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:'''
 
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Proposed Time: Sunday Late Morning to include 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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'''Where:''' [http://intl-pag.org/TownCountryMap.pdf Town and Country Hotel], Hampton Room
  
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'''Where:''' Town and Country Hotel, Room TBA
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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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- We will have 5 speakers from groups who are current or potential collaborators
  
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'''What:'''
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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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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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'''who: '''
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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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- We will have a 'working lunch' where folks can mingle and continue discussions
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From Mary Schaeffer:
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We will be exploring the new PO release as working on term matching to some developmental stages for a Maize Gene Atlas.  
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==Agenda:==
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'''10:30am: Welcome and Opening'''
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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'''
 +
 
 +
*'''10:35am: Ramona Walls, Plant Ontology Consortium'''
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Title:  Introduction to the Plant Ontology- Where does my project fit in?
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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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The sequencing group is turning in a final set of models soon, that MaizeGDB will be guardians of, starting Jan 2011.  We anticipate loading into
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Title: Plant Ontology and the Maize B73 Gene Atlas Wisconsin 2010
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MaizeGDB, both Nimblegen and RNA_Seq expression data from the same group for a Maize Gene Atlas.
 
  
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I anticipate being able to provide associations for gene models expressed highly. There are 61 tissues, at various plant growth stages, so this will be a substantial number of associations.  
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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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'''PJ: Would you be mapping the RNAseq data and the Array data to gene/gene models?'''
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[[Media:Schaeffer_MaizeGDB.pdf ]]
  
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MS: Initially they will be mapped to coordinates, and by inference then, to gene models. We are in close contact with CSH on the release of the
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*'''10:55am: Claude dePamphilis [http://www.floralgenome.org/ Floral Genome Project],'''
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new models.
 
  
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About adequacy of the PO, my sense is that all seems cool.  The current listing is a bit drafty in parts, and I am conferring as I work through the
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Title: The Floral Genome/Ancestral Angiosperm/and Amborella genome projects- Challenges for Applying Ontologies.
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list with the authors. Perhaps of better utility to you, would be how each 'tissue' is annotated to the PO terms? 
 
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Maybe I could present this in the workshop Laurel is organizing re use of PO?
 
  
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In any case, I will have the 'mappings' soon.  
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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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*'''11:10am: Stefan Rensing, [http://www.cosmoss.org/ ''Physcomitrella patens'' Resource]'''
  
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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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Title: MO - Moss/Bryophyte Ontology within PO
  
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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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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]]
  
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* TAIR email: curator@arabidopsis.org
 
  
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* '''11:25am: Nick Provart [http://bar.utoronto.ca/ BAR]'''
  
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Title: Identification of Expressologs in Plant Species using Gene Expression Compendia
  
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* [http://www.plexdb.org/index.php Plex DB] who?
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[[Media: Provart_PO.pdf]]
  
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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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* Physco group: Rensing and Lang  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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*'''11:40am: Ken McNally IRRI [http://beta.irri.org/index.php/Home/Welcome/Frontpage.html IRRI] '''
  
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* Brian Smith White- NCBI [http://intl-pag.org/19/19-ncbi.html NCBI Workshop]
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Title: Ontological Implications from Sequencing the Global Rice Collections
  
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* Helen Parkinson- Array Express EBI
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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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[[Media: KMcNally_IRRI.pdf]]
  
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* Genevestigator: contact ?  (support@genevestigator.com)  [https://www.genevestigator.com/gv/doc/ontologies.jsp Ontologies]
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'''11:55am: Closing Comments and Summary'''
  
 +
Pankaj Jaiswal,  Plant Ontology Consortium
  
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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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==Build-Your-Own Sandwich Buffet Lunch==
  
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*'''Soup du Jour'''
  
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*'''Sandwich Buffet:'''
  
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[http://msbarker.com/ Michael Barker] see 
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Selection of Sliced Meats and Cheeses
  
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Assorted Freshly Baked Deli Breads
  
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Others:?
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Condiments to include leaf lettuce, sliced tomatoes, onions, mayonnaise and mustards
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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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Crisp potato chips
  
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* SoyBase- Rex Nelson?
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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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* PlantTribes:  to: PI: Claude dePamphilis (Penn State) cwd3@psu.edu
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Pasta Salad Primavera
  
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* TraitNet:  Coordinators Farshid Ahrestani (fa2260@columbia.edu) and Dan Bunker (dbunker@njit.edu)
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Marinated Tomatoes and Cucumbers
  
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* CIMMYT, Mexico Generation Challenge Program:  Rosemary Shretha
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Variety of Seasonal Greens with Choice of Dressings
  
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* BRENDA to:project leader Prof. Dr. Dietmar Schomburg
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*'''Deserts:'''
  
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* UniProt  "contact us" page
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Assorted whole fresh fruits
  
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* BAR:  Nicholas Provert and Rohan Patel
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Chef's Sweets Table
  
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* Trish Whetzel and BioPortal-
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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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