Thursday Feb 6th, 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. Update from IT group- Data Store, AmiGO2, Justin Elser  :

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