Difference between revisions of "Planteome Ontology Development and Coordination Working Group"
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'''[[Ontology_Group_Meeting:_Monday_January_5th,_2015]]''' | '''[[Ontology_Group_Meeting:_Monday_January_5th,_2015]]''' | ||
+ | |||
+ | Kick Off Meeting: Monday January 5th, 2015 | ||
+ | |||
+ | Who: EA, LC and PJ | ||
+ | |||
+ | '''Goal: Discuss the coordination between the NSF Planteome Project and the Crop Ontology.''' | ||
+ | |||
+ | '''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: Planteome-CO Coordination meeting at PAG Jan 12th''' | ||
+ | |||
'''[[Crop Ontology and Planteome Project Meeting Monday Jan 12th @ PAG 2015]]''' | '''[[Crop Ontology and Planteome Project Meeting Monday Jan 12th @ PAG 2015]]''' |
Revision as of 20:17, 7 February 2015
Go back to Planteome_Wiki_Home Page
Ontology_Group_Meeting:_Monday_January_5th,_2015
Kick Off Meeting: Monday January 5th, 2015
Who: EA, LC and PJ
Goal: Discuss the coordination between the NSF Planteome Project and the Crop Ontology.
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: Planteome-CO Coordination meeting at PAG Jan 12th
Crop Ontology and Planteome Project Meeting Monday Jan 12th @ PAG 2015
Planteome_Ontology_Working_Group_Meeting- Jan 22, 2015