginella</i>), pteridophytes (ferns) and gymnosperms (conifers and cycads). We are also adding additional species-specific terms to accommodate annotations from Vitaceae (grape), Rosaceae (apple, cherry), Fabaceae (<i>Medicago</i> and soybean), Compositeae (sunflower), Solanaceae (potato, tomato), Poaceae (wheat, barley, oat, <i>Sorghum</i> and <i>Brachypodium</i>), Salicaceae (poplar) and Malvaceae (cotton). The development of the PO is coordinated with the development of the Gene Ontology (GO), and together these resources can be used to provide a comprehensive picture of the function, location and phenotypic effects of genes and gene products. The Plant Ontology project is funded by the National Science Foundation, USA and includes collaborations with groups from around the world. | ||
Latest revision as of 12:43, 26 March 2010
ASPB 2010 Oral presentation for mini-symposium
The Plant Ontology: A Database for Plant Genomics
Cooper, Laurel D., (cooperl@science.oregonstate.edu) Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR
Elser, Justin, Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR
Walls, Ramona L., The New York Botanical Garden, Bronx, NY
Stevenson, Dennis Wm., The New York Botanical Garden, Bronx, NY
Smith, Barry, Department of Philosophy, University at Buffalo, NY
Mungall, Chris Lawrence Berkeley National Lab, Berkeley, CA
Gandolfo, Maria A., Department of Plant Biology, Cornell University, Ithaca, NY
Jaiswal, Pankaj, Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR
As data is generated from the various plant genome and comparative genomics projects, the working vocabulary from group to group and species to species can be disparate. To enable researchers across species to draw conclusions from known or predicted experiments, we are developing controlled vocabularies (ontologies) to describe plant morphologies, anatomical structures, and growth and developmental stages. Since the inception of the Plant Ontology (PO) database in 2003, plant biologists have been able to annotate and describe tissue and/or growth stage specific expression of proteins, genes, and phenotypes that were observed in experiments by utilizing PO terms in the database. There are currently over 1,100 terms documented in the PO, with over 500,000 associations, of which over 85% have been added within the last year. Currently, we are in the process of expanding the coverage of PO to non-angiosperm plants to include mosses (Physcomitrella), Lycopods (Selaginella), pteridophytes (ferns) and gymnosperms (conifers and cycads). We are also adding additional species-specific terms to accommodate annotations from Vitaceae (grape), Rosaceae (apple, cherry), Fabaceae (Medicago and soybean), Compositeae (sunflower), Solanaceae (potato, tomato), Poaceae (wheat, barley, oat, Sorghum and Brachypodium), Salicaceae (poplar) and Malvaceae (cotton). The development of the PO is coordinated with the development of the Gene Ontology (GO), and together these resources can be used to provide a comprehensive picture of the function, location and phenotypic effects of genes and gene products. The Plant Ontology project is funded by the National Science Foundation, USA and includes collaborations with groups from around the world.
