Planteome Ontology Development and Coordination Working Group

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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

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