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'''Date''': October 11-12, 2017
'''Date''': October 11-12, 2017


'''Venue''': Jackson Lab, Bar Habor, Maine
[[PRO Consortium Workshop 2019]]


----
'''Venue''': [https://barharbormainehotel.com/ Atlantic Oceanside Hotel], Bar Harbor, MN


== '''Goals and outcomes''' ==
==Goals==


The goals of this meeting are:
The goals of this meeting are:
*1. To review the current state of the Protein Ontology and its relation to other protein-related information resources, especially UniProt and GO and to document these relations with a view to publication.
*2. To evaluate current competing approaches to gene annotation in PRO and in other OBO Foundry ontologies and to document the implications of this evaluation with a view to publication.
*3. To assess progress in the use of advanced computational techniques, including Natural Language Processing, in the development of the PRO.
*4. To examine the actual and potential contribution of PRO to the understanding of disease across organisms.
*5. To advance the treatment of protein-related clinical and translational data from the perspective of consistency, discoverability and support for diagnosis.


*1. To contribute to the ontological understanding of phenotype and disease across organisms
==White Papers==
*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 [http://obofoundry.org/ro/ 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 -- focus on PTMs, sites
 
*Relating to PRO's interactions with external resources:
:'''UniProt''': Draft of policies/recommendations regarding accession/site tracking for UniProt and PRO
 
Benefits and limitations of PRO
 
PRO and PTM knowledge networks


Developing PROs scope for annotating diseases
[https://buffalo.box.com/s/i1saod7olqdxc3c5n4vgikbpwxmk7qx7 PRO Family Relations]


=='''Schedule: Tuesday, October, 10, 2017==
[https://buffalo.box.com/s/hx6wd7eeyg6iw6q1kn7h956zyzpqs62w Functional Annotation of Proteins]


19:00 Informal reception for early arrivals in conference hotel
==Schedule: Wednesday, October, 11, 2017==


=='''Schedule: Wednesday, October, 11, 2017==
'''Introductory Session: The Landscape of the Protein Ontology'''


<u>Chair: TBD</u> '''The future of the PRO'''
:8:45 Cathy Wu: Protein Ontology: Its current state and future development [https://buffalo.box.com/s/ahra2it1glmtsqm2e96yhgsp20u9jou3 Slides]


Sites
:9:30 Susan Gregurick: NIH 2018 Priorities in Data Science and Computational Science [https://buffalo.box.com/s/8002lr7syg8gf2blt6hyjg7q69ka63b7 Slides]
PTMs


'''PRO and Related Resources'''


8:45 Cathy Wu: Protein Ontology: Its current state and future development
:9:45 Darren Natale: Implementation of the  PRO Sites Ontology [https://buffalo.box.com/s/2an2i0wcfn7r3m5dld2q6tilr03oy0gg Slides]


TBD: ProKinO: Protein Kinase Ontology Browser
:10:25 Karen Ross: PRO Collaborations (ProKinO, NeXtProt ...) [https://buffalo.box.com/s/zpicxbl4qj4b5y1o69bq3te8gkd8bakq Slides]


TBD: NeXtProt
:10:45 Break


Pamela VanAuken: Noctua
:11:00 Erich Baker and Elissa Chesler: GeneWeaver [https://buffalo.box.com/s/lglbejd3men722onm6m5xs1a5nsxmar4 Slides]


Cindy Smith: The Alliance of Genome Resources
:11:30 Cindy Smith: Disease Ontology at MGI [https://buffalo.box.com/s/mc67ue7h306aimgdipf0l16yok4t2u5h Slides]


10:30 Break
:12:00 Kimberley VanAuken: Noctua and GO-CAM
[https://buffalo.box.com/s/c855q50pges44czj6v6hro7rf2c8r6u1 Slides]


10:45 '''PRO and software / NLP / SPARQL'''
:12:30 Lunch
 
Chair: Alex Diehl
 
ChuMing: Writing SPARQL queries for PRO
 
Alex Diehl: PRO and the Antibody Ontology
 
Alex Diehl: PRO the Cell Ontology (HIPC, cell populations, the Antibody Panel Ontology)
 
PRO and its relations to the experimental community
 
PRO curation/development and NLP
 
12:30 Lunch
 
13:30


'''PRO and Disease'''
'''PRO and Disease'''


Chair: Barry Smith
Chair: Darren Natale
 
Judith Blake (MGI): Disease Ontology -- overview of available resources
 
Elissa Chesler (MGI): MGI effort to combine variant data with disease forms; Genereader resource, PRO IDs for variants
 
Barry Smith Protein-Disease Relations
 
Other large-scale frameworks working with protein variants
 
14:30 Break


14:45
:13:30 Judith Blake: Alliance of Genome Resources [https://buffalo.box.com/s/gu31c0z6vkgbd950tf4uft47zdd4ij6p Slides]


16:00 Close
:14:00 Chris Mungall: An Update on OBO / MONARCH [https://buffalo.box.com/s/uppgc4r87jn80xcpn4etiu2th19wfyax Slides]


=='''Schedule: Thursday, October 12, 2017'''==
:14:30 Barry Smith: How to define 'causally upstream of'


Venue: JAX
:15:00 Break


8:00 Continental breakfast
:15:15 Peter McGarvey: Genome Annotation, ClinGen and PRO [https://buffalo.box.com/s/gu31c0z6vkgbd950tf4uft47zdd4ij6p Slides]


'''GO, PRO and UniProt: How they should work together'''
:15:45 Peter d'Eustachio: Reactome, PRO, GO, Phenotypes,
Complexes [https://buffalo.box.com/s/bo5yiutb082sp8qlc6egyh3o3aed6xwr Slides]


Chair: TBD
:16:15 Alexander Diehl: Cells, Proteins, Antibodies and Diseases [https://buffalo.box.com/s/xpjpn5kilahkvtt69gp4p7f28axewitm Slides]


9:00 Alex Bateman (EBI)
17:00 '''Discussion of the representation of PRO annotations'''
:Chair: Barry Smith
:Participants: Alan Ruttenberg and Darren Natale


10:30 Break
:18:00 Working dinner


10:45
==Schedule: Thursday, October 12, 2017==


12:00 Lunch
'''GO, PRO and UniProt'''


12:45 '''PRO and OBO Foundry
Chair: Cathy Wu


Chair: TBD
:8:45 Maria Martin: Representing UniProt


Scope of PRO
:9:30 Chris Mungall: Representing GO


Treatment of protein complexes
:9:45 GO, PRO and UniProt: How will they work together


Alan Ruttenberg: How genes are referenced in OBO Foundry? in PRO?
:10:30 Break


Participants: Chris Mungall, Darren Natale
:10:45 Julie Cowart: Data Access and Writing SPARQL Queries [https://buffalo.box.com/s/6u4ef8l0gjylwgsdbv5eb9ww4yhmkja2 Slides]


Proper treatment of functions in PRO
:11:15 Alan Ruttenberg: Discussion of how genes are referenced in OBO Foundry and in PRO: why do they differ?


14:00 Close of Plenary Sessions
:11:45 Cecilia Arighi: The role of NLP in PRO curation [https://buffalo.box.com/s/ykzpfu5quyx44qr3fenoqqi45o084x3b Slides]


:12:15 Lunch


13:00 '''Discussion of how genes are referenced in OBO Foundry and in PRO: why do they differ?'''
:Chair: Barry Smith
:Participants: David Hill, Chris Mungall, Darren Natale, Alan Ruttenberg.


14:00 Working group meetings
:14:00 '''Roundtable on killer apps for PRO'''


17:00 Close
:16:00 Close


----
----
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== '''Participants''' ==
== '''Participants''' ==


:Cecilia Arighi (Delaware / PRO)
*=online
:Erich Baker (Baylor))
:Cecilia Arighi (Delaware / PRO)*
:Alex Bateman (EBI)
:Erich Baker (Baylor)
:Judith Blake (JAX)
:Judith Blake (JAX)
:Chuming Chen (Delaware)*
:Elissa Chesler (JAX)
:Elissa Chesler (JAX)
:? Karen Christie (JAX)
:Julie Cowart (Delaware)*
:Alex Diehl (Buffalo)
:Mary Dolan (JAX)
:Peter d'Eustachio (NYU)*
:Alexander Diehl (Buffalo)
:Harold Drabkin (JAX)
:Harold Drabkin (JAX)
:? Gang Fu (NCBI / NIH)
:Susan Gregurick (NIH / NIGMS)*
:? John S. Garavelli (Delaware)
:David Hill (JAX)
:? Donna Maglott (NIH / NLM / NCBI)
:Stanley Laulederkind (Medical College of Wisconsin)
:Peter McGarvey (Georgetown)
:Maria Martin (EBI)
:Chris Mungall (LBNL)
:Darren Natale (Georgetown)
:Darren Natale (Georgetown)
:? Veerasamy “Ravi” Ravichandran (NIH / NIGMS)
:Li Ni (JAX)
:? Karen Ross (Delaware)
:Karen Ross (Delaware)*
:Alan Ruttenberg (Buffalo)
:Alan Ruttenberg (Buffalo)
:Cynthia Smith (JAX)
:Cynthia Smith (JAX)

Latest revision as of 19:49, 13 June 2019

Date: October 11-12, 2017

PRO Consortium Workshop 2019

Venue: Atlantic Oceanside Hotel, Bar Harbor, MN

Goals

The goals of this meeting are:

  • 1. To review the current state of the Protein Ontology and its relation to other protein-related information resources, especially UniProt and GO and to document these relations with a view to publication.
  • 2. To evaluate current competing approaches to gene annotation in PRO and in other OBO Foundry ontologies and to document the implications of this evaluation with a view to publication.
  • 3. To assess progress in the use of advanced computational techniques, including Natural Language Processing, in the development of the PRO.
  • 4. To examine the actual and potential contribution of PRO to the understanding of disease across organisms.
  • 5. To advance the treatment of protein-related clinical and translational data from the perspective of consistency, discoverability and support for diagnosis.

White Papers

PRO Family Relations

Functional Annotation of Proteins

Schedule: Wednesday, October, 11, 2017

Introductory Session: The Landscape of the Protein Ontology

8:45 Cathy Wu: Protein Ontology: Its current state and future development Slides
9:30 Susan Gregurick: NIH 2018 Priorities in Data Science and Computational Science Slides

PRO and Related Resources

9:45 Darren Natale: Implementation of the PRO Sites Ontology Slides
10:25 Karen Ross: PRO Collaborations (ProKinO, NeXtProt ...) Slides
10:45 Break
11:00 Erich Baker and Elissa Chesler: GeneWeaver Slides
11:30 Cindy Smith: Disease Ontology at MGI Slides
12:00 Kimberley VanAuken: Noctua and GO-CAM
Slides
12:30 Lunch

PRO and Disease

Chair: Darren Natale

13:30 Judith Blake: Alliance of Genome Resources Slides
14:00 Chris Mungall: An Update on OBO / MONARCH Slides
14:30 Barry Smith: How to define 'causally upstream of'
15:00 Break
15:15 Peter McGarvey: Genome Annotation, ClinGen and PRO Slides
15:45 Peter d'Eustachio: Reactome, PRO, GO, Phenotypes,

Complexes Slides

16:15 Alexander Diehl: Cells, Proteins, Antibodies and Diseases Slides

17:00 Discussion of the representation of PRO annotations

Chair: Barry Smith
Participants: Alan Ruttenberg and Darren Natale
18:00 Working dinner

Schedule: Thursday, October 12, 2017

GO, PRO and UniProt

Chair: Cathy Wu

8:45 Maria Martin: Representing UniProt
9:30 Chris Mungall: Representing GO
9:45 GO, PRO and UniProt: How will they work together
10:30 Break
10:45 Julie Cowart: Data Access and Writing SPARQL Queries Slides
11:15 Alan Ruttenberg: Discussion of how genes are referenced in OBO Foundry and in PRO: why do they differ?
11:45 Cecilia Arighi: The role of NLP in PRO curation Slides
12:15 Lunch

13:00 Discussion of how genes are referenced in OBO Foundry and in PRO: why do they differ?

Chair: Barry Smith
Participants: David Hill, Chris Mungall, Darren Natale, Alan Ruttenberg.
14:00 Roundtable on killer apps for PRO
16:00 Close

Participants

*=online
Cecilia Arighi (Delaware / PRO)*
Erich Baker (Baylor)
Judith Blake (JAX)
Chuming Chen (Delaware)*
Elissa Chesler (JAX)
Julie Cowart (Delaware)*
Mary Dolan (JAX)
Peter d'Eustachio (NYU)*
Alexander Diehl (Buffalo)
Harold Drabkin (JAX)
Susan Gregurick (NIH / NIGMS)*
David Hill (JAX)
Stanley Laulederkind (Medical College of Wisconsin)
Peter McGarvey (Georgetown)
Maria Martin (EBI)
Chris Mungall (LBNL)
Darren Natale (Georgetown)
Li Ni (JAX)
Karen Ross (Delaware)*
Alan Ruttenberg (Buffalo)
Cynthia Smith (JAX)
Barry Smith (Buffalo)
Kimberley VanAuken (CalTech)
Laurens Wilming (JAX)
Cathy Wu (Delaware / PRO)

Please contact Barry Smith for further information.

Sponsors

The Protein Ontology Consortium
National Center for Ontological Research
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