Difference between revisions of "PAG 2011 Collaborators Workshop"

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'''This page is under construction.....'''
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==Date and Time:==
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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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When: TBA
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'''Where:''' [http://intl-pag.org/TownCountryMap.pdf 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.
  
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who:
 
  
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* [http://solgenomics.net/tools/onto/index.pl Solanaceae Genome network (SGN)];  Lukas Mueller + Naama Menda; see [http://intl-pag.org/19/19-solan.html Solanaceae Workshop]
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- We will have 5 speakers from groups who are current or potential collaborators
  
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* [http://www.gramene.org/plant_ontology/ Gramene] Gramene See: [http://intl-pag.org/19/19-gramene.html Gramene workshop at PAG]
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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.   
  
 +
- Each speaker will have about 10-15 minutes, including time for questions, (~ 5-10 slides)
  
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* TAIR email: curator@arabidopsis.org
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- We will have a 'working lunch' where folks can mingle and continue discussions
  
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* MaizeGDB: Carolyn Lawrence, Mary Schaeffer, Jack Gardiner. No generic contact address
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==Agenda:==
  
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* [http://www.plexdb.org/index.php Plex DB] who?
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'''10:30am: Welcome and Opening'''
  
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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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Laurel Cooper, Coordinator, Plant Ontology Consortium
  
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* Physco group: Rensing and Lang  see [http://intl-pag.org/19/19-lower.html Non-seed plant workshop]
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'''List of Speakers and Topics: Talks will be followed by time for discussion and networking lunch'''
  
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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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*'''10:35am: Ramona Walls, Plant Ontology Consortium'''
  
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* Brian Smith White- NCBI [http://intl-pag.org/19/19-ncbi.html NCBI Workshop]
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Title: Introduction to the Plant Ontology- Where does my project fit in?
  
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* Helen Parkinson- Array Express EBI
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[[Media:Walls_PO_intro.pdf]]
  
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*'''10:40am:  Mary Schaeffer, [http://www.maizegdb.org/ MaizeGDB]'''
  
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* Genevestigator: contact ?  (support@genevestigator.com)  [https://www.genevestigator.com/gv/doc/ontologies.jsp Ontologies]
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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.
  
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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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[[Media:Schaeffer_MaizeGDB.pdf ]]
  
 +
*'''10:55am: Claude dePamphilis [http://www.floralgenome.org/ Floral Genome Project],'''
  
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Title: The Floral Genome/Ancestral Angiosperm/and Amborella genome projects- Challenges for Applying Ontologies.
  
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[http://msbarker.com/ Michael Barker] see 
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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. .
 +
 +
[[Media:DePamphilis_Ontology.pdf]]
  
  
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Others:?
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*'''11:10am: Stefan Rensing, [http://www.cosmoss.org/ ''Physcomitrella patens'' Resource]'''
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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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Title: MO - Moss/Bryophyte Ontology within PO
  
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* SoyBase- Rex Nelson?
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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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* OryzaBase: to: Yukiko Yamazaki
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[[Media:Rensing_MO.pdf]]
  
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* PlantTribes:  to: PI: Claude dePamphilis (Penn State) cwd3@psu.edu
 
  
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* TraitNet: Coordinators Farshid Ahrestani (fa2260@columbia.edu) and Dan Bunker (dbunker@njit.edu)
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* '''11:25am: Nick Provart [http://bar.utoronto.ca/ BAR]'''
  
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* CIMMYT, Mexico Generation Challenge Program: Rosemary Shretha
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Title: Identification of Expressologs in Plant Species using Gene Expression Compendia
  
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* BRENDA to:project leader Prof. Dr. Dietmar Schomburg
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[[Media: Provart_PO.pdf]]
  
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* UniProt  "contact us" page
 
  
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* BAR:  Nicholas Provert and Rohan Patel
 
  
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* Trish Whetzel and BioPortal-
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*'''11:40am: Ken McNally IRRI [http://beta.irri.org/index.php/Home/Welcome/Frontpage.html IRRI] '''
  
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Title: Ontological Implications from Sequencing the Global Rice Collections
  
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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).
  
 +
[[Media: KMcNally_IRRI.pdf]]
  
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What:
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'''11:55am: Closing Comments and Summary'''
  
 +
Pankaj Jaiswal,  Plant Ontology Consortium
  
 +
==Build-Your-Own Sandwich Buffet Lunch==
  
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Where:
+
*'''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'''

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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