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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
 
*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
 
Relations between GO, UniProt, PRO
The future development of PRO and of PRO’s role in the Alliance of Genome Resources
Use of Noctua for GO annotation, use of PRO in Noctua
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]


[https://buffalo.box.com/s/hx6wd7eeyg6iw6q1kn7h956zyzpqs62w Functional Annotation of Proteins]


=='''Schedule: Tuesday, October, 10, 2017==
==Schedule: Wednesday, October, 11, 2017==


19:00 Informal reception for early arrivals in conference hotel
'''Introductory Session: The Landscape of the Protein Ontology'''


=='''Schedule: Wednesday, October, 11, 2017==
:8:45 Cathy Wu: Protein Ontology: Its current state and future development [https://buffalo.box.com/s/ahra2it1glmtsqm2e96yhgsp20u9jou3 Slides]


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


8:45 Cathy Wu (Delaware/Georgetown): [http://ncor.buffalo.edu/2014/PRO/Wu.pdf ​Current Status and Future Goals of the Protein Ontology]
'''PRO and Related Resources'''


9:45 Peter d'Eustachio (NYU): [http://ncor.buffalo.edu/2014/PRO/d'Eustachio.pptx PRO, Reactome and Disease Pathways]
:9:45 Darren Natale: Implementation of the  PRO Sites Ontology [https://buffalo.box.com/s/2an2i0wcfn7r3m5dld2q6tilr03oy0gg Slides]


10:30 Break
:10:25 Karen Ross: PRO Collaborations (ProKinO, NeXtProt ...) [https://buffalo.box.com/s/zpicxbl4qj4b5y1o69bq3te8gkd8bakq Slides]


10:45 Olivier Bodenreider (NLM): [http://ncor.buffalo.edu/2014/PRO/Bodenreider.pdf Ontologies in the NLM]
:10:45 Break


11:25 Sirarat Sarntivijai (FDA): [http://ncor.buffalo.edu/2014/PRO/Sarntivijai.ppt Using the Protein Ontology: The View from the Outside]
:11:00 Erich Baker and Elissa Chesler: GeneWeaver [https://buffalo.box.com/s/lglbejd3men722onm6m5xs1a5nsxmar4 Slides]


11:55 Carol Bean (Stanford / NCBO): The Future of the [http://bioportal.bioontology.org/ Bioportal]
:11:30 Cindy Smith: Disease Ontology at MGI [https://buffalo.box.com/s/mc67ue7h306aimgdipf0l16yok4t2u5h Slides]


12:15 Lunch
:12:00 Kimberley VanAuken: Noctua and GO-CAM
[https://buffalo.box.com/s/c855q50pges44czj6v6hro7rf2c8r6u1 Slides]


<u>Chair: Peter d'Eustachio</u>
:12:30 Lunch


13:00 Sandra Orchard (EBI): [http://ncor.buffalo.edu/2014/PRO/Orchard.pptx PRO and IntAct]
'''PRO and Disease'''


14:00 Evan Bolton (NCBI): [http://ncor.buffalo.edu/2014/PRO/Bolton.pdf PubChemRDF: Towards a Semantic Description of PubChem]
Chair: Darren Natale


14:40 Lynn Schriml (Baltimore): [http://ncor.buffalo.edu/2014/PRO/Schriml.pdf Collaboration of PRO and PubChem with the Disease Ontology]
:13:30 Judith Blake: Alliance of Genome Resources [https://buffalo.box.com/s/gu31c0z6vkgbd950tf4uft47zdd4ij6p Slides]


15:20 Break
:14:00 Chris Mungall: An Update on OBO / MONARCH [https://buffalo.box.com/s/uppgc4r87jn80xcpn4etiu2th19wfyax Slides]


<u>Chair: Darren Natale</u>
:14:30 Barry Smith: How to define 'causally upstream of'


15:40 Veerasamy “Ravi” Ravichandran (NIGMS): [http://ncor.buffalo.edu/2014/PRO/Ravichandran.pptx NIGMS and the Protein Ontology]
:15:00 Break


16:00 John Westbrook (PDB): [http://ncor.buffalo.edu/2014/PRO/Westbrook.pdf PRO Represention of Proteins Observed in 3D Experimental Structure Data]  
:15:15 Peter McGarvey: Genome Annotation, ClinGen and PRO [https://buffalo.box.com/s/gu31c0z6vkgbd950tf4uft47zdd4ij6p Slides]


16:40 Alexander Diehl (Buffalo): [http://ncor.buffalo.edu/2014/PRO/Diehl.pptx PRO and the NIF / ImmPort Antibody Registries]
:15:45 Peter d'Eustachio: Reactome, PRO, GO, Phenotypes,
Complexes [https://buffalo.box.com/s/bo5yiutb082sp8qlc6egyh3o3aed6xwr Slides]


17:20 Close
:16:15 Alexander Diehl: Cells, Proteins, Antibodies and Diseases [https://buffalo.box.com/s/xpjpn5kilahkvtt69gp4p7f28axewitm Slides]


18:00 Working Dinner: Cafe Divan, 1834 Wisconsin Ave
17:00 '''Discussion of the representation of PRO annotations'''
:Chair: Barry Smith
:Participants: Alan Ruttenberg and Darren Natale


=='''Schedule: Thursday, October 12, 2017'''==
:18:00 Working dinner


Venue: JAX
==Schedule: Thursday, October 12, 2017==


8:00 Continental breakfast
'''GO, PRO and UniProt'''


<u>Chair: TBD</u> '''PRO and UniProt'''
Chair: Cathy Wu


9:00 Alex Bateman (EBI)
:8:45 Maria Martin: Representing UniProt


10:30 Break
:9:30 Chris Mungall: Representing GO


10:45  
:9:45 GO, PRO and UniProt: How will they work together


12:30 Lunch
:10:30 Break


<u>Chair: Cecilia Arrighi</u>
:10:45 Julie Cowart: Data Access and Writing SPARQL Queries [https://buffalo.box.com/s/6u4ef8l0gjylwgsdbv5eb9ww4yhmkja2 Slides]


13:30 Judith Blake (Jackson Lab): [http://ncor.buffalo.edu/2014/PRO/Blake.pptx Ontologies, Databases, Knowledgebases: How Should They Interoperate?]
:11:15 Alan Ruttenberg: Discussion of how genes are referenced in OBO Foundry and in PRO: why do they differ?


14:00 Barry Smith (Buffalo): [http://ncor.buffalo.edu/2014/PRO/Smith.ppt Introduction to the Relation Ontology]
:11:45 Cecilia Arighi: The role of NLP in PRO curation [https://buffalo.box.com/s/ykzpfu5quyx44qr3fenoqqi45o084x3b Slides]


14:15 Darren Natale: [http://ncor.buffalo.edu/2014/PRO/Natale.pptx Relations linking Proteins to Diseases]
:12:15 Lunch


14:30 Break
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.


14:45 Gilbert S. Omenn (Michigan): [http://ncor.buffalo.edu/2014/PRO/Omenn.pptx The Human Proteome Project]
:14:00 '''Roundtable on killer apps for PRO'''


16:00 Close
:16:00 Close


----
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Line 112: Line 104:
== '''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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