Abstract-BSA2010 - Revision history

Rwalls: moved Abstract to Abstract-BSA2010: clarity

2010-08-06T16:42:43Z

moved Abstract to Abstract-BSA2010: clarity

Rwalls: moved Oral presentation for Developmental and Structural Section to Abstract: make room for pdf of presentation

2010-08-06T16:41:49Z

moved Oral presentation for Developmental and Structural Section to Abstract: make room for pdf of presentation

Cooperl at 17:42, 29 March 2010

2010-03-29T17:42:37Z

Rwalls at 12:34, 26 March 2010

2010-03-26T12:34:19Z

Rwalls: add authors

2010-03-26T12:33:31Z

add authors

Rwalls at 12:30, 26 March 2010

2010-03-26T12:30:36Z

Rwalls: added Botany abstract

2010-03-26T12:30:11Z

added Botany abstract

New page

Botany 2010 Oral presentation for Structural and Developmental Section

'''The Plant Ontology: a tool for structural, developmental, and molecular plant biologists'''

The Plant Ontology (PO: http://www.plantontlogy.org) was developed to accommodate functional annotation efforts by plant databases in particular and the plant research community in general. Participating databases such as TAIR, NASC, Gramene, and MaizeGDB, have been using the PO since 2003 to describe structure- and growth-stage-specific expression of genes, proteins, and phenotypes from mutants and natural variants. The PO consists of two interrelated ontologies: 1. Plant Structure and 2. Plant Growth and Developmental Stages. Each ontology consists of a structured vocabulary that includes both definitions of terms and relationships among terms. In addition, there are links to annotations for associated genes, literature references, and images. To date there are over 1100 terms in the PO and over 500,000 associations. The original scope of the PO was a few model angiosperm species (Zea mays, Arabidopsis thaliana, and Oryza sativa), but with the expansion of sequencing information from new genomes, the PO is also expanding. We are working to encompass all land plants, making new cross-taxon comparisons possible. Additional species-specific terms will accommodate annotations from Vitis, Helianthus, Populus, Gossypium, Rosaceae (Malus and Prunus), Fabaceae (Medicago and Glycine), Solanaceae (Solanum and Lycopersicum), and Poaceae (Triticum, Hordeum, Avena, Sorghum, and Brachypodium). Coverage of non-angiosperm plants includes bryophytes such as Physcomitrella, Marchantia, and Selaginella, pteridophytes, and gymnosperms. The main purpose of the PO is to facilitate cross database querying and to foster consistent use of vocabularies in annotation. With the addition of non-angiosperm terminology and the continued addition of reference images, the PO also provides a novel reference and teaching tool that can be used as a guide to plant structures, their relationships and parts, and common growth and development landmarks in the lifecycles of plants across multiple taxa. This presentation will provide an overview of the ontologies being developed, the annotation database, and their possible applications.

← Older revision		Revision as of 17:42, 29 March 2010
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−	The Plant Ontology (PO: http://www.~~plantontlogy~~.org) was developed to accommodate functional annotation efforts by plant databases in particular and the plant research community in general. Participating databases such as TAIR, NASC, Gramene, and MaizeGDB, have been using the PO since 2003 to describe structure- and growth-stage-specific expression of genes, proteins, and phenotypes from mutants and natural variants. The PO consists of two interrelated ontologies: 1. Plant Structure and 2. Plant Growth and Developmental Stages. Each ontology consists of a structured vocabulary that includes both definitions of terms and relationships among terms. In addition, there are links to annotations for associated genes, literature references, and images. To date there are over 1100 terms in the PO and over 500,000 associations. The original scope of the PO was a few model angiosperm species (<i>Zea mays</i>, <i>Arabidopsis thaliana</i>, and <i>Oryza sativa</i>), but with the expansion of sequencing information from new genomes, the PO is also expanding. We are working to encompass all land plants, making new cross-taxon comparisons possible. Additional species-specific terms will accommodate annotations from <i>Vitis</i>, <i>Helianthus</i>, <i>Populus</i>, <i>Gossypium</i>, Rosaceae (<i>Malus</i> and <i>Prunus</i>), Fabaceae (<i>Medicago</i> and <i>Glycine</i>), Solanaceae (<i>Solanum</i> and <i>Lycopersicum</i>), and Poaceae (<i>Triticum</i>, <i>Hordeum</i>, <i>Avena</i>, <i>Sorghum</i>, and <i>Brachypodium</i>). Coverage of non-angiosperm plants includes bryophytes such as <i>Physcomitrella</i>, <i>Marchantia</i>, and <i>Selaginella</i>, pteridophytes, and gymnosperms. The main purpose of the PO is to facilitate cross database querying and to foster consistent use of vocabularies in annotation. With the addition of non-angiosperm terminology and the continued addition of reference images, the PO also provides a novel reference and teaching tool that can be used as a guide to plant structures, their relationships and parts, and common growth and development landmarks in the lifecycles of plants across multiple taxa. This presentation will provide an overview of the ontologies being developed, the annotation database, and their possible applications.	+	The Plant Ontology (PO: http://www.plantontology.org) was developed to accommodate functional annotation efforts by plant databases in particular and the plant research community in general. Participating databases such as TAIR, NASC, Gramene, and MaizeGDB, have been using the PO since 2003 to describe structure- and growth-stage-specific expression of genes, proteins, and phenotypes from mutants and natural variants. The PO consists of two interrelated ontologies: 1. Plant Structure and 2. Plant Growth and Developmental Stages. Each ontology consists of a structured vocabulary that includes both definitions of terms and relationships among terms. In addition, there are links to annotations for associated genes, literature references, and images. To date there are over 1100 terms in the PO and over 500,000 associations. The original scope of the PO was a few model angiosperm species (<i>Zea mays</i>, <i>Arabidopsis thaliana</i>, and <i>Oryza sativa</i>), but with the expansion of sequencing information from new genomes, the PO is also expanding. We are working to encompass all land plants, making new cross-taxon comparisons possible. Additional species-specific terms will accommodate annotations from <i>Vitis</i>, <i>Helianthus</i>, <i>Populus</i>, <i>Gossypium</i>, Rosaceae (<i>Malus</i> and <i>Prunus</i>), Fabaceae (<i>Medicago</i> and <i>Glycine</i>), Solanaceae (<i>Solanum</i> and <i>Lycopersicum</i>), and Poaceae (<i>Triticum</i>, <i>Hordeum</i>, <i>Avena</i>, <i>Sorghum</i>, and <i>Brachypodium</i>). Coverage of non-angiosperm plants includes bryophytes such as <i>Physcomitrella</i>, <i>Marchantia</i>, and <i>Selaginella</i>, pteridophytes, and gymnosperms. The main purpose of the PO is to facilitate cross database querying and to foster consistent use of vocabularies in annotation. With the addition of non-angiosperm terminology and the continued addition of reference images, the PO also provides a novel reference and teaching tool that can be used as a guide to plant structures, their relationships and parts, and common growth and development landmarks in the lifecycles of plants across multiple taxa. This presentation will provide an overview of the ontologies being developed, the annotation database, and their possible applications.

@@ Line 3: / Line 3: @@
 '''The Plant Ontology: a tool for structural, developmental, and molecular plant biologists'''
-Walls, Ramona L (rwalls@nybg.org) The New York Botanical Garden, Bronx, NY
+Walls, Ramona L., (rwalls@nybg.org) The New York Botanical Garden, Bronx, NY
-Cooper, Laurel D Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR
+Cooper, Laurel D., Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR
-Elser, Justin Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR
+Elser, Justin, Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR
-Stevenson, Dennis W 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
+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
+Gandolfo, Maria A., Department of Plant Biology, Cornell University, Ithaca, NY
-Jaiswal, Pankaj Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR
+Jaiswal, Pankaj, Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR
 The Plant Ontology (PO: http://www.plantontlogy.org) was developed to accommodate functional annotation efforts by plant databases in particular and the plant research community in general. Participating databases such as TAIR, NASC, Gramene, and MaizeGDB, have been using the PO since 2003 to describe structure- and growth-stage-specific expression of genes, proteins, and phenotypes from mutants and natural variants. The PO consists of two interrelated ontologies: 1. Plant Structure and 2. Plant Growth and Developmental Stages. Each ontology consists of a structured vocabulary that includes both definitions of terms and relationships among terms. In addition, there are links to annotations for associated genes, literature references, and images. To date there are over 1100 terms in the PO and over 500,000 associations. The original scope of the PO was a few model angiosperm species (<i>Zea mays</i>, <i>Arabidopsis thaliana</i>, and <i>Oryza sativa</i>), but with the expansion of sequencing information from new genomes, the PO is also expanding. We are working to encompass all land plants, making new cross-taxon comparisons possible. Additional species-specific terms will accommodate annotations from <i>Vitis</i>, <i>Helianthus</i>, <i>Populus</i>, <i>Gossypium</i>, Rosaceae (<i>Malus</i> and <i>Prunus</i>), Fabaceae (<i>Medicago</i> and <i>Glycine</i>), Solanaceae (<i>Solanum</i> and <i>Lycopersicum</i>), and Poaceae (<i>Triticum</i>, <i>Hordeum</i>, <i>Avena</i>, <i>Sorghum</i>, and <i>Brachypodium</i>). Coverage of non-angiosperm plants includes bryophytes such as <i>Physcomitrella</i>, <i>Marchantia</i>, and <i>Selaginella</i>, pteridophytes, and gymnosperms. The main purpose of the PO is to facilitate cross database querying and to foster consistent use of vocabularies in annotation. With the addition of non-angiosperm terminology and the continued addition of reference images, the PO also provides a novel reference and teaching tool that can be used as a guide to plant structures, their relationships and parts, and common growth and development landmarks in the lifecycles of plants across multiple taxa. This presentation will provide an overview of the ontologies being developed, the annotation database, and their possible applications.

← Older revision		Revision as of 12:33, 26 March 2010
Line 2:		Line 2:

	'''The Plant Ontology: a tool for structural, developmental, and molecular plant biologists'''		'''The Plant Ontology: a tool for structural, developmental, and molecular plant biologists'''
		+
		+	Walls, Ramona L (rwalls@nybg.org) The New York Botanical Garden, Bronx, NY
		+
		+	Cooper, Laurel D Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR
		+
		+	Elser, Justin Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR
		+
		+	Stevenson, Dennis W 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
		+

	The Plant Ontology (PO: http://www.plantontlogy.org) was developed to accommodate functional annotation efforts by plant databases in particular and the plant research community in general. Participating databases such as TAIR, NASC, Gramene, and MaizeGDB, have been using the PO since 2003 to describe structure- and growth-stage-specific expression of genes, proteins, and phenotypes from mutants and natural variants. The PO consists of two interrelated ontologies: 1. Plant Structure and 2. Plant Growth and Developmental Stages. Each ontology consists of a structured vocabulary that includes both definitions of terms and relationships among terms. In addition, there are links to annotations for associated genes, literature references, and images. To date there are over 1100 terms in the PO and over 500,000 associations. The original scope of the PO was a few model angiosperm species (<i>Zea mays</i>, <i>Arabidopsis thaliana</i>, and <i>Oryza sativa</i>), but with the expansion of sequencing information from new genomes, the PO is also expanding. We are working to encompass all land plants, making new cross-taxon comparisons possible. Additional species-specific terms will accommodate annotations from <i>Vitis</i>, <i>Helianthus</i>, <i>Populus</i>, <i>Gossypium</i>, Rosaceae (<i>Malus</i> and <i>Prunus</i>), Fabaceae (<i>Medicago</i> and <i>Glycine</i>), Solanaceae (<i>Solanum</i> and <i>Lycopersicum</i>), and Poaceae (<i>Triticum</i>, <i>Hordeum</i>, <i>Avena</i>, <i>Sorghum</i>, and <i>Brachypodium</i>). Coverage of non-angiosperm plants includes bryophytes such as <i>Physcomitrella</i>, <i>Marchantia</i>, and <i>Selaginella</i>, pteridophytes, and gymnosperms. The main purpose of the PO is to facilitate cross database querying and to foster consistent use of vocabularies in annotation. With the addition of non-angiosperm terminology and the continued addition of reference images, the PO also provides a novel reference and teaching tool that can be used as a guide to plant structures, their relationships and parts, and common growth and development landmarks in the lifecycles of plants across multiple taxa. This presentation will provide an overview of the ontologies being developed, the annotation database, and their possible applications.		The Plant Ontology (PO: http://www.plantontlogy.org) was developed to accommodate functional annotation efforts by plant databases in particular and the plant research community in general. Participating databases such as TAIR, NASC, Gramene, and MaizeGDB, have been using the PO since 2003 to describe structure- and growth-stage-specific expression of genes, proteins, and phenotypes from mutants and natural variants. The PO consists of two interrelated ontologies: 1. Plant Structure and 2. Plant Growth and Developmental Stages. Each ontology consists of a structured vocabulary that includes both definitions of terms and relationships among terms. In addition, there are links to annotations for associated genes, literature references, and images. To date there are over 1100 terms in the PO and over 500,000 associations. The original scope of the PO was a few model angiosperm species (<i>Zea mays</i>, <i>Arabidopsis thaliana</i>, and <i>Oryza sativa</i>), but with the expansion of sequencing information from new genomes, the PO is also expanding. We are working to encompass all land plants, making new cross-taxon comparisons possible. Additional species-specific terms will accommodate annotations from <i>Vitis</i>, <i>Helianthus</i>, <i>Populus</i>, <i>Gossypium</i>, Rosaceae (<i>Malus</i> and <i>Prunus</i>), Fabaceae (<i>Medicago</i> and <i>Glycine</i>), Solanaceae (<i>Solanum</i> and <i>Lycopersicum</i>), and Poaceae (<i>Triticum</i>, <i>Hordeum</i>, <i>Avena</i>, <i>Sorghum</i>, and <i>Brachypodium</i>). Coverage of non-angiosperm plants includes bryophytes such as <i>Physcomitrella</i>, <i>Marchantia</i>, and <i>Selaginella</i>, pteridophytes, and gymnosperms. The main purpose of the PO is to facilitate cross database querying and to foster consistent use of vocabularies in annotation. With the addition of non-angiosperm terminology and the continued addition of reference images, the PO also provides a novel reference and teaching tool that can be used as a guide to plant structures, their relationships and parts, and common growth and development landmarks in the lifecycles of plants across multiple taxa. This presentation will provide an overview of the ontologies being developed, the annotation database, and their possible applications.

@@ Line 1: / Line 1: @@
-Botany 2010 Oral presentation for Structural and Developmental Section
+Botany 2010 Oral presentation for Developmental and Structural Section
 '''The Plant Ontology: a tool for structural, developmental, and molecular plant biologists'''
 The Plant Ontology (PO: http://www.plantontlogy.org) was developed to accommodate functional annotation efforts by plant databases in particular and the plant research community in general. Participating databases such as TAIR, NASC, Gramene, and MaizeGDB, have been using the PO since 2003 to describe structure- and growth-stage-specific expression of genes, proteins, and phenotypes from mutants and natural variants. The PO consists of two interrelated ontologies: 1. Plant Structure and 2. Plant Growth and Developmental Stages. Each ontology consists of a structured vocabulary that includes both definitions of terms and relationships among terms. In addition, there are links to annotations for associated genes, literature references, and images. To date there are over 1100 terms in the PO and over 500,000 associations. The original scope of the PO was a few model angiosperm species (<i>Zea mays</i>, <i>Arabidopsis thaliana</i>, and <i>Oryza sativa</i>), but with the expansion of sequencing information from new genomes, the PO is also expanding. We are working to encompass all land plants, making new cross-taxon comparisons possible. Additional species-specific terms will accommodate annotations from <i>Vitis</i>, <i>Helianthus</i>, <i>Populus</i>, <i>Gossypium</i>, Rosaceae (<i>Malus</i> and <i>Prunus</i>), Fabaceae (<i>Medicago</i> and <i>Glycine</i>), Solanaceae (<i>Solanum</i> and <i>Lycopersicum</i>), and Poaceae (<i>Triticum</i>, <i>Hordeum</i>, <i>Avena</i>, <i>Sorghum</i>, and <i>Brachypodium</i>). Coverage of non-angiosperm plants includes bryophytes such as <i>Physcomitrella</i>, <i>Marchantia</i>, and <i>Selaginella</i>, pteridophytes, and gymnosperms. The main purpose of the PO is to facilitate cross database querying and to foster consistent use of vocabularies in annotation. With the addition of non-angiosperm terminology and the continued addition of reference images, the PO also provides a novel reference and teaching tool that can be used as a guide to plant structures, their relationships and parts, and common growth and development landmarks in the lifecycles of plants across multiple taxa. This presentation will provide an overview of the ontologies being developed, the annotation database, and their possible applications.

← Older revision	Revision as of 16:42, 6 August 2010
(No difference)

← Older revision	Revision as of 16:41, 6 August 2010
(No difference)