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


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


=='''Schedule: Wednesday, October, 11, 2017==
[https://buffalo.box.com/s/hx6wd7eeyg6iw6q1kn7h956zyzpqs62w Functional Annotation of Proteins]


<u>Chair: Barry Smith</u>
==Schedule: Wednesday, October, 11, 2017==


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


9:45 Peter d'Eustachio (NYU): [http://ncor.buffalo.edu/2014/PRO/d'Eustachio.pptx PRO, Reactome and Disease Pathways]
:8:45 Cathy Wu: Protein Ontology: Its current state and future development [https://buffalo.box.com/s/ahra2it1glmtsqm2e96yhgsp20u9jou3 Slides]


10:30 Break
:9:30 Susan Gregurick: NIH 2018 Priorities in Data Science and Computational Science [https://buffalo.box.com/s/8002lr7syg8gf2blt6hyjg7q69ka63b7 Slides]


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


11:25 Sirarat Sarntivijai (FDA): [http://ncor.buffalo.edu/2014/PRO/Sarntivijai.ppt Using the Protein Ontology: The View from the Outside]
:9:45 Darren Natale: Implementation of the  PRO Sites Ontology [https://buffalo.box.com/s/2an2i0wcfn7r3m5dld2q6tilr03oy0gg Slides]


11:55 Carol Bean (Stanford / NCBO): The Future of the [http://bioportal.bioontology.org/ Bioportal]
:10:25 Karen Ross: PRO Collaborations (ProKinO, NeXtProt ...) [https://buffalo.box.com/s/zpicxbl4qj4b5y1o69bq3te8gkd8bakq Slides]


12:15 Lunch
:10:45 Break


<u>Chair: Peter d'Eustachio</u>
:11:00 Erich Baker and Elissa Chesler: GeneWeaver [https://buffalo.box.com/s/lglbejd3men722onm6m5xs1a5nsxmar4 Slides]


13:00 Sandra Orchard (EBI): [http://ncor.buffalo.edu/2014/PRO/Orchard.pptx PRO and IntAct]
:11:30 Cindy Smith: Disease Ontology at MGI [https://buffalo.box.com/s/mc67ue7h306aimgdipf0l16yok4t2u5h Slides]


14:00 Evan Bolton (NCBI): [http://ncor.buffalo.edu/2014/PRO/Bolton.pdf PubChemRDF: Towards a Semantic Description of PubChem]
:12:00 Kimberley VanAuken: Noctua and GO-CAM
[https://buffalo.box.com/s/c855q50pges44czj6v6hro7rf2c8r6u1 Slides]


14:40 Lynn Schriml (Baltimore): [http://ncor.buffalo.edu/2014/PRO/Schriml.pdf Collaboration of PRO and PubChem with the Disease Ontology]
:12:30 Lunch


15:20 Break
'''PRO and Disease'''


<u>Chair: Darren Natale</u>
Chair: Darren Natale


15:40 Veerasamy “Ravi” Ravichandran (NIGMS): [http://ncor.buffalo.edu/2014/PRO/Ravichandran.pptx NIGMS and the Protein Ontology]
:13:30 Judith Blake: Alliance of Genome Resources [https://buffalo.box.com/s/gu31c0z6vkgbd950tf4uft47zdd4ij6p Slides]


16:00 John Westbrook (PDB): [http://ncor.buffalo.edu/2014/PRO/Westbrook.pdf PRO Represention of Proteins Observed in 3D Experimental Structure Data]  
:14:00 Chris Mungall: An Update on OBO / MONARCH [https://buffalo.box.com/s/uppgc4r87jn80xcpn4etiu2th19wfyax Slides]


16:40 Alexander Diehl (Buffalo): [http://ncor.buffalo.edu/2014/PRO/Diehl.pptx PRO and the NIF / ImmPort Antibody Registries]
:14:30 Barry Smith: How to define 'causally upstream of'


17:20 Close
:15:00 Break


18:00 Working Dinner: Cafe Divan, 1834 Wisconsin Ave
:15:15 Peter McGarvey: Genome Annotation, ClinGen and PRO [https://buffalo.box.com/s/gu31c0z6vkgbd950tf4uft47zdd4ij6p Slides]


=='''Schedule: Thursday, October 12, 2017'''==
:15:45 Peter d'Eustachio: Reactome, PRO, GO, Phenotypes,
Complexes [https://buffalo.box.com/s/bo5yiutb082sp8qlc6egyh3o3aed6xwr 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]
:16:15 Alexander Diehl: Cells, Proteins, Antibodies and Diseases [https://buffalo.box.com/s/xpjpn5kilahkvtt69gp4p7f28axewitm Slides]


8:00 Continental breakfast
17:00 '''Discussion of the representation of PRO annotations'''
:Chair: Barry Smith
:Participants: Alan Ruttenberg and Darren Natale


<u>Chair: Alexander Diehl</u>
:18:00 Working dinner


9:00 Donna Maglott (NIH): [http://ncor.buffalo.edu/2014/PRO/Maglott.pptx PRO and Medical Genetics resources at NCBI]
==Schedule: Thursday, October 12, 2017==


9:40 Paul Martin Thomas (Northwestern): [http://ncor.buffalo.edu/2014/PRO/Thomas.pdf Descriptive and Quantitative Top Down Proteomics]
'''GO, PRO and UniProt'''


10:20 John Garavelli (Delaware): [http://ncor.buffalo.edu/2014/PRO/Garavelli.ppt Use Cases for Modified Protein Interactions (for UniProt, PRO and proteomics)]
Chair: Cathy Wu


10:30 Break
:8:45 Maria Martin: Representing UniProt


10:45 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]
:9:30 Chris Mungall: Representing GO


11.15 Alan Ruttenberg and Jonathan Bona (Buffalo): [http://goo.gl/i1bMRo Issues surrounding coordination of UniProtKB and the Protein Ontology]
: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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== '''Participants''' ==
== '''Participants''' ==


:Cecilia Arighi (Delaware / PRO)
*=online
:Alex Bateman (EBI)
:Cecilia Arighi (Delaware / PRO)*
:Erich Baker (Baylor)
:Judith Blake (JAX)
:Judith Blake (JAX)
:? Karen Christie (JAX)
:Chuming Chen (Delaware)*
:Alex Diehl (Buffalo)
:Elissa Chesler (JAX)
:Julie Cowart (Delaware)*
: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)
:Barry Smith (Buffalo)  
:Barry Smith (Buffalo)  
:Kimberley VanAuken (CalTech)
:Kimberley VanAuken (CalTech)
:Laurens Wilming (JAX)
:Cathy Wu (Delaware / PRO)
:Cathy Wu (Delaware / 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
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