PRO Consortium Workshop 2017: Difference between revisions

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:12:00 Lunch
:12:00 Lunch


:12:45 '''Debate: How genes are referenced in OBO Foundry and in PRO: why do they differ?'''
'''Debate: How genes are referenced in OBO Foundry and in PRO: why do they differ?'''


Chair: Barry Smith
:12:45 Debate, with Chris Mungall, Darren Natale, Alan Ruttenberg, Chair: Barry Smith
(will be moved to working dinner if space needed)


:Participants: Chris Mungall, Darren Natale, Alan Ruttenberg (will be moved to working dinner if space needed)
:14:00 Close of Plenary Sessions


14:00 Close of Plenary Sessions
:14:00 Working group / breakout meetings
 
:Proposed topics:
14:00 Working group meetings
::PURLs for genes
::Domains/families in PRO
::PRO in enrichment analysis/geneweaver
::Noctua


17:00 Close
17:00 Close

Revision as of 17:53, 30 September 2017

Date: October 11-12, 2017

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
  • 2. To assess progress in the use of advanced computational techniques, including Natural Language Processing, in the development of the PRO
  • 3. To examine the actual and potential contribution of PRO to the understanding of disease across organisms
  • 4. To review PRO's role in the field of immunology informatics
  • 5. To advance the treatment of protein-related clinical and translational data from the perspective of consistency, discoverability and support for diagnosis
  • 6. To evaluate competing approaches to PRO annotation

Schedule: Tuesday, October, 10, 2017

19:00 Informal reception for early arrivals in conference hotel

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
Sites, PTMs
9:30 Susan Gregurick: NIH 2018 Priorities in Data Science and Computational Science

PRO and Related Resources

9:45 Karen Ross: PRO Collaborations (ProKinO, NeXtProt ...)
10:15 Erich Baker and Elissa Chesler: GeneWeaver
10:45 Break
11:00 Cindy Smith: The Alliance of Genome Resources
11:30 Kimberley VanAuken: Noctua
12:00 Cecilia Arighi: The role of NLP in PRO curation
12:30 Lunch

PRO and Disease

Chair: Darren Natale

13:30 Judith Blake: Disease Ontology -- overview of available resources
14:00 Chris Mungall: MONARCH
14:30 Elissa Chesler: MGI effort to combine variant data with disease forms; Genereader resource, PRO IDs for variants
15:00 Break
15:15 Peter McGarvey: Genome Annotation, ClinGen and PRO
15:45 Peter d'Eustachio : PRO and Reactome
16:15 Alexander Diehl: PRO, the Antibody Ontology and the Cell Ontology
  • HIPC, cell populations, the Antibody Panel Ontology, Cell types vs. cell states -- when do combinations of protein markers

The Value of PRO Annotations in Enabling Interconnection of Biomedical Ontologies and Databases

17:00 *This session will include a debate between Alan Ruttenberg, Chris Mungall, David Hill and Darren Natale on the proper representation of PRO annotations
18:00 Working dinner

Schedule: Thursday, October 12, 2017

8:00 Continental breakfast

GO, PRO and UniProt

Chair: Cathy Wu

8:45 Alex Bateman (EBI)
9:15 Maria Martin (EBI) TBD
9:45 Discussion of GO, PRO and UniProt: How they should work together
10:30 Break
11:00 Julie Cowart: Writing SPARQL queries for PRO
11:30 Alan Ruttenberg: Enhanced SPARQL queries for PRO
12:00 Lunch

Debate: How genes are referenced in OBO Foundry and in PRO: why do they differ?

12:45 Debate, with Chris Mungall, Darren Natale, Alan Ruttenberg, Chair: Barry Smith

(will be moved to working dinner if space needed)

14:00 Close of Plenary Sessions
14:00 Working group / breakout meetings
Proposed topics:
PURLs for genes
Domains/families in PRO
PRO in enrichment analysis/geneweaver
Noctua

17:00 Close


Participants

*=online
Cecilia Arighi (Delaware / PRO)*
Erich Baker (Baylor)
Alex Bateman (EBI)*
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