Planteome Ontology Development and Coordination Working Group: Difference between revisions

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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 03:17, 8 February 2015

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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/)

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


Tues Feb 10th, 2015

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