Tuesday Jan 6th, 2015
Planteome- cROP Meeting: Tuesday Jan 6th, 2015
Who: PJ, LC, JE, DWS, CM, ST, GG, JD Not available: EA, EZ, BS
Name Role Major Focus Pankaj Jaiswal, Oregon State University Lead PI plant systems biology and bioinformatics Laurel Cooper, Oregon State University Senior Personnel, project Coordinator, Bioinformatic Scientist Curation, data analysis, gene expression, genomics, project coordination Dennis W. Stevenson, New York Botanical Garden CO-PI Plant anatomy and development, evolution and classification, genomics, taxonomy Elizabeth Arnaud, Bioversity International/CGIAR, France CO-PI Lead on Crop Ontology- crop-specific trait and germplasm ontologies for agronomic databases of crops Sinisa Todorovic, Oregon State University CO-PI Computer vision, machine learning, and artificial intelligence Eugene Zhang, Oregon State University CO-PI Computer graphics, scientific visualization, and geometric modeling Christopher Mungall, Lawrence Berkeley National Laboratory CO-PI Functional Genomics, Gene Ontology, Disease Phenotype Informatics, Logic-based modeling and programming Barry Smith, University at Buffalo Ontology consultant Ontology and its applications, especially in biomedical informatics Georgios V. Gkoutos, University of Aberystwyth, UK Senior Personnel, collaborator Molecular informatics and bioinformatics, association of genotype to phenotype John Doonan, University of Aberystwyth, UK Senior Personnel, collaborator Director National Plant Phenomics Centre, High throughput phenotyping - gene discovery and plant breeding. Integration of phenomic and genomic data Justin Elser, Oregon State University Bioinformatics Researcher Data analysis, System Administration
Agenda:
Introductions again, since we have not all met for about a year.
See Above
B. Questions about grant, hiring etc GG, CM, have not received the subcontract paperwork, PJ will follow up on DWS just received his 12-29 Can start billing the grant back dated to Dec 1st
C. Setting some initial priorities:
The NSF agreed to fund the cROP proposal for an initial three year period. After the first two years are completed, we will have a reverse site visit, at which time they may fund an additional (4th) year.
PJ will circulate revised timeline
Three major components: Reference Ontologies- PO, TO, PSO, EO, GO, PATO, ChEBI Continued and new development Training users and curators Cross linkings to the crop-specific ontologies at the CO moving repositories to centralized platform at GitHub Transition to AmiGO 2- new functionalities Who: Laurel, Elizabeth, new curator to be hired, Chris, Dennis with Barry’s advice, others?
Accumulating annotations and large datasets, data warehouse- IT group Collaboration with data generating projects such as CO/IBP Annotations to sequenced plant genomes- approximately 100 done now Who: Eugene?, JE, new programmer, others?
Image annotations with ontologies, Collaboration with iplant Bisque (from UCSD) developers Building on AISO, machine learning approaches integration of annotations and images Who: Sinisia, grad student, iPlant contacts: Nirav + ?, others?
Potential hires joining the project:
Ez, ST will have grad students
DWS- will start advertising, may have opssible candidtate
CM- Seth is already present
PJ: programmer and curator
EA???
Can help advertising through FB, mailing lists
Other Project info: New planteome wiki to be set up tracker for issues Need new Logo or modify cROP one? Will look into other web conf calling tools- Google hangouts, Go to Meetings, others?
Potential members for Project Advisory Board: Sandra Knapp Melissa Haendel Alejandra Gandolfo Ruth Bastow other suggestions? Someone more from the computer sciences field?
D. Planning for monthly all-hands meetings and group meetings
LC will send out a doodle poll to find a good day/time for the monthly all-hands meetings
Group meeting will be set up with the interested people on each part of the project.
E. Other items?
DWS: Is redoing the Glossary for the textbook he has authored and will include link to PO terms and definitions.
