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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 All-Hands Monthly meetings

Planteome_cROP_Grant_Proposal

Scientific Advisory Board

Position Paper- Setting Standards for Plant Phenotyping

Planteome Collaborations

Planteome Project Working Groups

Planteome Ontology Development and Coordination Working Group

Planteome_Image_Annotation_Working_Group

Data storage and AmiGO2 Working Group

Planteome Outreach

2015:

Plant and Animal Genome Meeting, January 9-13, 2015 San Diego, CA

Link to Conference program: Plant and Animal Genome Meeting XXIII

  • DivSeek Meeting- Friday January 9th from 8am-5pm
  • Systems Biology and Ontologies Workshop, Saturday January 10th from 8:00-10:10 AM. Organizers: Laurel Cooper, Sushma Naithani and Pankaj Jaiswal
  • Plant Phenotypes Workshop, Sunday, January 11, 2015. Organizers: Mary Schaeffer and Chi-Ren Shyu
  • Crop Ontology Meeting Monday, January 12, 2015. Organizers: Elizabeth Arnaud and Rex Nelson

2015 Maize Genetics Conference- March 12-15, 2015, St. Charles, Illinois, USA

Upcoming Meetings of Interest:

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