Difference between revisions of "Planteome Ontology Development and Coordination Working Group"
(Replaced content with "Go back to Planteome_Wiki_Home Page =Tues Feb 10th, 2015=") |
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Go back to [[Planteome_Wiki_Home]] Page | 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/)''' | ||
+ | * 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'' | ||
=Tues Feb 10th, 2015= | =Tues Feb 10th, 2015= |
Revision as of 20:25, 7 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/)
- 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