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

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

5. Upcoming:

Planteome Ontology Development and Coordination Working Group