PAG 2011 Collaborators Workshop

Date and Time:

Sunday, January 16th, Late Morning to include a buffet lunch

Time: 10:30-1:00 pm (will wrap up in time to get to 1:30 sessions)

Where: Town and Country Hotel, Windsor Room

See list of other potential speakers and invitees PAG 2011 PO Workshop Invitees and Speakers

Summary and Objectives:

- We have about 4 or 5 speakers from groups that use the PO or share annotations with us, or who we would like to develop collaborations with

- The goal is to show a range of uses and highlight the utility of the Plant Ontology to the plant science community.

- Each speaker will have about 10 minutes, including time for questions, (~ 5-10 slides)

- We will have a 'working lunch' where folks can mingle and continue discussions

Agenda:

10:30am: Introduction and Welcome (Laurel Cooper, Coordinator, Plant Ontology Consortium)

10:40am: Mary Schaeffer, MaizeGDB

Title: TBA

The Plant Ontology is being utilized as they develop a Maize Gene Atlas. They are working on a large set of Nimblegen and RNA_Seq expression data, from 61 tissues, at various plant growth stages. These data will be added to the Plant Ontology's existing annotations.

* MaizeGDB: Carolyn Lawrence, Mary Schaeffer, Jack Gardiner.

Mary Schaeffer has said that their group can come and she has offered to speak about how the PO is being utilized as they develop a Maize Gene Atlas. They are working on a large set of Nimblegen and RNA_Seq expression data, from 61 tissues, at various plant growth stages.

They are working on initially mapping the expressed sequences to coordinates, and by inference then, to gene models.

They anticipate being able to provide associations for gene models expressed highly to the PO. This will be a substantial number of associations.

Mary has suggested that she could discuss how each 'tissue' is annotated to the PO terms.

Groups to Invite:

These groups will be represented at PAG:

• Gramene See: Gramene workshop at PAG

• Plex DB Roger P. Wise

• Blake Meyer (meyers@dbi.udel.edu) see International Arabidopsis Informatics Consortium (IAIC) Workshop

• Physcomitrella group: Stefan Rensing, University of Freiburg, Germany and Daniel Lang,

see: Cosmoss, the Physcomitrella patens resource site. see: Non-seed plant workshop

• Genome Database for Roseae (GDR), Univ of Washington see Fruit and Nut workshop

Doreen Main WSU, Nahla Bassil, USDA-ARS Corvallis

• Qifa Zhang Rice Gene Expression Atlas paper

• Brian Smith White- NCBI NCBI Workshop

• Michael Barker, see:Speciation Genomics Workshop

• Cesare Gessler, ETH Zurich??

• TAIR, Eva Huala, Kate Dreher (PMN), (Tanya Bernadini?) email: curator@arabidopsis.org

• GrainGenes (curators@pw.usda.gov); David Matthews:(matthews@greengenes.cit.cornell.edu); Victoria Carollo (vcarollo@pw.usda.gov)

• Solanaceae Genome network (SGN); Lukas Mueller (but not Naama Menda); see Solanaceae Workshop

• SoyBase- Rex Nelson

• Trish Whetzel and BioPortal

• PlantTribes to: PI: Claude dePamphilis (Penn State) cwd3@psu.edu

• RoBust: Root and Bulb Genomics Database Phillipp Simon

• Richard Bruskiewich, IRRI International Rice Research Institute

• Grape Genomics: International Grape Genome Project Workshop:

Grant Cramer, University of Nevada, Reno (cramer@unr.edu), Anne-Francoise Adam-Blondon, INRA (adam@evry.inra.fr) and others?

• Boinformatics Workshop Dr. Alexander Souvorov, NCBI/NLM/NIH (souvorov@ncbi.nlm.nih.gov)

"Annotation of Glycine max and Zea mays genomes"

• Mutation Screening workshop

-Ryohei Terauchi , Iwate Biotechnology Research Center (Japan) (terauchi@ibrc.or.jp) "Large-scale EMS mutant screen and Next-Gen Sequencing: Rapid gene isolation in rice"

-John B. Hays, Oregon Sate University (USA) (haysj@science.oregonstate.edu) "Evolutionarily conserved guardians of the plant genome: DNA mismatch repair and DNA-damage responses"

• Root Genomics Workshop

-Michelle Watt, CSIRO Plant Industry, Australia ( michelle.watt@csiro.au) "Genetic Improvement Of Wheat Root Architecture: Opportunities From Diverse Grasses With Sequenced Genomes"

-Phylogenomics- Claude dePamphilis, Penn State University and Jim Leebens-Mack, University of Georgia

- Joshua Der

• Chris Rawlings (RRes-Roth) <chris.rawlings@bbsrc.ac.uk>

Others:

• Genevestigator: contact? (support@genevestigator.com) Ontologies

• VirtualPlant who, use their "contact us" form? Virtual plant

• Gene Ontology

• Shoshi Kikuchi, National Institute of Agrobiological Sciences, Japan

• Helen Parkinson- Array Express EBI

• Nottingham Arabidopsis NASC Ontology page

• OryzaBase: to: Yukiko Yamazaki

• TraitNet: Coordinators Farshid Ahrestani (fa2260@columbia.edu) and Dan Bunker (dbunker@njit.edu)

• CIMMYT, Mexico Generation Challenge Program: Rosemary Shrestha, Elizabeth Arnaud? see: GCP workshop

• BRENDA to:project leader Prof. Dr. Dietmar Schomburg

• UniProt "contact us" page ? Rachel Huntley, someone doing plant annotations from SwissProt

• BAR: Nicholas Provert and Rohan Patel

• Nori Kurata see Rice Atlas paper preprint- Plant and Cell Physiology

• Robert Furbank, IRRI