Difference between revisions of "PAG 2011 Collaborators Workshop"

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'''This page is under construction.....'''
 
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==Date and Time:==
 
==Date and Time:==
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Sunday, January 16th,  Late Morning to include a buffet lunch
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'''Sunday, January 16th''',  Late Morning to include a buffet lunch
  
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Time 10:30-1:00 pm (will wrap up in time to get to 1:30 sessions)
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Time: 10:30-1:00 pm (will wrap up in time to get to 1:30 sessions)
  
  
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'''Where:''' [http://www.towncountry.com/ Town and Country Hotel], Windsor Room
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'''Where:''' [http://intl-pag.org/TownCountryMap.pdf Town and Country Hotel], Hampton Room
  
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==Summary and Objectives:==
  
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The goal of the workshop is to develop and enrich collaborations with other groups in the Plant Sciences and to demonstrate the utility of the PO in annotating large plant genomics datasets.
  
  
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'''What:'''
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- We will have 5 speakers from groups who are current or potential collaborators
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The plan will be to have about 5 speakers from groups that use the PO or send annotations to us. 
 
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The goal is to show a range of types of uses and highlight the utility of the PO to the plant science community. 
 
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Each speaker will have about 10 minutes, including time for questions, (~ 5-10 slides)?
 
  
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We will plan to have a 'working lunch' where folks can mingle and continue discussions
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- The goal is to show a range of uses and highlight the utility of the Plant Ontology to the plant science community. 
  
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'''who: List of Speakers: '''
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- Each speaker will have about 10-15 minutes, including time for questions, (~ 5-10 slides)
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'''* MaizeGDB:  Carolyn Lawrence, Mary Schaeffer, Jack Gardiner.'''
 
  
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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.
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- We will have a 'working lunch' where folks can mingle and continue discussions
  
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They are working on initially mapping the expressed sequences to coordinates, and by inference then, to gene models.
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==Agenda:==
  
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They anticipate being able to provide associations for gene models expressed highly to the PO.  This will be a substantial number of associations.
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'''10:30am: Welcome and Opening'''
  
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Mary has suggested that she could discuss how each 'tissue' is annotated to the PO terms. 
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Laurel Cooper, Coordinator, Plant Ontology Consortium
  
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'''List of Speakers and Topics: Talks will be followed by time for discussion and networking lunch'''
  
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==Other Potential Speakers==
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*'''10:35am: Ramona Walls, Plant Ontology Consortium'''
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* Physcomitrella group: [https://www.cosmoss.org/physcome_project/wiki/Moss_Ontology MO-PO Mappings]
 
  
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-[http://plantco.de/ Stefan Rensing], University of Freiburg, Germany and Daniel Lang,  
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Title:  Introduction to the Plant Ontology- Where does my project fit in?
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see: [http://www.cosmoss.org/ Cosmoss], the ''Physcomitrella patens'' resource site.  see: [http://intl-pag.org/19/19-lower.html Non-seed plant workshop]
 
  
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*[http://floralgenome.org/tribe.php Floral Genome Project]  
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[[Media:Walls_PO_intro.pdf]]
  
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-[http://cwd.huck.psu.edu/ Claude dePamphilis], Penn State University and
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*'''10:40am:  Mary Schaeffer, [http://www.maizegdb.org/ MaizeGDB]'''
  
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-[http://www.plantbio.uga.edu/~jleebensmack/JLMmain.html Jim Leebens-Mack] , University of Georgia 
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Title: Plant Ontology and the Maize B73 Gene Atlas Wisconsin 2010
  
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* [http://www.rosaceae.org/ Genome Database for Roseae] (GDR), Univ of Washington  
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Summary:
 +
The Plant Ontology is being utilized as MaizeGBD develops 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.
  
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-see [http://intl-pag.org/19/19-fruits.html Fruit and Nut workshop]
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[[Media:Schaeffer_MaizeGDB.pdf ]]
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-Doreen Main (dorrie@wsu.edu) WSU, Nahla Bassil (attending), USDA-ARS Corvallis
 
  
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* [http://phenotypercn.org/ Phenotype Ontology Research Coordination Network (RCN)]
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*'''10:55am: Claude dePamphilis [http://www.floralgenome.org/ Floral Genome Project],'''
  
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Eva Huala (huala@acoma.stanford.edu) 
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Title: The Floral Genome/Ancestral Angiosperm/and Amborella genome projects- Challenges for Applying Ontologies.
  
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* Rosemary Shrestha- Generation Challenge Program
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Summary:  An overview of their work on a number of basal species in the '''Floral Genome / Ancestral Angiosperm / and Amborella genome projects'''. This will include some of the results that have come along the from both developmental studies and transcriptome studies that may be of interest to plant ontology specialists. There are certainly some challenges for applying ontologies from other organisms on these plants, and work is needed to generate useful comparative ontologies. .
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* Rex Nelson- [http://soybase.org/ SoyBase]
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[[Media:DePamphilis_Ontology.pdf]]
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* Lukas Mueller- SGN
 
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* Kate or someone from TAIR
 
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==Groups to Invite:==
 
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These groups will be represented at PAG:
 
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* [http://www.gramene.org/plant_ontology/ Gramene] See: [http://intl-pag.org/19/19-gramene.html Gramene workshop at PAG]
 
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* [http://www.plexdb.org/index.php Plex DB]  Roger P. Wise
 
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* Blake Meyer (meyers@dbi.udel.edu) see [http://intl-pag.org/19/19-iaic.html International Arabidopsis Informatics Consortium (IAIC) Workshop]
 
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* Physcomitrella group: [http://plantco.de/ Stefan Rensing], University of Freiburg, Germany and Daniel Lang, 
 
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see: [http://www.cosmoss.org/ Cosmoss], the ''Physcomitrella patens'' resource site.  see: [http://intl-pag.org/19/19-lower.html Non-seed plant workshop]
 
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* [http://www.rosaceae.org/ Genome Database for Roseae] (GDR), Univ of Washington  see [http://intl-pag.org/19/19-fruits.html Fruit and Nut workshop]
 
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Doreen Main WSU, Nahla Bassil, USDA-ARS Corvallis
 
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* [http://qifa.ncpgr.cn/ Qifa Zhang] Rice Gene Expression Atlas paper
 
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* Brian Smith White- NCBI [http://intl-pag.org/19/19-ncbi.html NCBI Workshop]
 
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*[http://msbarker.com/res.htm Michael Barker], see:[http://intl-pag.org/19/19-speciation.html Speciation Genomics Workshop]
 
  
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* Cesare  Gessler,  ETH Zurich??
 
  
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* TAIR, Eva Huala, Kate Dreher (PMN), (Tanya Bernadini?)  email: curator@arabidopsis.org  
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*'''11:10am: Stefan Rensing, [http://www.cosmoss.org/ ''Physcomitrella patens'' Resource]'''
  
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*GrainGenes (curators@pw.usda.gov); David Matthews:(matthews@greengenes.cit.cornell.edu); Victoria Carollo (vcarollo@pw.usda.gov)
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Title: MO - Moss/Bryophyte Ontology within PO
  
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* [http://solgenomics.net/tools/onto/index.pl Solanaceae Genome network (SGN)];  Lukas Mueller (but not Naama Menda); see [http://intl-pag.org/19/19-solan.html Solanaceae Workshop]
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Summary: Stefan's group is developing a moss ontology. He will tell us about how they are developing the PO to MO mappings and annotating the ''Physcomitrella'' genome and transcriptome.
  
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* [http://soybase.org/ SoyBase]- Rex Nelson
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[[Media:Rensing_MO.pdf]]
  
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* Trish Whetzel and [http://bioportal.bioontology.org/ BioPortal]
 
  
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* [http://fgp.huck.psu.edu/tribedb/index.pl PlantTribes] to: PI: Claude dePamphilis (Penn State) cwd3@psu.edu
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* '''11:25am: Nick Provart [http://bar.utoronto.ca/ BAR]'''
  
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* [http://robust.genome.com/  RoBust: Root and Bulb Genomics Database] [http://www.horticulture.wisc.edu/PhilippSimon Phillipp Simon]
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Title: Identification of Expressologs in Plant Species using Gene Expression Compendia
  
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* Richard Bruskiewich, IRRI  International Rice Research Institute
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[[Media: Provart_PO.pdf]]
  
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* Grape Genomics: [http://intl-pag.org/19/19-grape.html International Grape Genome Project Workshop]:
 
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Grant Cramer, University of Nevada, Reno (cramer@unr.edu), Anne-Francoise Adam-Blondon, INRA (adam@evry.inra.fr)
 
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and others?
 
  
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* [http://intl-pag.org/19/19-bioinformatics.html Boinformatics Workshop] Dr. Alexander Souvorov, NCBI/NLM/NIH (souvorov@ncbi.nlm.nih.gov)
 
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"Annotation of Glycine max and Zea mays genomes"
 
  
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* [http://intl-pag.org/19/19-mut-screening.html Mutation Screening workshop]
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*'''11:40am: Ken McNally IRRI [http://beta.irri.org/index.php/Home/Welcome/Frontpage.html IRRI] '''
  
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-Ryohei Terauchi , Iwate Biotechnology Research Center (Japan) (terauchi@ibrc.or.jp)
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Title: Ontological Implications from Sequencing the Global Rice Collections
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"Large-scale EMS mutant screen and Next-Gen Sequencing: Rapid gene isolation in rice"
 
  
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-John B. Hays, Oregon Sate University (USA) (haysj@science.oregonstate.edu)
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Summary: Sequencing of genetic resource accessions in Rice. They are characterizing the 120,000 rice accessions (both genotypic and phenotypic diversity).
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"Evolutionarily conserved guardians of the plant genome: DNA mismatch repair and DNA-damage responses"
 
  
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*[http://intl-pag.org/19/19-root.html Root Genomics Workshop]  
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[[Media: KMcNally_IRRI.pdf]]
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-Michelle Watt, CSIRO Plant Industry, Australia ( michelle.watt@csiro.au)
 
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"Genetic Improvement Of Wheat Root Architecture: Opportunities From Diverse Grasses With Sequenced Genomes"
 
  
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-Phylogenomics- [http://cwd.huck.psu.edu/ Claude dePamphilis], Penn State University and   Jim Leebens-Mack, University of Georgia
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'''11:55am: Closing Comments and Summary'''
  
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- [http://www.personal.psu.edu/jpd18/blogs/about.html Joshua Der]
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Pankaj Jaiswal,  Plant Ontology Consortium
  
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* [http://www.rothamsted.bbsrc.ac.uk/bab/ Chris Rawlings] (RRes-Roth) <chris.rawlings@bbsrc.ac.uk>
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==Build-Your-Own Sandwich Buffet Lunch==
  
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==Others:==
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*'''Soup du Jour'''
  
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* Genevestigator: contact?  (support@genevestigator.com)  [https://www.genevestigator.com/gv/doc/ontologies.jsp Ontologies]
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*'''Sandwich Buffet:'''
  
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* VirtualPlant who, use their "contact us" form?  [http://virtualplant.bio.nyu.edu/cgi-bin/vpweb2/ Virtual plant]
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Selection of Sliced Meats and Cheeses
  
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* [http://www.geneontology.org/ Gene Ontology]
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Assorted Freshly Baked Deli Breads
  
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* Shoshi Kikuchi, National Institute of Agrobiological Sciences, Japan
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Condiments to include leaf lettuce, sliced tomatoes, onions, mayonnaise and mustards
  
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* Helen Parkinson- Array Express EBI
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Crisp potato chips
  
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* Nottingham Arabidopsis [http://arabidopsis.info/cgi-bin/ontology/nasc_po/go.cgi?search_constraint=terms&action=replace_tree&session_id=8730b1287179734 NASC Ontology page]
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*'''Salad Selections:'''
  
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* OryzaBase:  to: Yukiko Yamazaki
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Red Potato Salad
  
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* TraitNet:  Coordinators Farshid Ahrestani (fa2260@columbia.edu) and Dan Bunker (dbunker@njit.edu)
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Pasta Salad Primavera
  
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* CIMMYT, Mexico Generation Challenge Program:  Rosemary Shrestha, Elizabeth Arnaud? see: [http://intl-pag.org/19/19-cp.html GCP workshop]
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Marinated Tomatoes and Cucumbers
  
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* BRENDA to:project leader Prof. Dr. Dietmar Schomburg
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Variety of Seasonal Greens with Choice of Dressings
  
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* UniProt  "contact us" page ? Rachel Huntley, someone doing plant annotations from SwissProt
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*'''Deserts:'''
  
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* BAR:  Nicholas Provert and Rohan Patel
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Assorted whole fresh fruits
  
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* [http://www.nig.ac.jp/section/kurata/kurata-e.html Nori Kurata] see [http://pcp.oxfordjournals.org/content/early/2010/11/09/pcp.pcq165.abstract Rice Atlas paper preprint- Plant and Cell Physiology]
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Chef's Sweets Table
  
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* [http://beta.irri.org/projects15/en/consortium-c4rice/502-profilerfurbank Robert Furbank, IRRI]
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*'''Freshly brewed coffee, decaffeinated coffee and tea'''

Latest revision as of 17:20, 1 November 2012

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, Hampton Room

Summary and Objectives:

The goal of the workshop is to develop and enrich collaborations with other groups in the Plant Sciences and to demonstrate the utility of the PO in annotating large plant genomics datasets.


- We will have 5 speakers from groups who are current or potential collaborators

- 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 10-15 minutes, including time for questions, (~ 5-10 slides)

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

Agenda:

10:30am: Welcome and Opening

Laurel Cooper, Coordinator, Plant Ontology Consortium

List of Speakers and Topics: Talks will be followed by time for discussion and networking lunch

  • 10:35am: Ramona Walls, Plant Ontology Consortium

Title: Introduction to the Plant Ontology- Where does my project fit in?

Media:Walls_PO_intro.pdf

Title: Plant Ontology and the Maize B73 Gene Atlas Wisconsin 2010

Summary: The Plant Ontology is being utilized as MaizeGBD develops 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.

Media:Schaeffer_MaizeGDB.pdf

Title: The Floral Genome/Ancestral Angiosperm/and Amborella genome projects- Challenges for Applying Ontologies.

Summary: An overview of their work on a number of basal species in the Floral Genome / Ancestral Angiosperm / and Amborella genome projects. This will include some of the results that have come along the from both developmental studies and transcriptome studies that may be of interest to plant ontology specialists. There are certainly some challenges for applying ontologies from other organisms on these plants, and work is needed to generate useful comparative ontologies. .

Media:DePamphilis_Ontology.pdf


Title: MO - Moss/Bryophyte Ontology within PO

Summary: Stefan's group is developing a moss ontology. He will tell us about how they are developing the PO to MO mappings and annotating the Physcomitrella genome and transcriptome.

Media:Rensing_MO.pdf


  • 11:25am: Nick Provart BAR

Title: Identification of Expressologs in Plant Species using Gene Expression Compendia

Media: Provart_PO.pdf


  • 11:40am: Ken McNally IRRI IRRI

Title: Ontological Implications from Sequencing the Global Rice Collections

Summary: Sequencing of genetic resource accessions in Rice. They are characterizing the 120,000 rice accessions (both genotypic and phenotypic diversity).

Media: KMcNally_IRRI.pdf

11:55am: Closing Comments and Summary

Pankaj Jaiswal, Plant Ontology Consortium

Build-Your-Own Sandwich Buffet Lunch

  • Soup du Jour
  • Sandwich Buffet:

Selection of Sliced Meats and Cheeses

Assorted Freshly Baked Deli Breads

Condiments to include leaf lettuce, sliced tomatoes, onions, mayonnaise and mustards

Crisp potato chips

  • Salad Selections:

Red Potato Salad

Pasta Salad Primavera

Marinated Tomatoes and Cucumbers

Variety of Seasonal Greens with Choice of Dressings

  • Deserts:

Assorted whole fresh fruits

Chef's Sweets Table

  • Freshly brewed coffee, decaffeinated coffee and tea
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