|
|
| Line 1: |
Line 1: |
| Go back to [[Planteome_Wiki_Home]] Page | | Go back to [[Planteome_Wiki_Home]] Page |
|
| |
|
| ==Kick Off Meeting: Monday January 5th, 2015==
| | [[Ontology_Working_Group_Meetings-_Jan_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= |