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:
Crop Ontology and Planteome Project Meeting Monday Jan 12th @ PAG 2015