Planteome Ontology Development and Coordination Working Group: Difference between revisions
Jump to navigation
Jump to search
| Line 13: | Line 13: | ||
* Traits may be in common, but also there is variation between crops | * Traits may be in common, but also there is variation between crops | ||
* CO provides community-specific vocabularies for integration of data annotations | * CO provides community-specific vocabularies for integration of data annotations | ||
'''2. Ontology development and serving to users:''' | '''2. Ontology development and serving to users:''' | ||
| Line 20: | Line 21: | ||
* Reference ontologies need to be updated and expanded: | * Reference ontologies need to be updated and expanded: | ||
** Core reference ontologies: PO, TO, GO, ENVO/EO, PATO, ChEBI | ** Core reference ontologies: PO, TO, GO, ENVO/EO, PATO, ChEBI | ||
** CO- species-specific vocabularies, | ** 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''' | '''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 | * 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''' | '''4. Online resources web services, provide links to databases''' | ||
Revision as of 00:19, 21 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:
- 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: