Planteome Ontology Development and Coordination Working Group: Difference between revisions

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* 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:'''
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* 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, onntologies
** CO- species-specific vocabularies, ontologies
* Need to be able to query across ontologies
* CO has a tailored helpdesk for the users- needs to be maintained
 
 


* Need to create cross links between the crop-specific ontologies and the reference ones-
* TO Development - could be opened to editing through Term Genie
* 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
* SKOS format, OBO, move towards using OWL- at least in the reference ontologies
* relations
* 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/)


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: