Thursday Feb 6th, 2015: Difference between revisions
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====Elizabeth Arnaud: CGIAR ==== | ====Elizabeth Arnaud: CGIAR Centers ==== | ||
Crop Ontologies (http://www.cropontology.org/) | Crop Ontologies (http://www.cropontology.org/) | ||
* Applied ontologies, crop specific ontologies and vocabularies for plant breeders communities | * Applied ontologies, crop specific ontologies and vocabularies for plant breeders communities traits, methods and scales | ||
* Align concepts with PO, TO, GO, PDO and expand the list of traits | |||
* Integrating descriptors for annotating germplasm=m and genetic experiments in the various CGIAR campuses | * Integrating descriptors for annotating germplasm=m and genetic experiments in the various CGIAR campuses | ||
* List of 8-10 crops and or clades | * List of 8-10 crops and or clades, and will add additional ones | ||
* Build common references and cross links | * Build common references and cross links | ||
* Contribute to development of the reference ontologies | * Contribute to development of the reference ontologies | ||
* Outreach to users on CGIARS campuses | * Outreach to users on CGIARS campuses | ||
* Key crops for the initial pilot cases: wheat, maize, rice | * Key crops for the initial pilot cases: wheat, maize, rice | ||
* Will also test alignment tools and | * Will also test alignment tools and annotation tools | ||
Revision as of 00:30, 6 February 2015
Planteome All-Hands Monthly Meeting- Thursday Feb 6th, 2015
Who: PJ, EA, LC, JE, JP, DWS, GG, EZ, BS; Not available: ST, CM, JD
Agenda:
A. Introductions, as some people have not met yet.
See details on last months page: Tuesday_Jan_6th,_2015
Barry Smith, University at Buffalo
- Head of the OBO Foundry, Ontology Consultant
- Guidance on ontology development, consistent structure for PO and can be extended to other ontologies
- Setting standards for ontologies
Georgios Gkoutos, University of Aberystwyth, UK:
- Roles- As laid out in the proposal, (Fibi? was this referring to the ERA-CAPs proposal??)
- create logical definitions for plant phenotype ontology
- Expand Plant Phenoment , along with Phenotype RCN
- Developed out of http://phenomebrowser.net/index.html
- Contribute to expanding the reference ontologies as need
- PATO partially funded from this project, will need to address needs of the Planteome as we move forward
- Should have an acknowledgment on the PATO web site:http://wiki.obofoundry.org/wiki/index.php/PATO:Main_Page
- Will be hiring a postdoc once the contracts are set up, somewhat of a lengthly procedure, will keep us posted
- Will be working with the ontology group and closely with John Doonan
John Doonan, University of Aberystwyth, UK (not present on the call)
- Senior person, collaborator- Director National Plant Phenomics Centre for the UK (http://www.plant-phenomics.ac.uk/en/)
- Tools and workflows developed in the project will be integrated into the NPPC, for the phenotype evaluation
Elizabeth Arnaud: CGIAR Centers
Crop Ontologies (http://www.cropontology.org/)
- Applied ontologies, crop specific ontologies and vocabularies for plant breeders communities traits, methods and scales
- Align concepts with PO, TO, GO, PDO and expand the list of traits
- Integrating descriptors for annotating germplasm=m and genetic experiments in the various CGIAR campuses
- List of 8-10 crops and or clades, and will add additional ones
- Build common references and cross links
- Contribute to development of the reference ontologies
- Outreach to users on CGIARS campuses
- Key crops for the initial pilot cases: wheat, maize, rice
- Will also test alignment tools and annotation tools
B. General Comments and Updates:
- Schedule will be: Monthly all hands meetings and the working groups will meet and report back to the group.
- PJ will circulate final version of the proposal in a cleaned up format
- Contracts work on an invoice system
- Planteome-Internal Mailing list has been set up, this will be a useful way to share information among the key people in the team.
- Planteome Wiki page has been set up with password protection
- Ontology Repositories at GitHub- in progress
C. :
- Progress on opening new Planteome-related positions in the Jaiswal Lab (software developer, curator)