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:

See details on last months page: Tuesday_Jan_6th,_2015

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

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

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

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

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

Justin E has been working with Seth Carbon and Chris Mungall on installing the SolR (http://en.wikipedia.org/wiki/Apache_Solr) system to run the AmiGO2 browser
Index based, dynamic, flexible and adaptable
Call last Friday- ideas for data visualizations,
Running, but needs some extension from the GO Schema for the new relations we use in the PO etc
Background: Plant Ontology has been run on MySQL database in the past, but now we are transitioning to the new NoSQL platform.
Has some visualization tools, for the ontologies rather than the data
Need some use cases for demonstration
Development version will be run from OSU, then eventually will be ported to the new Live site at iPlant
Also involves contributions from Eugene Zhang and his two grad students- who will share tasks, one main one secondary
JE can add the needed access for the people involved
JE will document steps in progress- see link to wiki page:http://wiki.planteome.org/index.php/AmiGO2_install