Difference between revisions of "PRO-PO-GO Meeting"

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'''PRO-PO-GO: Challenges of Ontology Coordination Across Organisms'''
+
'''PRO-PO-GO: International Coordination Meeting for Ontology-Based Efforts for Plant Biology'''
  
−
'''A meeting designed to promote the coordination of the Gene, Protein, and Plant Ontologies and of other reference ontologies used  in plant biology'''
+
'''A meeting to promote the coordination of the Gene, Protein, and Plant Ontologies and of other reference ontologies used  in plant biology'''
  
 
'''Venue''': [http://www.ramada.com/hotels/new-york/amherst/ramada-amherst-conference-center/hotel-overview?partner_id=&hotel_id=17590&group_code=&campaign_code=&propId=RA17590&brand_id=RA&checkout_date=&modify=false&useWRPoints=false&children=0&corporate_id=&ratePlan=&teens=0&affiliate_id=&altPropId=17590&brand_code=BH%2CDI%2CRA%2CBU%2CHJ%2CKG%2CMT%2CSE%2CTL%2CWG%2CWY%2CPX%2CWT%2CWP%2CPN&iata=&rate_code=&adults=1&checkin_date=&rooms=1 Ramada Inn], Amherst, NY 14221
 
'''Venue''': [http://www.ramada.com/hotels/new-york/amherst/ramada-amherst-conference-center/hotel-overview?partner_id=&hotel_id=17590&group_code=&campaign_code=&propId=RA17590&brand_id=RA&checkout_date=&modify=false&useWRPoints=false&children=0&corporate_id=&ratePlan=&teens=0&affiliate_id=&altPropId=17590&brand_code=BH%2CDI%2CRA%2CBU%2CHJ%2CKG%2CMT%2CSE%2CTL%2CWG%2CWY%2CPX%2CWT%2CWP%2CPN&iata=&rate_code=&adults=1&checkin_date=&rooms=1 Ramada Inn], Amherst, NY 14221
  
−
'''Date''': May 15-16, 2013. The meeting will start at 10am on May 15 and conclude at 4pm on May 16.
+
'''Date''': May 15-16, 2013. The meeting will start at 9am on May 15 and conclude at 4pm on May 16.
  
 
----
 
----
Line 14: Line 14:
  
 
*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 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:  
−
:a. To enhance the PO treatment of plant-related proteins  
+
:a. To enhance the treatment of plant-related proteins in the Protein Ontology
−
:b. To address issues concerning reuse of GO terms to describe plant-related proteins, for example as concerns treatment of plant life cycle and development stages
+
: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
 
*2.    To address general issues which arise when ontologies need to be extended to cover multiple species of organisms  
 
*2.    To address general issues which arise when ontologies need to be extended to cover multiple species of organisms  
 
*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
 
*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
 
*4. To contribute to the ontological understanding of phenotype and disease across organisms.
 
*4. To contribute to the ontological understanding of phenotype and disease across organisms.
−
*5. To identify potentially fruitful applications which enhanced ontology coordination might bring.
+
*5. To identify potentially fruitful applications which enhanced ontology coordination might bring.
 +
 
 +
== '''cROP: Common Reference Ontologies for Plants''' ==
 +
Yellow = cROP ontologies for plants; Blue = general reference ontologies; Pink = to be developed by cROP
  
 
[[File:cROP.jpg]]
 
[[File:cROP.jpg]]
−
:Yellow = cROP ontologies for plants; Blue = general reference ontologies; Pink = to be developed by cROP
+
−
 
 
  
 
----
 
----
  
−
== '''Draft Schedule''' ==
+
=='''Schedule''' ==
  
−
'''Wednesday, May 15, 2013'''
+
==='''Wednesday, May 15, 2013'''===
  
−
8:15 Registration and continental breakfast  
+
8:00 Registration and continental breakfast  
  
−
9:00 From the OBO Foundry to [http://wiki.plantontology.org/index.php/The_cROP_(Common_Reference_Ontologies_for_Plants)_Initiative cROP] (Common Reference Ontologies for Plants)
+
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]
  
 +
[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''
 
:Outline of the cROP Framework (Pankaj Jaiswal)
 
:Outline of the cROP Framework (Pankaj Jaiswal)
−
:Overview of general ontologies used within the cROP Framework
+
:Overview of cROP ontologies  
 +
::Presentations will focus on:
 +
*Current or planned treatment of multiple organism types
 +
*Important applications of these ontologies
 +
*Experiences in the use of these ontologies in coordination (prototypically via use of terms from coordinating ontologies in cross-product definitions)
 +
 
 
:Molecules:
 
:Molecules:
−
::Protein Ontology (PRO) (Cathy Wu)
+
::Protein Ontology (PRO) (Cathy Wu) [http://ontology.buffalo.edu/13/PRO-PO-GO/PRO-Wu-5-15-13.pptx Slides]
−
::CHEBI (Janna Hastings)
+
::CHEBI and Natural Products of Plant Origin (Janna Hastings) [http://ontology.buffalo.edu/13/PRO-PO-GO/chebi-and-plants.pptx Slides]
  
 
:Cells
 
:Cells
 
::GO-Cellular Component (Alex Diehl)
 
::GO-Cellular Component (Alex Diehl)
−
::Cell Type Ontology (CL) (Alex Diehl)
+
::Cell Type Ontology (CL) (Alex Diehl)  
−
:::Use of PRO in defining Cell Types
+
::Use of PRO in defining Cell Types (Alex Diehl)
−
::Plant cell branch of the Plant Ontology (PO)
+
:::[http://ontology.buffalo.edu/13/PRO-PO-GO/Diehl.pptx Diehl Slides]
 +
::Plant Cell branch of the Plant Ontology (PO) (Laurel Cooper)
  
−
:Presentations should focus on:
+
:Organisms
−
::Current or planned treatment of multiple organism types
+
::Plant Ontology (PO) (Laurel Cooper)
−
::Important applications of these ontologies
+
:::[http://ontology.buffalo.edu/13/PRO-PO-GO/Cooper.pptx Cooper Slides]
−
::Experiences in the use of these ontologies in coordination
 
  
 
10:30 Break
 
10:30 Break
  
−
10:45 The Coordinating Role of the Gene Ontology (Jane Lomax)
+
10:45 The Coordinating Role of the Gene Ontology (Jane Lomax) [http://ontology.buffalo.edu/13/PRO-PO-GO/GO-Lomax.pptx Lomax slides]
 +
 
 +
[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]
 +
 
 
:Questions to be addressed include:
 
:Questions to be addressed include:
 
::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?
 
::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?
 
::How are growth and development terms to be dealt with across organisms?
 
::How are growth and development terms to be dealt with across organisms?
 
::What are the lessons learned from the GO's experience in coordinating with other ontologies using GO terms in definitions?
 
::What are the lessons learned from the GO's experience in coordinating with other ontologies using GO terms in definitions?
 +
::Need for mechanisms of alerting each other to changes in ontology structure, e.g term obsoletions
 +
 +
* Use of PO for relevant GO logical definitions (Tanya Berardini) [http://ontology.buffalo.edu/13/PRO-PO-GO/PRO_PO_GO_TB.pptx Slides]
 +
::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)?
  
 
12:00 Lunch
 
12:00 Lunch
  
−
13:00 Traits and Phenotypes  
+
13:00 '''Traits and Phenotypes Webex Session #2'''
−
:Phenotypic Quality Ontology ([http://obofoundry.org/wiki/index.php/PATO:Main_Page PATO])  
+
 
−
::Includes treatment of population phenotypes and of the Population and Community Ontology [https://code.google.com/p/popcomm-ontology/ (PCO)] (Ramona Walls)
+
[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]
−
:Plant Trait Ontology ([http://crop.cgrb.oregonstate.edu/amigo/cgi-bin/crop_amigo/browse.cgi?action=plus_node&target=TO:0000387 TO]) (Pankaj Jaiswal)
+
 
−
::Critical remarks on PATO and TO (Barry Smith)
+
: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]
 +
:Automated tools to help construction of Trait Ontologies (Chris Mungall) [http://ontology.buffalo.edu/13/PRO-PO-GO/Mungall%20TraitOntologies.pptx Slides]
 +
: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]
 +
: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]
  
 
14:30 Break
 
14:30 Break
  
−
15:00 Defining Disease Across Organisms (Judith Blake)
+
15:00 Critical remarks on PATO and TO (Barry Smith) [http://ontology.buffalo.edu/13/PRO-PO-GO/TO.pptx Slides]
−
:Defining Disease
+
[https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=74933542&rKey=0bd434529a0c206f Streaming recording link]
−
:The [http://wiki.plantontology.org/index.php/Plant_Disease_Ontology Plant Disease Ontology] and the [http://ceur-ws.org/Vol-897/session1-paper01.pdf Plant Infectious Disease Ontology] (Ramona Walls)
 
−
:Use of PRO in defining diseases
 
  
−
17:00 Close
+
[https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=74933542&rKey=65ddcc0e6dda1b9e Webex Download recording link]
  
−
18:00 Working Dinner
+
:Defining Disease Across Organisms (Judith Blake)[http://ontology.buffalo.edu/13/PRO-PO-GO/blakeP0-PRO-GO.pptx Slides]
 +
::Defining Disease
 +
::Disease as a Subtype of Stress (Pankaj Jaiswal/Laurel Cooper) [http://ontology.buffalo.edu/13/PRO-PO-GO/Plant-Stress-Ontology.pptx Slides]
 +
::Plant Stresses and the [http://wiki.plantontology.org/index.php/Plant_Environment_Ontology Plant Environment Ontology] (EO) 
 +
::[http://wiki.plantontology.org/index.php/Plant_Disease_Ontology Plant Disease Ontology]
 +
:::[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]
 +
  
−
'''Thursday, May 16th, 2013'''
+
17:30 Close
  
−
8:15 Continental breakfast
+
18:00 Working Dinner in the Ramada Inn Restaurant
  
−
9:00 The Coordinating Role of the Protein Ontology
+
==='''Thursday, May 16th, 2013'''===
−
:PRO and Model Organism Research: Maintaining Ontologies Across Multiple Species
+
 
−
:PRO and UniProt
+
8:00 Continental breakfast
 +
 
 +
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]
 +
''Note: Audio only, variable quality ''
 +
:The Representation of Proteins in UniProtKB (Claire O'Donovan) [http://ontology.buffalo.edu/13/PRO-PO-GO/PRO-PO-GOClaire.pptx Slides]
 +
:The Integration of the Protein Ontology and UniProtKB (Cathy Wu) [http://ontology.buffalo.edu/13/PRO-PO-GO/PRO-&-UniProt-Wu.pptx Slides]
  
 
10:30 Break
 
10:30 Break
  
−
11:00 cROP Ontologies as Annotation Resources for New Plant Genomes  
+
10:45 Ontologies Across Species
 +
 +
[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''
 +
 
 +
:[http://www.topdownproteomics.org/ Top-Down Proteomics] (Paul Martin Thomas) [http://ontology.buffalo.edu/13/PRO-PO-GO/PMT-PROPOGO.pptx Slides]
 +
:Maintaining Ontologies as They Scale Across Multiple Species (Darren Natale) [http://ontology.buffalo.edu/13/PRO-PO-GO/PRO-PO-GO-DN.pptx Slides]
 +
: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]
 +
::Species-Neutral vs. Multi-Species Ontology (Barry Smith) [http://ontology.buffalo.edu/13/PRO-PO-GO/Foundry-efforts.pptx Slides]
  
 
12:30 Lunch
 
12:30 Lunch
  
−
13:30 Documenting Success Stories in Application of Annotated Genome Data
+
13:30 Documenting Success Stories and On-Going Projects (Dennis W. Stevenson) [http://ontology.buffalo.edu/13/PRO-PO-GO/Stevenson-Buffalo.pptx Slides]
−
:This is a discussion of ontology annotations; we will alert attendees to bring success stories regarding use of annotations in areas such as
+
 
−
::Diversity research (Inter-Species)
+
[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!''
−
::Discovering similarities and dissimilarities within organisms (Intra-Species)
+
 
−
::Identification of species for forensic purposes
+
::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]
−
::What are the structures involved in given biological processes (for example pollination)?
+
 
−
::What are the biological processes involved in phenomena such as disease)?
+
::The [http://www.iplantcollaborative.org/ iPlant Ontology Strategy] (Ramona Walls) [http://ontology.buffalo.edu/13/PRO-PO-GO/iPlant_for_PROPOGO.pptx Slides]
 +
 
 +
::[http://www.morphobank.org/ Morphobank] (Ramona Walls and Dennis Stevenson)
 +
 +
[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!
 +
 
 +
::[[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]
 +
 
 +
::Plant Phenotype Pilot Project (Laurel Cooper) [http://ontology.buffalo.edu/13/PRO-PO-GO/PPPP-Cooper-5-16-13.pptx Slides]
 +
 
 +
::Bioportal Slices (Trish Whetzel) [http://ontology.buffalo.edu/13/PRO-PO-GO/Whetzel-PROPOGO.ppt Slides]
  
 
16:00 Close
 
16:00 Close
Line 105: Line 150:
 
----
 
----
  
−
== '''Participants will include:''' ==
+
== '''Participants''' ==
  
 
PO Consortium
 
PO Consortium
 
:Laurel Cooper (Oregon)
 
:Laurel Cooper (Oregon)
 
:Pankaj Jaiswal (Oregon)
 
:Pankaj Jaiswal (Oregon)
 +
:Justin Preece (Oregon)
 
:Barry Smith (Buffalo)  
 
:Barry Smith (Buffalo)  
 
:Dennis Wm. Stevenson (New York Botanical Gardens)
 
:Dennis Wm. Stevenson (New York Botanical Gardens)
Line 117: Line 163:
 
:Jane Lomax (EBI)
 
:Jane Lomax (EBI)
 
:Chris Mungall (Berkeley)  
 
:Chris Mungall (Berkeley)  
 +
:Tanya Berardini (Stanford)
 +
:Eva Huala (Stanford)
  
 
PRO Consortium  
 
PRO Consortium  
Line 131: Line 179:
  
 
UniProt
 
UniProt
−
:Claire O'Donovan (EBI)  
+
:Claire O'Donovan (EBI)
 +
 
 +
Top-Down Proteomics
 +
:Paul Martin Thomas (Northwestern)
 +
 
 +
Ensembl Plants
 +
:Dan Bolser (EBI)  
  
 
CHEBI
 
CHEBI
−
:Janna Hastings (EBI, Geneva)
+
:Janna Hastings (EBI / Geneva)
 +
 
 +
PATO
 +
:George Gkoutos (Cambridge)
 +
 
 +
Immune Epitope Database
 +
:James Overton 
  
 
Arabidopsis Information Portal
 
Arabidopsis Information Portal
Line 145: Line 205:
 
:Tanya Berardini (Stanford)
 
:Tanya Berardini (Stanford)
 
:Eva Huala (Stanford)
 
:Eva Huala (Stanford)
 +
 +
NCBO
 +
:Trish Whetzel (Stanford)
  
 
Other participants:
 
Other participants:
 
:Alexander Cox (Buffalo)
 
:Alexander Cox (Buffalo)
−
:William Hogan (Arkansas)
 
 
:Mark Jensen (Buffalo)
 
:Mark Jensen (Buffalo)
 +
:Patrick Ray (Buffalo)
  
−
A limited number of places are available for additional participants. Please contact [mailto:phismith@buffalo.edu Barry Smith] for further information.
+
Please contact [mailto:phismith@buffalo.edu Barry Smith] for further information.
−
 
 
−
Note that this meeting is co-located with the BFO 2.0 meeting, which will take place in Buffalo on May 13-14:
 
  
−
http://ncorwiki.buffalo.edu/index.php/2013_BFO_Meeting
+
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.
  
−
'''Sponsors'''  
+
== '''Sponsors''' ==
 +
 
:[http://www.plantontology.org/ The Plant Ontology]
 
:[http://www.plantontology.org/ The Plant Ontology]
 
:[http://pir.georgetown.edu/pro/ The Protein Ontology]
 
:[http://pir.georgetown.edu/pro/ The Protein Ontology]
−
:[http://bioontologies.org The National Center for Biomedical Ontology]
+
:[http://bioontologies.org National Center for Biomedical Ontology]
 +
:[http://ncor.buffalo.edu National Center for Ontological Research]

Latest revision as of 22:36, 6 December 2013

PRO-PO-GO: International Coordination Meeting for Ontology-Based Efforts for Plant Biology

A meeting to promote the coordination of the Gene, Protein, and Plant Ontologies and of other reference ontologies used in plant biology

Venue: Ramada Inn, Amherst, NY 14221

Date: May 15-16, 2013. The meeting will start at 9am on May 15 and conclude at 4pm on May 16.

Goals

The goals of this meeting are:

  • 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:
a. To enhance the treatment of plant-related proteins in the Protein Ontology
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
  • 2. To address general issues which arise when ontologies need to be extended to cover multiple species of organisms
  • 3. To contribute to the cROP (Common Reference Ontologies for Plants) initiative
  • 4. To contribute to the ontological understanding of phenotype and disease across organisms.
  • 5. To identify potentially fruitful applications which enhanced ontology coordination might bring.

cROP: Common Reference Ontologies for Plants

Yellow = cROP ontologies for plants; Blue = general reference ontologies; Pink = to be developed by cROP

CROP.jpg


Schedule

Wednesday, May 15, 2013

8:00 Registration and continental breakfast

9:00 From the OBO Foundry to cROP Slides

Webex recording Webex download link Note: No audio

Outline of the cROP Framework (Pankaj Jaiswal)
Overview of cROP ontologies
Presentations will focus on:
  • Current or planned treatment of multiple organism types
  • Important applications of these ontologies
  • Experiences in the use of these ontologies in coordination (prototypically via use of terms from coordinating ontologies in cross-product definitions)
Molecules:
Protein Ontology (PRO) (Cathy Wu) Slides
CHEBI and Natural Products of Plant Origin (Janna Hastings) Slides
Cells
GO-Cellular Component (Alex Diehl)
Cell Type Ontology (CL) (Alex Diehl)
Use of PRO in defining Cell Types (Alex Diehl)
Diehl Slides
Plant Cell branch of the Plant Ontology (PO) (Laurel Cooper)
Organisms
Plant Ontology (PO) (Laurel Cooper)
Cooper Slides

10:30 Break

10:45 The Coordinating Role of the Gene Ontology (Jane Lomax) Lomax slides

Webex Streaming recording link Webex Download recording link

Questions to be addressed include:
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?
How are growth and development terms to be dealt with across organisms?
What are the lessons learned from the GO's experience in coordinating with other ontologies using GO terms in definitions?
Need for mechanisms of alerting each other to changes in ontology structure, e.g term obsoletions
  • Use of PO for relevant GO logical definitions (Tanya Berardini) Slides
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)?

12:00 Lunch

13:00 Traits and Phenotypes Webex Session #2

Streaming recording link Download recording link

Phenotypic Quality Ontology (PATO) (George Gkoutos) Slides
Automated tools to help construction of Trait Ontologies (Chris Mungall) Slides
The treatment of population phenotypes and use of the Population and Community Ontology (PCO) (Ramona Walls) Slides
Plant Trait Ontology (TO) (Pankaj Jaiswall/Laurel Cooper) Slides

14:30 Break

15:00 Critical remarks on PATO and TO (Barry Smith) Slides Streaming recording link

Webex Download recording link

Defining Disease Across Organisms (Judith Blake)Slides
Defining Disease
Disease as a Subtype of Stress (Pankaj Jaiswal/Laurel Cooper) Slides
Plant Stresses and the Plant Environment Ontology (EO)
Plant Disease Ontology
Plant Infectious Disease Ontology (Ramona Walls) slides


17:30 Close

18:00 Working Dinner in the Ramada Inn Restaurant

Thursday, May 16th, 2013

8:00 Continental breakfast

9:00 PRO and UniProt Streaming recording link Download recording link Note: Audio only, variable quality

The Representation of Proteins in UniProtKB (Claire O'Donovan) Slides
The Integration of the Protein Ontology and UniProtKB (Cathy Wu) Slides

10:30 Break

10:45 Ontologies Across Species

Streaming recording link Download recording link Note: Audio quite poor

Top-Down Proteomics (Paul Martin Thomas) Slides
Maintaining Ontologies as They Scale Across Multiple Species (Darren Natale) Slides
Interface Points between the cROP plant ontologies and the Protein Ontology (Cathy Wu) Slides
Species-Neutral vs. Multi-Species Ontology (Barry Smith) Slides

12:30 Lunch

13:30 Documenting Success Stories and On-Going Projects (Dennis W. Stevenson) Slides

Streaming recording link:Part One Download recording link: Part One Warning- large file!

GO Annotation of 23 Plant Genomes in Ensembl Plants (Dan Bolser) Slides
The iPlant Ontology Strategy (Ramona Walls) Slides
Morphobank (Ramona Walls and Dennis Stevenson)

Streaming recording link:Part Two Download recording link: Part Two Warning- large file!

AISO: Annotation of Image Segments using Ontologies (Justin Preece) Webex Session #3 Slides
Plant Phenotype Pilot Project (Laurel Cooper) Slides
Bioportal Slices (Trish Whetzel) Slides

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Participants

PO Consortium

Laurel Cooper (Oregon)
Pankaj Jaiswal (Oregon)
Justin Preece (Oregon)
Barry Smith (Buffalo)
Dennis Wm. Stevenson (New York Botanical Gardens)

GO Consortium

Judith Blake (JAX)
Jane Lomax (EBI)
Chris Mungall (Berkeley)
Tanya Berardini (Stanford)
Eva Huala (Stanford)

PRO Consortium

Cathy Wu (Delaware)
Darren Natale (Georgetown)
Alan Ruttenberg (Buffalo)

Cell Ontology

Alex Diehl (Buffalo)

BFO

Stefan Schulz (Graz)
Selja Seppälä (Buffalo)

UniProt

Claire O'Donovan (EBI)

Top-Down Proteomics

Paul Martin Thomas (Northwestern)

Ensembl Plants

Dan Bolser (EBI)

CHEBI

Janna Hastings (EBI / Geneva)

PATO

George Gkoutos (Cambridge)

Immune Epitope Database

James Overton

Arabidopsis Information Portal

Christopher D. Town (J. Craig Venter Institute)

The iPlant Collaborative

Ramona Walls

TAIR

Tanya Berardini (Stanford)
Eva Huala (Stanford)

NCBO

Trish Whetzel (Stanford)

Other participants:

Alexander Cox (Buffalo)
Mark Jensen (Buffalo)
Patrick Ray (Buffalo)

Please contact Barry Smith for further information.

Note that this meeting is co-located with the BFO 2.0 meeting, which will take place in Buffalo on May 13-14.

Sponsors

The Plant Ontology
The Protein Ontology
National Center for Biomedical Ontology
National Center for Ontological Research
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