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[[Planteome All-Hands Monthly meetings]] | [[Planteome All-Hands Monthly meetings]] | ||
The Planteome Project (http://planteome.org/) is a newly funded ([http://www.nsf.gov/awardsearch/showAward?AWD_ID=1340112 NSF Award #1340112]) initiative which will be create a centralized platform where reference ontologies for plants will be used to access cutting-edge data resources for plant traits, phenotypes, diseases, genomes and semantically-queried genetic diversity and gene expression data across a wide range of plant species. The Planteome will develop the Plant Trait Ontology (TO), the Plant Stress Ontology (PSO), and the Plant Environment Ontology (EO) besides taking over the development of Plant Ontology (PO). It will also include relevant aspects of ontologies such as Gene Ontology (GO), Cell type (CL), Chemical Entities (ChEBI), Protein Ontology and the Phenotypic Qualities Ontology (PATO). The Planteome fits into the existing biological ontology landscape, and will be an active participant in the OBO Foundry (http://obofoundry.org/crit.shtml), adhering to all of its principles. We will collaborate with the existing reference ontologies and contribute to their enrichment in terms and definitions of common importance to plant biology. | The Planteome Project (http://planteome.org/) is a newly-funded ([http://www.nsf.gov/awardsearch/showAward?AWD_ID=1340112 NSF Award #1340112]) initiative which will be create a centralized platform where reference ontologies for plants will be used to access cutting-edge data resources for plant traits, phenotypes, diseases, genomes and semantically-queried genetic diversity and gene expression data across a wide range of plant species. The Planteome will develop the Plant Trait Ontology (TO), the Plant Stress Ontology (PSO), and the Plant Environment Ontology (EO) besides taking over the development of Plant Ontology (PO). It will also include relevant aspects of ontologies such as Gene Ontology (GO), Cell type (CL), Chemical Entities (ChEBI), Protein Ontology and the Phenotypic Qualities Ontology (PATO). The Planteome fits into the existing biological ontology landscape, and will be an active participant in the OBO Foundry (http://obofoundry.org/crit.shtml), adhering to all of its principles. We will collaborate with the existing reference ontologies and contribute to their enrichment in terms and definitions of common importance to plant biology. | ||
==Specific Aims of the Project:== | |||
* Bulleted list item | |||
Aim-1: Develop a set of common reference ontologies to describe major knowledge domains of plant biology, comprising plant phenotype and traits, environments, and biotic and abiotic stresses, including plant diseases: | |||
* Bulleted list item | |||
Aim-2. Develop standards, workflows and tools for ontology development, curation and improved annotation of genes, genomes, phenotype and germplasm. | |||
* Bulleted list item | |||
Aim-3: Develop an online informatics portal and data warehouse for ontology-based, annotated plant genome data and plant genomes. | |||
In order to maintain high quality standards for data annotation and provide a common place to find these annotations, we are proposing a new web portal and a data warehouse to host and serve the reference ontologies and the associated annotation data. | |||
* Bulleted list item | |||
Aim-4: Develop smart and semantic data query, analysis, visualization, and community-based annotation and curation tools. | |||
* Bulleted list item | |||
Aim-5: Outreach involving K-12 and undergraduate students, and the plant research community: | |||
== Planteome Project Working Groups: == | == Planteome Project Working Groups: == | ||
Revision as of 22:03, 8 February 2015
About the Planteome Project
Planteome All-Hands Monthly meetings
The Planteome Project (http://planteome.org/) is a newly-funded (NSF Award #1340112) initiative which will be create a centralized platform where reference ontologies for plants will be used to access cutting-edge data resources for plant traits, phenotypes, diseases, genomes and semantically-queried genetic diversity and gene expression data across a wide range of plant species. The Planteome will develop the Plant Trait Ontology (TO), the Plant Stress Ontology (PSO), and the Plant Environment Ontology (EO) besides taking over the development of Plant Ontology (PO). It will also include relevant aspects of ontologies such as Gene Ontology (GO), Cell type (CL), Chemical Entities (ChEBI), Protein Ontology and the Phenotypic Qualities Ontology (PATO). The Planteome fits into the existing biological ontology landscape, and will be an active participant in the OBO Foundry (http://obofoundry.org/crit.shtml), adhering to all of its principles. We will collaborate with the existing reference ontologies and contribute to their enrichment in terms and definitions of common importance to plant biology.
Specific Aims of the Project:
- Bulleted list item
Aim-1: Develop a set of common reference ontologies to describe major knowledge domains of plant biology, comprising plant phenotype and traits, environments, and biotic and abiotic stresses, including plant diseases:
- Bulleted list item
Aim-2. Develop standards, workflows and tools for ontology development, curation and improved annotation of genes, genomes, phenotype and germplasm.
- Bulleted list item
Aim-3: Develop an online informatics portal and data warehouse for ontology-based, annotated plant genome data and plant genomes. In order to maintain high quality standards for data annotation and provide a common place to find these annotations, we are proposing a new web portal and a data warehouse to host and serve the reference ontologies and the associated annotation data.
- Bulleted list item
Aim-4: Develop smart and semantic data query, analysis, visualization, and community-based annotation and curation tools.
- Bulleted list item
Aim-5: Outreach involving K-12 and undergraduate students, and the plant research community:
Planteome Project Working Groups:
Planteome Ontology Development and Coordination Working Group