Protein Ontology Workshop: Difference between revisions

Latest revision as of 18:58, 5 September 2017

Date: June 18-19, 2014

Venue: Georgetown University

Goals and outcomes

The goals of this meeting are:

1. To contribute to the ontological understanding of phenotype and disease across organisms
2. To advance the treatment of protein-related clinical and translational data from the perspective of consistency, discoverability and support for diagnosis
3. To advance coordination between the Protein Ontology and other protein-related information resources

Desired outcomes are of two sorts:

Relating to disease:

We will seek greater clarity as to

- how proteomic information in general and the PRO in particular can help us to understand the relationship between genotype and phenotype, for example in understanding disease etiology

- which relations we should use in linking the protein entities represented in the PRO to disease entities

- which are the important entities on the protein side that need to be linked

Relating to PRO's interactions with external resources:

UniProt: Draft of policies/recommendations regarding accession/site tracking for UniProt and PRO

IntAct: Identify points of agreement and discrepancy in curation pipelines and resolve as appropriate. Reach agreements for example on reciprocal links and accession issues

Schedule: Wednesday, June 18, 2014

Chair: Barry Smith

8:45 Cathy Wu (Delaware/Georgetown): Current Status and Future Goals of the Protein Ontology

9:45 Peter d'Eustachio (NYU): PRO, Reactome and Disease Pathways

10:30 Break

10:45 Olivier Bodenreider (NLM): Ontologies in the NLM

11:25 Sirarat Sarntivijai (FDA): Using the Protein Ontology: The View from the Outside

11:55 Carol Bean (Stanford / NCBO): The Future of the Bioportal

12:15 Lunch

Chair: Peter d'Eustachio

13:00 Sandra Orchard (EBI): PRO and IntAct

14:00 Evan Bolton (NCBI): PubChemRDF: Towards a Semantic Description of PubChem

14:40 Lynn Schriml (Baltimore): Collaboration of PRO and PubChem with the Disease Ontology

15:20 Break

Chair: Darren Natale

15:40 Veerasamy “Ravi” Ravichandran (NIGMS): NIGMS and the Protein Ontology

16:00 John Westbrook (PDB): PRO Represention of Proteins Observed in 3D Experimental Structure Data

16:40 Alexander Diehl (Buffalo): PRO and the NIF / ImmPort Antibody Registries

17:20 Close

18:00 Working Dinner: Cafe Divan, 1834 Wisconsin Ave

Schedule: Thursday, June 19th, 2014

Venue: Conference Room #1300, Harris Building, Georgetown University, 3300 Whitehaven Street NW

8:00 Continental breakfast

Chair: Alexander Diehl

9:00 Donna Maglott (NIH): PRO and Medical Genetics resources at NCBI

9:40 Paul Martin Thomas (Northwestern): Descriptive and Quantitative Top Down Proteomics

10:20 John Garavelli (Delaware): Use Cases for Modified Protein Interactions (for UniProt, PRO and proteomics)

10:30 Break

10:45 Alexander Cox (Buffalo): Neurofibrillary Tangles and Amyloid Plaques: The Treatment of Protein Aggregates in the Protein Ontology

11.15 Alan Ruttenberg and Jonathan Bona (Buffalo): Issues surrounding coordination of UniProtKB and the Protein Ontology

12:30 Lunch

Chair: Cecilia Arrighi

13:30 Judith Blake (Jackson Lab): Ontologies, Databases, Knowledgebases: How Should They Interoperate?

14:00 Barry Smith (Buffalo): Introduction to the Relation Ontology

14:15 Darren Natale: Relations linking Proteins to Diseases

14:30 Break

14:45 Gilbert S. Omenn (Michigan): The Human Proteome Project

16:00 Close

Participants

Cecilia Arighi (Delaware / PRO)

Carol Bean (NCBO / Stanford)

Judith Blake (JAX)

Olivier Bodenreider (NIH / NLM / LHC)

Evan Bolton (NIH / NCBI)

Jonathan Bona (Buffalo)

Karen Christie (JAX)

Alexander Cox (Buffalo)

Peter d'Eustachio (NYU / Reactome)

Alex Diehl (Buffalo)

Harold Drabkin (JAX)

Gang Fu (NCBI / NIH)

John S. Garavelli (Delaware)

Donna Maglott (NIH / NLM / NCBI)

John Mattison (Global Alliance for Genomics and Health)

Darren Natale (Georgetown)

Claire O'Donovan (EBI / UniProt)

Gilbert S. Omenn (Michigan)

Sandra Orchard (EBI / IntAct)

Veerasamy “Ravi” Ravichandran (NIH / NIGMS)

Karen Ross (Delaware)

Alan Ruttenberg (Buffalo)

Sirarat Sarntivijai (FDA)

Selja Seppälä (Buffalo)

Lynn Schriml (Baltimore)

Barry Smith (Buffalo)

Paul Martin Thomas (Top Down Proteomics / Northwestern)

John Westbrook (PDB / Rutgers)

Cathy Wu (Delaware / PRO)

Please contact Barry Smith for further information.

Protein Ontology Workshop: Difference between revisions

Latest revision as of 18:58, 5 September 2017

Contents

Goals and outcomes

Schedule: Wednesday, June 18, 2014

Schedule: Thursday, June 19th, 2014

Participants

Sponsors

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@@ Line 1: / Line 1: @@
-'''PRO-PO-GO: International Coordination Meeting for Ontology-Based Efforts for Plant Biology'''
+'''Date''': June 18-19, 2014
-'''A meeting to promote the coordination of the Gene, Protein, and Plant Ontologies and of other reference ontologies used  in plant biology'''
+'''Venue''': Georgetown University
-'''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 9am on May 15 and conclude at 4pm on May 16.
+== '''Goals and outcomes''' ==
-----
+The goals of this meeting are:
-== '''Goals''' ==
+*1. To contribute to the ontological understanding of phenotype and disease across organisms
+*2. To advance the treatment of protein-related clinical and translational data from the perspective of consistency, discoverability and support for diagnosis
+*3. To advance coordination between the Protein Ontology and other protein-related information resources
-The goals of this meeting are:
+Desired outcomes are of two sorts:
-*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:
+*Relating to disease:
-:a.	To enhance the treatment of plant-related proteins in the Protein Ontology
+: We will seek greater clarity as to
-: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
+: - how proteomic information in general and the PRO in particular can help us to understand the relationship between genotype and phenotype, for example in understanding disease etiology
-*2.     To address general issues which arise when ontologies need to be extended to cover multiple species of organisms
+: - which [http://obofoundry.org/ontology/ro.html relations] we should use in linking the protein entities represented in the PRO to disease entities
-*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
+: - which are the important entities on the protein side that need to be linked
-*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''' ==
+*Relating to PRO's interactions with external resources:
-Yellow = cROP ontologies for plants; Blue = general reference ontologies; Pink = to be developed by cROP
+:'''UniProt''': Draft of policies/recommendations regarding accession/site tracking for UniProt and PRO
+:'''IntAct''': Identify points of agreement and discrepancy in curation pipelines and resolve as appropriate. Reach agreements for example on reciprocal links and accession issues
-[[File:cROP.jpg]]
+=='''Schedule: Wednesday, June 18, 2014==
-----
+<u>Chair: Barry Smith</u>
-=='''Schedule''' ==
+:45 Cathy Wu (Delaware/Georgetown): [http://ncor.buffalo.edu/2014/PRO/Wu.pdf Current Status and Future Goals of the Protein Ontology]
-==='''Wednesday, May 15, 2013'''===
+:45 Peter d'Eustachio (NYU): [http://ncor.buffalo.edu/2014/PRO/d'Eustachio.pptx PRO, Reactome and Disease Pathways]
-:00 Registration and continental breakfast
+:30 Break
-: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]
+:45 Olivier Bodenreider (NLM): [http://ncor.buffalo.edu/2014/PRO/Bodenreider.pdf Ontologies in the NLM]
-[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''
+:25 Sirarat Sarntivijai (FDA): [http://ncor.buffalo.edu/2014/PRO/Sarntivijai.ppt Using the Protein Ontology: The View from the Outside]
-: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:
+:55 Carol Bean (Stanford / NCBO): The Future of the [http://bioportal.bioontology.org/ Bioportal]
-::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) [http://ontology.buffalo.edu/13/PRO-PO-GO/chebi-and-plants.pptx Slides]
-:Cells
+:15 Lunch
-::GO-Cellular Component (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)
-:Organisms
+<u>Chair: Peter d'Eustachio</u>
-::Plant Ontology (PO) (Laurel Cooper)
-:::[http://ontology.buffalo.edu/13/PRO-PO-GO/Cooper.pptx Cooper Slides]
-:30 Break
+:00 Sandra Orchard (EBI): [http://ncor.buffalo.edu/2014/PRO/Orchard.pptx PRO and IntAct]
-:45 The Coordinating Role of the Gene Ontology (Jane Lomax) [http://ontology.buffalo.edu/13/PRO-PO-GO/GO-Lomax.pptx Lomax slides]
+:00 Evan Bolton (NCBI): [http://ncor.buffalo.edu/2014/PRO/Bolton.pdf PubChemRDF: Towards a Semantic Description of PubChem]
-[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]
+:40 Lynn Schriml (Baltimore): [http://ncor.buffalo.edu/2014/PRO/Schriml.pdf Collaboration of PRO and PubChem with the Disease Ontology]
-:Questions to be addressed include:
+:20 Break
-::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) [http://ontology.buffalo.edu/13/PRO-PO-GO/PRO_PO_GO_TB.pptx Slides]
+<u>Chair: Darren Natale</u>
-::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)?
-:00 Lunch
+:40 Veerasamy “Ravi” Ravichandran (NIGMS): [http://ncor.buffalo.edu/2014/PRO/Ravichandran.pptx NIGMS and the Protein Ontology]
-:00 '''Traits and Phenotypes Webex Session #2'''
+:00 John Westbrook (PDB): [http://ncor.buffalo.edu/2014/PRO/Westbrook.pdf PRO Represention of Proteins Observed in 3D Experimental Structure Data]
-[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]
+:40 Alexander Diehl (Buffalo): [http://ncor.buffalo.edu/2014/PRO/Diehl.pptx PRO and the NIF / ImmPort Antibody Registries]
-: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]
-:30 Break
+:20 Close
-:00 Critical remarks on PATO and TO (Barry Smith) [http://ontology.buffalo.edu/13/PRO-PO-GO/TO.pptx Slides]
+:00 Working Dinner: Cafe Divan, 1834 Wisconsin Ave
-[https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=74933542&rKey=0bd434529a0c206f Streaming recording link]
-[https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=74933542&rKey=65ddcc0e6dda1b9e Webex Download recording link]
+=='''Schedule: Thursday, June 19th, 2014'''==
-:Defining Disease Across Organisms (Judith Blake)[http://ontology.buffalo.edu/13/PRO-PO-GO/blakeP0-PRO-GO.pptx Slides]
+Venue: Conference Room #1300, Harris Building, Georgetown University,  [https://www.google.com/maps/place/3300+Whitehaven+St+NW/@38.917007,-77.06752,17z/data=!3m1!4b1!4m2!3m1!1s0x89b7b630848d084f:0x22bd0eb5dab5a2ff 3300 Whitehaven Street NW]
-::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]
-:30 Close
+:00 Continental breakfast
-:00 Working Dinner in the Ramada Inn Restaurant
+<u>Chair: Alexander Diehl</u>
-==='''Thursday, May 16th, 2013'''===
+:00 Donna Maglott (NIH): [http://ncor.buffalo.edu/2014/PRO/Maglott.pptx PRO and Medical Genetics resources at NCBI]
-:00 Continental breakfast
+:40 Paul Martin Thomas (Northwestern): [http://ncor.buffalo.edu/2014/PRO/Thomas.pdf Descriptive and Quantitative Top Down Proteomics]
-:00 PRO and UniProt
+:20 John Garavelli (Delaware): [http://ncor.buffalo.edu/2014/PRO/Garavelli.ppt Use Cases for Modified Protein Interactions (for UniProt, PRO and proteomics)]
-[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]
 :30 Break
-:45 Ontologies Across Species
+:45 Alexander Cox (Buffalo): [http://ncor.buffalo.edu/2014/PRO/Cox.pptx Neurofibrillary Tangles and Amyloid Plaques: The Treatment of Protein Aggregates in the Protein Ontology]
-[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]
+.15 Alan Ruttenberg and Jonathan Bona (Buffalo): [http://goo.gl/i1bMRo Issues surrounding coordination of UniProtKB and the Protein Ontology]
-: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]
 :30 Lunch
-:30 Documenting Success Stories and On-Going Projects (Dennis W. Stevenson) [http://ontology.buffalo.edu/13/PRO-PO-GO/Stevenson-Buffalo.pptx Slides]
+<u>Chair: Cecilia Arrighi</u>
-[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!''
+:30 Judith Blake (Jackson Lab): [http://ncor.buffalo.edu/2014/PRO/Blake.pptx Ontologies, Databases, Knowledgebases: How Should They Interoperate?]
-::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]
+:00 Barry Smith (Buffalo): [http://ncor.buffalo.edu/2014/PRO/Smith.ppt Introduction to the Relation Ontology]
-::The [http://www.iplantcollaborative.org/ iPlant Ontology Strategy] (Ramona Walls) [http://ontology.buffalo.edu/13/PRO-PO-GO/iPlant_for_PROPOGO.pptx Slides]
+:15 Darren Natale: [http://ncor.buffalo.edu/2014/PRO/Natale.pptx Relations linking Proteins to Diseases]
-::[http://www.morphobank.org/ Morphobank] (Ramona Walls and Dennis Stevenson)
+:30 Break
-[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]
+:45 Gilbert S. Omenn (Michigan): [http://ncor.buffalo.edu/2014/PRO/Omenn.pptx The Human Proteome Project]
-::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]
 :00 Close
@@ Line 152: / Line 105: @@
 == '''Participants''' ==
-PO Consortium
+:Cecilia Arighi (Delaware / PRO)
-:Laurel Cooper (Oregon)
+:Carol Bean (NCBO / Stanford)
-:Pankaj Jaiswal (Oregon)
-:Justin Preece (Oregon)
-:Barry Smith (Buffalo)
-:Dennis Wm. Stevenson (New York Botanical Gardens)
-GO Consortium
 :Judith Blake (JAX)
-:Jane Lomax (EBI)
+:Olivier Bodenreider (NIH / NLM / LHC)
-:Chris Mungall (Berkeley)
+:Evan Bolton (NIH / NCBI)
-:Tanya Berardini (Stanford)
+:Jonathan Bona (Buffalo)
-:Eva Huala (Stanford)
+:Karen Christie (JAX)
+:Alexander Cox (Buffalo)
-PRO Consortium
+:Peter d'Eustachio (NYU / Reactome)
-:Cathy Wu (Delaware)
+:Alex Diehl (Buffalo)
+:Harold Drabkin (JAX)
+:Gang Fu (NCBI / NIH)
+:John S. Garavelli (Delaware)
+:Donna Maglott (NIH / NLM / NCBI)
+:John Mattison (Global Alliance for Genomics and Health)
 :Darren Natale (Georgetown)
+:Claire O'Donovan (EBI / UniProt)
+:Gilbert S. Omenn (Michigan)
+:Sandra Orchard (EBI / IntAct)
+:Veerasamy “Ravi” Ravichandran (NIH / NIGMS)
+:Karen Ross (Delaware)
 :Alan Ruttenberg (Buffalo)
+:Sirarat Sarntivijai (FDA)
-Cell Ontology
-:Alex Diehl (Buffalo)
-BFO
-:Stefan Schulz (Graz)
 :Selja Seppälä (Buffalo)
+:Lynn Schriml (Baltimore)
-UniProt
+:Barry Smith (Buffalo)
-:Claire O'Donovan (EBI)
+:Paul Martin Thomas ([http://www.kelleher.northwestern.edu/research/top-down-proteomics Top Down Proteomics] / Northwestern)
+:John Westbrook (PDB / Rutgers)
-Top-Down Proteomics
+:Cathy Wu (Delaware / PRO)
-: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 [mailto:phismith@buffalo.edu Barry Smith] for further information.
-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''' ==
-:[http://www.plantontology.org/ The Plant Ontology]
+:[http://pir.georgetown.edu/pro/ The Protein Ontology Consortium]
-:[http://pir.georgetown.edu/pro/ The Protein Ontology]
 :[http://bioontologies.org National Center for Biomedical Ontology]
 :[http://ncor.buffalo.edu National Center for Ontological Research]