PRO Consortium Workshop 2017

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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 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: Tuesday, October, 10, 2017

~19:00 Informal reception for early arrivals in conference hotel. Details will follow by email.

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

PRO and Related Resources

9:45 Darren Natale: Implementation of the PRO Sites Ontology
10:25 Karen Ross: PRO Collaborations (ProKinO, NeXtProt ...)
10:45 Break
11:00 Erich Baker and Elissa Chesler: GeneWeaver
11:30 Cindy Smith: The Alliance of Genome Resources
12:00 Kimberley VanAuken: Noctua
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

17:00 Debate: On the proper representation of PRO annotations

Chair: Barry Smith
Participants: Alan Ruttenberg, Chris Mungall, David Hill and Darren Natale
18:00 Working dinner

Schedule: Thursday, October 12, 2017

8:00 Continental breakfast

GO, PRO and UniProt

Chair: Cathy Wu

8:45 Maria Martin (EBI): Representing UniProt
9:30 Chris Mungall (LBL, Berkeley): Representing GO
9:45 Discussion of GO, PRO and UniProt: How they will work together
10:30 Break
10:45 Julie Cowart: Writing SPARQL queries for PRO
11:15 Alan Ruttenberg: Enhanced SPARQL queries for PRO
11:45 Cecilia Arighi: The role of NLP in PRO curation
12:15 Lunch

13:00 Debate: How genes are referenced in OBO Foundry and in PRO: why do they differ?

Chair: Barry Smith
Participants; 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