Planteome Ontology Development and Coordination Working Group

Kick Off Meeting: Monday January 5th, 2015

Goal: Discuss the coordination between the NSF Planteome Project and the Crop Ontology.

Who: EA, LC and PJ

1. Progress and Updates on the Crop Ontology (http://www.cropontology.org/)

• Annotation of phenotyping data through the IBP (https://www.integratedbreeding.net)
• Ontology manager on https://www.integratedbreeding.net/
• CO traits used to populate
• Agtrials (http://www.agtrials.org/) on CIAT another source
• Involvement of ICRISAT
• Genebank accessions- done at some centers e.g. CP
• Traits may be in common, but also there is variation between crops
• CO provides community-specific vocabularies for integration of data annotations

2. Ontology development and serving to users:

• With NSF's investment, they have certain requirements- need to minimize the duplication of efforts
• Centralized location for the ontology repositories- can be served to various portals as needed- such as the CO webpage the users are familiar with
• Need reliable system of versioning for the ontologies- Are the CO ones versioned currently?
• Reference ontologies need to be updated and expanded:
  • Core reference ontologies: PO, TO, GO, ENVO/EO, PATO, ChEBI
  • CO- species-specific vocabularies, ontologies
• CO has a tailored helpdesk for the users- needs to be maintained

• TO Development - could be opened to editing through Term Genie

3. Annotations and linking- vision of how the data is going to be shared

• SKOS format, OBO, move towards using OWL- at least in the reference ontologies
• Relations
• Need to be able to query across ontologies
• Need to create cross links between the crop-specific ontologies and the reference ones
• Design pilot project- pick a select group to focus on- will discuss further

4. Online resources web services, provide links to databases

• APIs can be set up as we move forward

5. Upcoming: