PRO Consortium Workshop 2019: Difference between revisions

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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]
:9:00 C
 
: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
:18:00 Working dinner


Line 74: Line 31:
Chair: Cathy Wu
Chair: Cathy Wu


:8:45 Maria Martin: Representing UniProt
:8:45  
 
: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
:15:00 Close


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Revision as of 16:38, 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