PRO Consortium Workshop 2017: Difference between revisions

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'''Date''': October 11-12, 2017
'''Date''': October 11-12, 2017
[[PRO Consortium Workshop 2019]]


'''Venue''': [https://barharbormainehotel.com/ Atlantic Oceanside Hotel], Bar Harbor, MN
'''Venue''': [https://barharbormainehotel.com/ Atlantic Oceanside Hotel], Bar Harbor, MN
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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.
*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 document the relation between PRO, UniProt and Go 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 evaluate current competing approaches to gene annotation in PRO and in other OBO Foundry ontologies, 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 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 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.
*6. To advance the treatment of protein-related clinical and translational data from the perspective of consistency, discoverability and support for diagnosis.


==Schedule: Tuesday, October, 10, 2017==
==White Papers==


19:00 Informal reception for early arrivals in conference hotel
[https://buffalo.box.com/s/i1saod7olqdxc3c5n4vgikbpwxmk7qx7 PRO Family Relations]
 
[https://buffalo.box.com/s/hx6wd7eeyg6iw6q1kn7h956zyzpqs62w Functional Annotation of Proteins]


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


:8:45 Cathy Wu: Protein Ontology: Its current state and future development
:8:45 Cathy Wu: Protein Ontology: Its current state and future development [https://buffalo.box.com/s/ahra2it1glmtsqm2e96yhgsp20u9jou3 Slides]
 
::Sites, PTMs


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


'''PRO and Related Resources'''
'''PRO and Related Resources'''


:9:45 Karen Ross: PRO Collaborations (ProKinO, NeXtProt ...)
:9:45 Darren Natale: Implementation of the  PRO Sites Ontology [https://buffalo.box.com/s/2an2i0wcfn7r3m5dld2q6tilr03oy0gg Slides]


:10:15 Darren Natale: PRO Site Ontology
:10:25 Karen Ross: PRO Collaborations (ProKinO, NeXtProt ...) [https://buffalo.box.com/s/zpicxbl4qj4b5y1o69bq3te8gkd8bakq Slides]


:10:45 Break
:10:45 Break


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


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


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


:12:30 Lunch
:12:30 Lunch
Line 47: Line 49:
Chair: Darren Natale
Chair: Darren Natale


:13:30 Judith Blake: Disease Ontology -- overview of available resources
:13:30 Judith Blake: Alliance of Genome Resources [https://buffalo.box.com/s/gu31c0z6vkgbd950tf4uft47zdd4ij6p Slides]


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


:14:30 Elissa Chesler: MGI effort to combine variant data with disease forms; Genereader resource, PRO IDs for variants
:14:30 Barry Smith: How to define 'causally upstream of'


:15:00 Break
:15:00 Break


:15:15 Peter McGarvey: Genome Annotation, ClinGen and PRO
:15:15 Peter McGarvey: Genome Annotation, ClinGen and PRO [https://buffalo.box.com/s/gu31c0z6vkgbd950tf4uft47zdd4ij6p Slides]
 
:15:45 Peter d'Eustachio : PRO and Reactome


:16:15 Alexander Diehl: PRO, the Antibody Ontology and the Cell Ontology
:15:45 Peter d'Eustachio: Reactome, PRO, GO, Phenotypes,
::*HIPC, cell populations, the Antibody Panel Ontology, Cell types vs. cell states -- when do combinations of protein markers
Complexes [https://buffalo.box.com/s/bo5yiutb082sp8qlc6egyh3o3aed6xwr Slides]


'''The Value of PRO Annotations in Enabling Interconnection of Biomedical Ontologies and Databases'''
:16:15 Alexander Diehl: Cells, Proteins, Antibodies and Diseases [https://buffalo.box.com/s/xpjpn5kilahkvtt69gp4p7f28axewitm Slides]


:17:00 *This session will include a debate between Alan Ruttenberg, Chris Mungall, David Hill and Darren Natale on the proper representation of PRO annotations
17:00 '''Discussion of the representation of PRO annotations'''
:Chair: Barry Smith
:Participants: Alan Ruttenberg and Darren Natale  


:18:00 Working dinner
:18:00 Working dinner


==Schedule: Thursday, October 12, 2017==
==Schedule: Thursday, October 12, 2017==
:8:00 Continental breakfast


'''GO, PRO and UniProt'''
'''GO, PRO and UniProt'''
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Chair: Cathy Wu
Chair: Cathy Wu


:8:45 Maria Martin (EBI): Representing UniProt
:8:45 Maria Martin: Representing UniProt


:9:30 Chris Mungall (LBL, Berkeley): Representing GO
:9:30 Chris Mungall: Representing GO


:9:45 Discussion of GO, PRO and UniProt: How they will work together
:9:45 GO, PRO and UniProt: How will they work together


:10:30 Break
:10:30 Break


:10:45 Julie Cowart: Writing SPARQL queries for PRO
:10:45 Julie Cowart: Data Access and Writing SPARQL Queries [https://buffalo.box.com/s/6u4ef8l0gjylwgsdbv5eb9ww4yhmkja2 Slides]


:11:15 Alan Ruttenberg: Enhanced SPARQL queries for PRO
: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
:11:45 Cecilia Arighi: The role of NLP in PRO curation [https://buffalo.box.com/s/ykzpfu5quyx44qr3fenoqqi45o084x3b Slides]


:12:15 Lunch
:12:15 Lunch


:13:00 '''Debate: How genes are referenced in OBO Foundry and in PRO: why do they differ?'''
13:00 '''Discussion of how genes are referenced in OBO Foundry and in PRO: why do they differ?'''
 
:Chair: Barry Smith
:with Chris Mungall, Darren Natale, Alan Ruttenberg, Chair: Barry Smith (will be moved to working dinner if space needed)
:Participants: David Hill, Chris Mungall, Darren Natale, Alan Ruttenberg.


:14:00 '''Roundtable on killer apps for PRO'''
:14:00 '''Roundtable on killer apps for PRO'''

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