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
*Align concepts with TO, PO, GO, PTO and expand the list of traits
* 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 algorithms
* 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
  • 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.  :

  1. Progress on opening new Planteome-related positions in the Jaiswal Lab (software developer, curator)