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| | '''Venue''': Georgetown University |
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| ''''''Venue''': Georgetown University
| | '''Date''': June (17)-18-19 2014. The meeting will start with dinner on Tuesday, June 17 and conclude at 4pm on June 19. |
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| '''Date''': June (17)-18-19 2014. The meeting will start with a working dinner on June 17 conclude at 4pm on June 19. | |
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| The goals of this meeting are: | | The goals of this meeting are: |
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| *1. To inform members of the Protein, Plant, Gene Ontology and related communities of developments in their respective ontologies in order to promote cross-ontology coordination. Specifically: | | *1. To contribute to the ontological understanding of phenotype and disease across organisms. |
| :a. To enhance the treatment of plant-related proteins in the Protein Ontology
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| :b. To address issues concerning reuse of GO terms to describe plant-related entities, for example in the treatment of plant life cycle and development stages
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| *2. To address general issues which arise when ontologies need to be extended to cover multiple species of organisms
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| *3. To contribute to the [http://wiki.plantontology.org/index.php/The_cROP_(Common_Reference_Ontologies_for_Plants)_Initiative cROP] (Common Reference Ontologies for Plants) initiative
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| *4. To contribute to the ontological understanding of phenotype and disease across organisms.
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| *5. To identify potentially fruitful applications which enhanced ontology coordination might bring.
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| == '''cROP: Common Reference Ontologies for Plants''' ==
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| Yellow = cROP ontologies for plants; Blue = general reference ontologies; Pink = to be developed by cROP
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| [[File:cROP.jpg]]
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| ----
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| =='''Schedule''' == | | =='''Schedule''' == |
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| ==='''Wednesday, May 15, 2013'''===
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| 8:00 Registration and continental breakfast
| | ==='''Wednesday, June 18, 2014"=== |
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| 9:00 From the OBO Foundry to [http://wiki.plantontology.org/index.php/The_cROP_(Common_Reference_Ontologies_for_Plants)_Initiative cROP] [http://ontology.buffalo.edu/13/PRO-PO-GO/PRO-PO-GO_jaiswal.pptx Slides]
| | 8:00 Continental Breakfast |
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| [https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=74908582&rKey=38cdc41908a25850 Webex recording] [https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=74908582&rKey=d18eb7ba9a466506 Webex download link] ''Note: No audio''
| | 9:00 The Coordinating Role of the Protein Ontology |
| :Outline of the cROP Framework (Pankaj Jaiswal)
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| :Overview of cROP ontologies
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| ::Presentations will focus on:
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| *Current or planned treatment of multiple organism types
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| *Important applications of these ontologies
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| *Experiences in the use of these ontologies in coordination (prototypically via use of terms from coordinating ontologies in cross-product definitions)
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| :Molecules:
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| ::Protein Ontology (PRO) (Cathy Wu) [http://ontology.buffalo.edu/13/PRO-PO-GO/PRO-Wu-5-15-13.pptx Slides]
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| ::CHEBI and Natural Products of Plant Origin (Janna Hastings) [http://ontology.buffalo.edu/13/PRO-PO-GO/chebi-and-plants.pptx Slides]
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| :Cells
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| ::GO-Cellular Component (Alex Diehl)
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| ::Cell Type Ontology (CL) (Alex Diehl)
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| ::Use of PRO in defining Cell Types (Alex Diehl)
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| :::[http://ontology.buffalo.edu/13/PRO-PO-GO/Diehl.pptx Diehl Slides]
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| ::Plant Cell branch of the Plant Ontology (PO) (Laurel Cooper)
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| :Organisms
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| ::Plant Ontology (PO) (Laurel Cooper)
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| :::[http://ontology.buffalo.edu/13/PRO-PO-GO/Cooper.pptx Cooper Slides]
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| 10:30 Break | | 10:30 Break |
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| 10:45 The Coordinating Role of the Gene Ontology (Jane Lomax) [http://ontology.buffalo.edu/13/PRO-PO-GO/GO-Lomax.pptx Lomax slides]
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| [https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=74912612&rKey=c6c506214779c91f Webex Streaming recording link] [https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=74912612&rKey=5814826c4db93864 Webex Download recording link]
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| :Questions to be addressed include:
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| ::How does the GO view the division of labor with regard to describing Biological Processes (BPs) which are not within the scope of the GO BP ontology especially in regard to stage ontologies such as the cell life cycle ontology or the PO plant development stage ontology?
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| ::How are growth and development terms to be dealt with across organisms?
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| ::What are the lessons learned from the GO's experience in coordinating with other ontologies using GO terms in definitions?
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| ::Need for mechanisms of alerting each other to changes in ontology structure, e.g term obsoletions
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| * Use of PO for relevant GO logical definitions (Tanya Berardini) [http://ontology.buffalo.edu/13/PRO-PO-GO/PRO_PO_GO_TB.pptx Slides]
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| ::What is the strategy and timeline for integrating PO into cross-product definitions of plant-relevant BPs (analogous to the way in which CHEBI, CL and PRO are currently being used)?
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| 12:00 Lunch | | 12:00 Lunch |
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| 13:00 '''Traits and Phenotypes Webex Session #2''' | | 13:00 |
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| [https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=74933527&rKey=c36aed5c505e65a6 Streaming recording link] [https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=74933527&rKey=18f5c06b9f26df0b Download recording link]
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| :Phenotypic Quality Ontology ([http://obofoundry.org/wiki/index.php/PATO:Main_Page PATO]) (George Gkoutos) [http://ontology.buffalo.edu/13/PRO-PO-GO/gkoutos.pptx Slides]
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| :Automated tools to help construction of Trait Ontologies (Chris Mungall) [http://ontology.buffalo.edu/13/PRO-PO-GO/Mungall%20TraitOntologies.pptx Slides]
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| :The treatment of population phenotypes and use of the Population and Community Ontology [https://code.google.com/p/popcomm-ontology/ (PCO)] (Ramona Walls) [http://ontology.buffalo.edu/13/PRO-PO-GO/Walls.pptx Slides]
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| :Plant Trait Ontology ([http://crop.cgrb.oregonstate.edu/amigo/cgi-bin/crop_amigo/browse.cgi?action=plus_node&target=TO:0000387 TO]) (Pankaj Jaiswall/Laurel Cooper) [http://ontology.buffalo.edu/13/PRO-PO-GO/Pankaj-TO.ppt Slides]
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| 14:30 Break | | 14:30 Break |
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| 15:00 Critical remarks on PATO and TO (Barry Smith) [http://ontology.buffalo.edu/13/PRO-PO-GO/TO.pptx Slides] | | 15:00 |
| [https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=74933542&rKey=0bd434529a0c206f Streaming recording link]
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| [https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=74933542&rKey=65ddcc0e6dda1b9e Webex Download recording link]
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| :Defining Disease Across Organisms (Judith Blake)[http://ontology.buffalo.edu/13/PRO-PO-GO/blakeP0-PRO-GO.pptx Slides]
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| ::Defining Disease
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| ::Disease as a Subtype of Stress (Pankaj Jaiswal/Laurel Cooper) [http://ontology.buffalo.edu/13/PRO-PO-GO/Plant-Stress-Ontology.pptx Slides]
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| ::Plant Stresses and the [http://wiki.plantontology.org/index.php/Plant_Environment_Ontology Plant Environment Ontology] (EO)
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| ::[http://wiki.plantontology.org/index.php/Plant_Disease_Ontology Plant Disease Ontology]
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| :::[http://ceur-ws.org/Vol-897/session1-paper01.pdf Plant Infectious Disease Ontology] (Ramona Walls) [http://ontology.buffalo.edu/13/PRO-PO-GO/IDOPlant_PROPOGO.pptx slides]
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| 17:30 Close | | 17:30 Close |
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| 18:00 Working Dinner in the Ramada Inn Restaurant | | 18:00 Working Dinner |
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| ==='''Thursday, May 16th, 2013'''=== | | ==='''Thursday, May 16th, 2013'''=== |
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| 9:00 PRO and UniProt | | 9:00 PRO and UniProt |
| [https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=74957937&rKey=4dfdfdb102c7199e Streaming recording link] [https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=74957937&rKey=f5ec44f0b3539591 Download recording link]
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| ''Note: Audio only, variable quality ''
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| :The Representation of Proteins in UniProtKB (Claire O'Donovan) [http://ontology.buffalo.edu/13/PRO-PO-GO/PRO-PO-GOClaire.pptx Slides]
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| :The Integration of the Protein Ontology and UniProtKB (Cathy Wu) [http://ontology.buffalo.edu/13/PRO-PO-GO/PRO-&-UniProt-Wu.pptx Slides]
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| 10:30 Break | | 10:30 Break |
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| 10:45 Ontologies Across Species | | 10:45 |
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| [https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=74957947&rKey=3a0cab23df398382 Streaming recording link] [https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=74957947&rKey=10130a499e510b69 Download recording link] ''Note: Audio quite poor''
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| :[http://www.topdownproteomics.org/ Top-Down Proteomics] (Paul Martin Thomas) [http://ontology.buffalo.edu/13/PRO-PO-GO/PMT-PROPOGO.pptx Slides]
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| :Maintaining Ontologies as They Scale Across Multiple Species (Darren Natale) [http://ontology.buffalo.edu/13/PRO-PO-GO/PRO-PO-GO-DN.pptx Slides]
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| :Interface Points between the cROP plant ontologies and the Protein Ontology (Cathy Wu) [http://ontology.buffalo.edu/13/PRO-PO-GO/PRO-&-cROP-Wu.pptx Slides]
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| ::Species-Neutral vs. Multi-Species Ontology (Barry Smith) [http://ontology.buffalo.edu/13/PRO-PO-GO/Foundry-efforts.pptx Slides]
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| 12:30 Lunch | | 12:30 Lunch |
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| 13:30 Documenting Success Stories and On-Going Projects (Dennis W. Stevenson) [http://ontology.buffalo.edu/13/PRO-PO-GO/Stevenson-Buffalo.pptx Slides] | | 13:30 |
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| [https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=74971907&rKey=64ecf69421d6415c Streaming recording link:Part One] [https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=74971907&rKey=edb5a27d850c37fc Download recording link: Part One] ''Warning- large file!''
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| ::GO Annotation of 23 Plant Genomes in [http://plants.ensembl.org/index.html Ensembl Plants] (Dan Bolser) [http://ontology.buffalo.edu/13/PRO-PO-GO/Bolser-Plant-Genomes-in-Ensembl.pdf Slides]
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| ::The [http://www.iplantcollaborative.org/ iPlant Ontology Strategy] (Ramona Walls) [http://ontology.buffalo.edu/13/PRO-PO-GO/iPlant_for_PROPOGO.pptx Slides]
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| ::[http://www.morphobank.org/ Morphobank] (Ramona Walls and Dennis Stevenson)
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| [https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=74971917&rKey=4ef0811756bbc81a Streaming recording link:Part Two] [https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=74971917&rKey=db8b51f216c825cf Download recording link: Part Two] Warning- large file!
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| ::[[AISO]]: Annotation of Image Segments using Ontologies (Justin Preece) Webex Session #3 [http://ontology.buffalo.edu/13/PRO-PO-GO/AISO_PRO-PO-GO_Demo.pptx Slides]
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| ::Plant Phenotype Pilot Project (Laurel Cooper) [http://ontology.buffalo.edu/13/PRO-PO-GO/PPPP-Cooper-5-16-13.pptx Slides]
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| ::Bioportal Slices (Trish Whetzel) [http://ontology.buffalo.edu/13/PRO-PO-GO/Whetzel-PROPOGO.ppt Slides]
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| 16:00 Close | | 16:00 Close |
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| == '''Participants''' == | | == '''Participants''' == |
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| PO Consortium
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| :Laurel Cooper (Oregon)
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| :Pankaj Jaiswal (Oregon)
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| :Justin Preece (Oregon)
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| :Barry Smith (Buffalo)
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| :Dennis Wm. Stevenson (New York Botanical Gardens)
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| GO Consortium
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| :Judith Blake (JAX) | | :Judith Blake (JAX) |
| :Jane Lomax (EBI) | | :Alex Diehl (Buffalo) |
| :Chris Mungall (Berkeley)
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| :Tanya Berardini (Stanford)
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| :Eva Huala (Stanford)
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| PRO Consortium
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| :Cathy Wu (Delaware)
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| :Darren Natale (Georgetown) | | :Darren Natale (Georgetown) |
| | :Claire O'Donovan (EBI) |
| :Alan Ruttenberg (Buffalo) | | :Alan Ruttenberg (Buffalo) |
| | | :Barry Smith (Buffalo) |
| Cell Ontology
| | :Cathy Wu (Delaware) |
| :Alex Diehl (Buffalo)
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| BFO
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| :Stefan Schulz (Graz)
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| :Selja Seppälä (Buffalo) | |
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| UniProt
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| :Claire O'Donovan (EBI)
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| Top-Down Proteomics
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| :Paul Martin Thomas (Northwestern)
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| Ensembl Plants
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| :Dan Bolser (EBI)
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| CHEBI
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| :Janna Hastings (EBI / Geneva)
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| PATO
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| :George Gkoutos (Cambridge) | |
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| Immune Epitope Database
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| :James Overton
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| Arabidopsis Information Portal
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| :Christopher D. Town (J. Craig Venter Institute)
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| The iPlant Collaborative
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| :Ramona Walls
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| TAIR
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| :Tanya Berardini (Stanford)
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| :Eva Huala (Stanford)
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| NCBO
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| :Trish Whetzel (Stanford)
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| Other participants:
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| :Alexander Cox (Buffalo)
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| :Mark Jensen (Buffalo)
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| :Patrick Ray (Buffalo)
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| Please contact [mailto:phismith@buffalo.edu Barry Smith] for further information. | | Please contact [mailto:phismith@buffalo.edu Barry Smith] for further information. |
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| Note that this meeting is co-located with the [http://ncorwiki.buffalo.edu/index.php/2013_BFO_Meeting BFO 2.0 meeting], which will take place in Buffalo on May 13-14.
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| == '''Sponsors''' == | | == '''Sponsors''' == |
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| :[http://www.plantontology.org/ The Plant Ontology]
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| :[http://pir.georgetown.edu/pro/ The Protein Ontology] | | :[http://pir.georgetown.edu/pro/ The Protein Ontology] |
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| | == '''Co-Sponsors''' == |
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| :[http://bioontologies.org National Center for Biomedical Ontology] | | :[http://bioontologies.org National Center for Biomedical Ontology] |
| :[http://ncor.buffalo.edu National Center for Ontological Research] | | :[http://ncor.buffalo.edu National Center for Ontological Research] |
