Planteome Ontology Development and Coordination Working Group: Difference between revisions

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'''[[Crop Ontology and Planteome Project Meeting Monday Jan 12th @ PAG 2015]]'''
'''[[Crop Ontology and Planteome Project Meeting Monday Jan 12th @ PAG 2015]]'''


==Planteome_Ontology_Working_Group_Meeting- Jan 22, 2015==
==[[Planteome_Ontology_Working_Group_Meeting- Jan 22, 2015]]==


Who: EA, LC and PJ
Who: EA, LC and PJ
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''To-do: create page for Scientific Advisory Board, Ontology Workshop''
''To-do: create page for Scientific Advisory Board, Ontology Workshop''


=Tues Feb 10th, 2015=
=Tues Feb 10th, 2015=

Revision as of 03:21, 8 February 2015

Go back to Planteome_Wiki_Home Page

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

Who: EA, LC and PJ Points of Discussion:

1. Planteome wiki set up

  • will add EA and others on her team as needed..
  • Will be closed, will have to login to access

2. Interaction with DivSeek.

  • Ruth Bastow is on the board and is interested in coordinating between the projects. DivSeek is a partnership, advisory board role may create COI?

3. Scientific Advisory Board- will have info on the wiki- create page for Scientific Advisory Board

  • Oversight, annual report, meeting in person or online
  • advocates to community, users and funding agencies
  • possibly representative from CG centers such as RH, PK

4. Prioritizing the CO vocabularies for cross referencing and curator training

  • Rice- IRRI is shorthanded right now, possible person is Berta Miro- associated with IRRI (Ajay Kohli)
  • Maize and wheat - CIMMYT- Rosemary; Project already underway with LC + Mary Schaeffer
    • WheatIS and WDIWG of the RDA- interested in using ontologies and setting standards
  • Soybean- USDA Rex Nelson
  • Potato - CIP Reinhard, Richard Finkers (also other solanaceae)

5. Planning is starting for Ontology Workshop in the Spring

  • Owl training, etc
  • more details TBA as they develop

6. Collaboration possibilities with PL, AV and CJ, from IRD in Montpellier

  • CJ will be in Stanford this spring, has money for a postdoc for a year which will go away without a project.
  • Southgreen platform, involvement with 3000 rice genomes project
  • Semantic integration

To-do: create page for Scientific Advisory Board, Ontology Workshop

Tues Feb 10th, 2015