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=<big>About the Planteome Project</big>= | |||
* The Planteome Project (http://planteome.org/) is a newly-funded ([http://www.nsf.gov/awardsearch/showAward?AWD_ID=1340112 NSF Award #1340112] Dec. 2014) initiative which will build on the work done in the Plant Ontology Project ([http://plantontology.org link]), and will 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 Project (http://planteome.org/) is a newly-funded ([http://www.nsf.gov/awardsearch/showAward?AWD_ID=1340112 NSF Award #1340112] Dec. 2014) initiative which will build on the work done in the Plant Ontology Project ([http://plantontology.org link]), and will 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 continue to develop and enrich the existing reference ontologies, the Plant Ontology (PO), Plant Trait Ontology (TO), and the Plant Environment Ontology (EO) and will encompass relevant aspects of other reference ontologies such as the Gene Ontology (GO), Cell type Ontology (CL), Chemical Entities of Biological Interest (ChEBI), Protein Ontology (PR) and the Phenotypic Qualities Ontology (PATO). | * The Planteome will continue to develop and enrich the existing reference ontologies, the Plant Ontology (PO), Plant Trait Ontology (TO), and the Plant Environment Ontology (EO) and will encompass relevant aspects of other reference ontologies such as the Gene Ontology (GO), Cell type Ontology (CL), Chemical Entities of Biological Interest (ChEBI), Protein Ontology (PR) 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 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= | |||
'''1. 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.''' | '''1. 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.''' | ||
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'''5. Outreach involving K-12 and undergraduate students, and the plant research community.''' | '''5. Outreach involving K-12 and undergraduate students, and the plant research community.''' | ||
=Planteome Project Management= | |||
==[[Planteome Outreach]]== | |||
==[[Planteome All-Hands Monthly meetings]]== | |||
[[Planteome_cROP_Grant_Proposal]] | [[Planteome_cROP_Grant_Proposal]] | ||
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[[Position Paper- Setting Standards for Plant Phenotyping]] | [[Position Paper- Setting Standards for Plant Phenotyping]] | ||
[[Planteome Collaborations]] | [[Planteome Collaborations]] [http://planteome.org/node/9?q=node/6] | ||
=Planteome Project Working Groups = | |||
[[Planteome Ontology Development and Coordination Working Group]] | [[Planteome Ontology Development and Coordination Working Group]] | ||
| Line 32: | Line 33: | ||
[[Data storage and AmiGO2 Working Group]] | [[Data storage and AmiGO2 Working Group]] | ||
Latest revision as of 17:22, 20 November 2015
About the Planteome Project
- The Planteome Project (http://planteome.org/) is a newly-funded (NSF Award #1340112 Dec. 2014) initiative which will build on the work done in the Plant Ontology Project (link), and will 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 continue to develop and enrich the existing reference ontologies, the Plant Ontology (PO), Plant Trait Ontology (TO), and the Plant Environment Ontology (EO) and will encompass relevant aspects of other reference ontologies such as the Gene Ontology (GO), Cell type Ontology (CL), Chemical Entities of Biological Interest (ChEBI), Protein Ontology (PR) 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
1. 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.
2. Standards, workflows and tools for ontology development, curation and improved annotation of genes, genomes, phenotype and germplasm.
3. An online informatics portal and data warehouse for ontology-based, annotated plant genome data and plant genomes.
4. Smart and semantic data query, analysis, visualization, and community-based annotation and curation tools.
5. Outreach involving K-12 and undergraduate students, and the plant research community.
Planteome Project Management
Planteome Outreach
Planteome All-Hands Monthly meetings
Position Paper- Setting Standards for Plant Phenotyping
Planteome Project Working Groups
Planteome Ontology Development and Coordination Working Group