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| Go back to [[Planteome_Wiki_Home]] Page | | Go back to [[Planteome_Wiki_Home]] Page |
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| ==Kick Off Meeting: Monday January 5th, 2015==
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| Who: EA, LC and PJ
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| '''Goal: Discuss the coordination between the NSF Planteome Project and the Crop Ontology.'''
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| '''1. Progress and Updates on the Crop Ontology (http://www.cropontology.org/)'''
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| * Annotation of phenotyping data through the IBP (https://www.integratedbreeding.net)
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| * Ontology manager on https://www.integratedbreeding.net/
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| * CO traits used to populate
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| * Agtrials (http://www.agtrials.org/) on CIAT another source
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| * Involvement of ICRISAT
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| * Genebank accessions- done at some centers e.g. CP
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| * Traits may be in common, but also there is variation between crops
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| * CO provides community-specific vocabularies for integration of data annotations
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| '''2. Ontology development and serving to users:'''
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| * With NSF's investment, they have certain requirements- need to minimize the duplication of efforts
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| * Centralized location for the ontology repositories- can be served to various portals as needed- such as the CO webpage the users are familiar with
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| * Need reliable system of versioning for the ontologies- Are the CO ones versioned currently?
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| * Reference ontologies need to be updated and expanded:
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| ** Core reference ontologies: PO, TO, GO, ENVO/EO, PATO, ChEBI
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| ** CO- species-specific vocabularies, ontologies
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| * CO has a tailored helpdesk for the users- needs to be maintained
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| * TO Development - could be opened to editing through Term Genie
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| '''3. Annotations and linking- vision of how the data is going to be shared'''
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| * SKOS format, OBO, move towards using OWL- at least in the reference ontologies
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| * Relations
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| * Need to be able to query across ontologies
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| * Need to create cross links between the crop-specific ontologies and the reference ones
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| * Design pilot project- pick a select group to focus on- will discuss further
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| '''4. Online resources web services, provide links to databases'''
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| * APIs can be set up as we move forward
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| '''5. Upcoming: Planteome-CO Coordination meeting at PAG Jan 12th'''
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| '''[[Crop Ontology and Planteome Project Meeting Monday Jan 12th @ PAG 2015]]'''
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| ==[[Planteome_Ontology_Working_Group_Meeting- Jan 22, 2015]]==
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| Who: EA, LC and PJ
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| Points of Discussion:
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| 1. Planteome wiki set up
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| * will add EA and others on her team as needed..
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| * Will be closed, will have to login to access
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| 2. Interaction with DivSeek.
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| * Ruth Bastow is on the board and is interested in coordinating between the projects. DivSeek is a partnership, advisory board role may create COI?
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| 3. Scientific Advisory Board- will have info on the wiki- create page for Scientific Advisory Board
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| * Oversight, annual report, meeting in person or online
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| * advocates to community, users and funding agencies
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| * possibly representative from CG centers such as RH, PK
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| 4. Prioritizing the CO vocabularies for cross referencing and curator training
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| * Rice- IRRI is shorthanded right now, possible person is Berta Miro- associated with IRRI (Ajay Kohli)
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| * Maize and wheat - CIMMYT- Rosemary; Project already underway with LC + Mary Schaeffer
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| ** WheatIS and WDIWG of the RDA- interested in using ontologies and setting standards
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| * Soybean- USDA Rex Nelson
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| * Potato - CIP Reinhard, Richard Finkers (also other solanaceae)
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| 5. Planning is starting for Ontology Workshop in the Spring
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| * Owl training, etc
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| * more details TBA as they develop
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| 6. Collaboration possibilities with PL, AV and CJ, from IRD in Montpellier
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| * CJ will be in Stanford this spring, has money for a postdoc for a year which will go away without a project.
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| * Southgreen platform, involvement with 3000 rice genomes project
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| * Semantic integration
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| ''To-do: create page for Scientific Advisory Board, Ontology Workshop''
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| =Tues Feb 10th, 2015= | | =Tues Feb 10th, 2015= |