Difference between revisions of "Planteome Ontology Development and Coordination Working Group"
From Planteome.org
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* With NSF's investment, they have certain requirements- need to minimize the duplication of efforts | * 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 | * 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 | + | * Need reliable system of versioning for the ontologies- Are the CO ones versioned currently? |
* Reference ontologies need to be updated and expanded | * Reference ontologies need to be updated and expanded | ||
− | + | * 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 | ||
+ | * 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''' | '''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 | ||
+ | |||
− | 4. Online resources web services, provide links to databases | + | '''4. Online resources web services, provide links to databases''' |
+ | * APIs |
Revision as of 12:40, 20 January 2015
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
- 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
- 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
4. Online resources web services, provide links to databases
- APIs