Difference between revisions of "PRO Consortium Workshop 2019"

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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 [https://buffalo.box.com/s/ahra2it1glmtsqm2e96yhgsp20u9jou3 Slides]
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:9:00 C
 
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:9:30 Susan Gregurick: NIH 2018 Priorities in Data Science and Computational Science [https://buffalo.box.com/s/8002lr7syg8gf2blt6hyjg7q69ka63b7 Slides]
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'''PRO and Related Resources'''
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:9:45 Darren Natale: Implementation of the  PRO Sites Ontology [https://buffalo.box.com/s/2an2i0wcfn7r3m5dld2q6tilr03oy0gg Slides]
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:10:25 Karen Ross: PRO Collaborations (ProKinO, NeXtProt ...) [https://buffalo.box.com/s/zpicxbl4qj4b5y1o69bq3te8gkd8bakq Slides]
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:10:45 Break
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:11:00 Erich Baker and Elissa Chesler: GeneWeaver [https://buffalo.box.com/s/lglbejd3men722onm6m5xs1a5nsxmar4 Slides]
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:11:30 Cindy Smith: Disease Ontology at MGI [https://buffalo.box.com/s/mc67ue7h306aimgdipf0l16yok4t2u5h Slides]
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:12:00 Kimberley VanAuken: Noctua and GO-CAM
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[https://buffalo.box.com/s/c855q50pges44czj6v6hro7rf2c8r6u1 Slides]
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:12:30 Lunch
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'''PRO and Disease'''
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Chair: Darren Natale
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:13:30 Judith Blake: Alliance of Genome Resources [https://buffalo.box.com/s/gu31c0z6vkgbd950tf4uft47zdd4ij6p Slides]
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:14:00 Chris Mungall: An Update on OBO / MONARCH [https://buffalo.box.com/s/uppgc4r87jn80xcpn4etiu2th19wfyax Slides]
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:14:30 Barry Smith: How to define 'causally upstream of'
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:15:00 Break
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:15:15 Peter McGarvey: Genome Annotation, ClinGen and PRO [https://buffalo.box.com/s/gu31c0z6vkgbd950tf4uft47zdd4ij6p Slides]
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:15:45 Peter d'Eustachio: Reactome, PRO, GO, Phenotypes,
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Complexes [https://buffalo.box.com/s/bo5yiutb082sp8qlc6egyh3o3aed6xwr Slides]
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:16:15 Alexander Diehl: Cells, Proteins, Antibodies and Diseases [https://buffalo.box.com/s/xpjpn5kilahkvtt69gp4p7f28axewitm Slides]
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17:00 '''Discussion of the representation of PRO annotations'''
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:Chair: Barry Smith
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:Participants: Alan Ruttenberg and Darren Natale
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:18:00 Working dinner
 
:18:00 Working dinner
  
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Chair: Cathy Wu
 
Chair: Cathy Wu
  
:8:45 Maria Martin: Representing UniProt
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:8:45  
 
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:9:30 Chris Mungall: Representing GO
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:9:45 GO, PRO and UniProt: How will they work together
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:10:30 Break
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:10:45 Julie Cowart: Data Access and Writing SPARQL Queries [https://buffalo.box.com/s/6u4ef8l0gjylwgsdbv5eb9ww4yhmkja2 Slides]
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:11:15 Alan Ruttenberg: Discussion of how genes are referenced in OBO Foundry and in PRO: why do they differ?
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:11:45 Cecilia Arighi: The role of NLP in PRO curation [https://buffalo.box.com/s/ykzpfu5quyx44qr3fenoqqi45o084x3b Slides]
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:12:15 Lunch
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13:00 '''Discussion of how genes are referenced in OBO Foundry and in PRO: why do they differ?'''
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:Chair: Barry Smith
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:Participants: David Hill, Chris Mungall, Darren Natale, Alan Ruttenberg.
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:14:00 '''Roundtable on killer apps for PRO'''
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:16:00 Close
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:15:00 Close
  
 
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Revision as of 12:38, 14 June 2019

Date: October 23-24, 2019

Venue:

Protein Informatics Resource
Georgetown University Medical Center
3300 Whitehaven Street, NW, Suite 1200
Washington, DC 20007, USA


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.


Schedule: Wednesday, October 23, 2019

Introductory Session: The Landscape of the Protein Ontology

9:00 C
18:00 Working dinner

Schedule: Thursday, October 24, 2019

GO, PRO and UniProt

Chair: Cathy Wu

8:45
15:00 Close

Participants

Alexander Bateman (EBI)*
Alexander Diehl (Buffalo)
Cecilia Arighi (Delaware / PRO)
Judith Blake (JAX)
Peter d'Eustachio (NYU)*
Alexander Diehl (Buffalo)
? Harold Drabkin (JAX)
Michelle Giglio (Baltimore)
Yongqun (Oliver) He (Michigan)
? Neil Kelleher
Birgit Meldal (EBI)*
Darren Natale (Georgetown)
Li Ni (JAX)
Bjoern Peters (San Diego)
? Karen Ross (Delaware)
Alan Ruttenberg (Buffalo)
?Stephan Schürer (Miami)
Barry Smith (Buffalo)
Cathy Wu (Delaware / PRO)
  • =online


Please contact Barry Smith for further information.

Sponsors

The Protein Ontology Consortium
National Center for Ontological Research