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

[[PRO Consortium Workshop 2019]]

'''Venue''': [https://barharbormainehotel.com/ 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==

[https://buffalo.box.com/s/i1saod7olqdxc3c5n4vgikbpwxmk7qx7 PRO Family Relations]

[https://buffalo.box.com/s/hx6wd7eeyg6iw6q1kn7h956zyzpqs62w 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 [https://buffalo.box.com/s/ahra2it1glmtsqm2e96yhgsp20u9jou3 Slides]

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

'''PRO and Related Resources'''

:9:45 Darren Natale: Implementation of the  PRO Sites Ontology [https://buffalo.box.com/s/2an2i0wcfn7r3m5dld2q6tilr03oy0gg Slides]

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

:10:45 Break

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

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

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

:12:30 Lunch

'''PRO and Disease'''

Chair: Darren Natale

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

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

:14:30 Barry Smith: How to define 'causally upstream of'

:15:00 Break

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

:15:45 Peter d'Eustachio: Reactome, PRO, GO, Phenotypes,
Complexes [https://buffalo.box.com/s/bo5yiutb082sp8qlc6egyh3o3aed6xwr Slides]

:16:15 Alexander Diehl: Cells, Proteins, Antibodies and Diseases [https://buffalo.box.com/s/xpjpn5kilahkvtt69gp4p7f28axewitm 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 [https://buffalo.box.com/s/6u4ef8l0gjylwgsdbv5eb9ww4yhmkja2 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 [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 '''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 [mailto:phismith@buffalo.edu Barry Smith] for further information.

== '''Sponsors''' ==
 
:[http://pir.georgetown.edu/pro/ The Protein Ontology Consortium]
:[http://ncor.buffalo.edu National Center for Ontological Research]