Difference between revisions of "PRO-PO-GO Meeting"
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| − | '''PRO-PO-GO: | + | '''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''' | '''A meeting to promote the coordination of the Gene, Protein, and Plant Ontologies and of other reference ontologies used in plant biology''' | ||
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'''Date''': May 15-16, 2013. The meeting will start at 9am 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. | ||
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| − | |||
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| Line 31: | Line 29: | ||
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| − | == '''Schedule''' == | + | =='''Schedule''' == |
| − | + | ==='''Wednesday, May 15, 2013'''=== | |
| − | |||
| − | '''Wednesday, May 15, 2013''' | ||
8:00 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] | + | 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 cROP ontologies | :Overview of cROP ontologies | ||
| Line 49: | Line 46: | ||
: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 and Natural Products of Plant Origin (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 (Alex Diehl) | |
| + | :::[http://ontology.buffalo.edu/13/PRO-PO-GO/Diehl.pptx Diehl Slides] | ||
::Plant Cell branch of the Plant Ontology (PO) (Laurel Cooper) | ::Plant Cell branch of the Plant Ontology (PO) (Laurel Cooper) | ||
:Organisms | :Organisms | ||
::Plant Ontology (PO) (Laurel Cooper) | ::Plant Ontology (PO) (Laurel Cooper) | ||
| + | :::[http://ontology.buffalo.edu/13/PRO-PO-GO/Cooper.pptx Cooper Slides] | ||
10:30 Break | 10:30 Break | ||
| − | 10:45 The Coordinating Role of the Gene Ontology (Jane Lomax) Webex | + | 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? | ||
| − | ::Use of PO for relevant GO logical definitions (Tanya Berardini) | + | ::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)? | ::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''' | |
| − | + | [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] | |
| − | :Phenotypic Quality Ontology ([http://obofoundry.org/wiki/index.php/PATO:Main_Page PATO]) ( | + | |
| − | ::The treatment of population phenotypes and use of the Population and Community Ontology [https://code.google.com/p/popcomm-ontology/ (PCO)] (Ramona Walls) | + | :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] |
| − | :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) | + | :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] |
| − | :Disease as a Subtype of Stress (Pankaj Jaiswal/Laurel Cooper) | + | |
| + | [https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=74933542&rKey=65ddcc0e6dda1b9e Webex Download recording link] | ||
| + | |||
| + | :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) | ::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://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://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] |
| + | |||
17:30 Close | 17:30 Close | ||
| Line 93: | Line 105: | ||
18:00 Working Dinner in the Ramada Inn Restaurant | 18:00 Working Dinner in the Ramada Inn Restaurant | ||
| − | '''Thursday, May 16th, 2013''' | + | ==='''Thursday, May 16th, 2013'''=== |
8:00 Continental breakfast | 8:00 Continental breakfast | ||
9:00 PRO and UniProt | 9:00 PRO and UniProt | ||
| − | :The Representation of Proteins in UniProtKB (Claire O'Donovan) | + | [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] |
| − | :The Integration of the Protein Ontology and UniProtKB (Cathy Wu) | + | ''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 | ||
| − | + | 10:45 Ontologies Across Species | |
| − | :Maintaining Ontologies as They Scale Across Multiple Species (Darren Natale) | + | |
| − | : | + | [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'' |
| − | :Interface Points between the cROP plant ontologies and the Protein Ontology (Cathy Wu) | + | |
| + | :[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 and On-Going Projects (Dennis W. Stevenson) | + | 13:30 Documenting Success Stories and On-Going Projects (Dennis W. Stevenson) [http://ontology.buffalo.edu/13/PRO-PO-GO/Stevenson-Buffalo.pptx Slides] |
| − | ::GO Annotation of 23 Plant Genomes in [http://plants.ensembl.org/index.html Ensembl Plants] (Dan Bolser) | + | |
| − | + | [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!'' | |
| − | ::The [http://www.iplantcollaborative.org/ iPlant Ontology Strategy] (Ramona Walls) | + | |
| + | ::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] | ||
| + | |||
| + | ::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) | ::[http://www.morphobank.org/ Morphobank] (Ramona Walls and Dennis Stevenson) | ||
| − | ::[[AISO]]: Annotation of Image Segments using Ontologies (Justin Preece) | + | |
| − | ::Plant Phenotype Pilot Project (Laurel Cooper) | + | [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 | ||
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
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:
- Cells
- GO-Cellular Component (Alex Diehl)
- Cell Type Ontology (CL) (Alex Diehl)
- Use of PRO in defining Cell Types (Alex Diehl)
- Plant Cell branch of the Plant Ontology (PO) (Laurel Cooper)
- Organisms
- Plant Ontology (PO) (Laurel Cooper)
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
- 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!
- Plant Phenotype Pilot Project (Laurel Cooper) Slides
- Bioportal Slices (Trish Whetzel) Slides
16:00 Close
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.
