PRO Consortium Workshop 2017

Date: October 11-12, 2017

Venue: Jackson Lab, Bar Habor, Maine

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Goals and outcomes

The goals of this meeting are:

• 1. To review the current state of the Protein Ontology and its relation to

contribute to the ontological understanding of phenotype and disease across organisms

• 2. To advance the treatment of protein-related clinical and translational data from the perspective of consistency, discoverability and support for diagnosis
• 3. To advance coordination between the Protein Ontology and other protein-related information resources

Desired outcomes are of two sorts:

• Relating to disease:

We will seek greater clarity as to

- how proteomic information in general and the PRO in particular can help us to understand the relationship between genotype and phenotype, for example in understanding disease etiology

- which relations we should use in linking the protein entities represented in the PRO to disease entities

- which are the important entities on the protein side that need to be linked -- focus on PTMs, sites

• Relating to PRO's interactions with external resources:

UniProt: Draft of policies/recommendations regarding accession/site tracking for UniProt and PRO

Benefits and limitations of PRO

PRO and PTM knowledge networks

Developing PROs scope for annotating diseases

Schedule: Tuesday, October, 10, 2017

19:00 Informal reception for early arrivals in conference hotel

Schedule: Wednesday, October, 11, 2017

8:45 Introductory Session: The Landscape of the Protein Ontology

Cathy Wu: Protein Ontology: Its current state and future development

Sites, PTMs

TBD: ProKinO: Protein Kinase Ontology Browser (action item)

TBD: NeXtProt

Pamela VanAuken: Noctua

Cindy Smith: The Alliance of Genome Resources

10:30 Break

10:45 PRO and SPARQL / PRO and NLP

Chair: TBD

Chuming Chen: Writing SPARQL queries for PRO

Alan Ruttenberg: Enhanced SPARQL queries for PRO

Cecilia Arighi: The role of NLP in PRO curation

12:30 Lunch

13:30 PRO and Disease

Chair: Barry Smith

Judith Blake: Disease Ontology -- overview of available resources

Chris Mungall: MONARCH

Elissa Chesler: MGI effort to combine variant data with disease forms; Genereader resource, PRO IDs for variants

Barry Smith: Protein-Disease Relations

Other large-scale frameworks working with protein variants

14:30 Break

14:45 PRO and Immunology

Chair: Darren Natale

Alex Diehl: PRO and the Antibody Ontology

Alex Diehl: PRO the Cell Ontology

HIPC, cell populations, the Antibody Panel Ontology, Cell types vs. cell states -- when do combinations of protein markers

16:00 Close

Schedule: Thursday, October 12, 2017

Venue: JAX

8:00 Continental breakfast

9:00 GO, PRO and UniProt: How they should work together

Chair: Cathy Wu

Alex Bateman (EBI)

10:30 Break

10:45 Alan Ruttenberg: Proposal regarding representation of PRO annotations

Responses by Chris Mungall, David Hill, Darren Natale

12:00 Lunch

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

Chair: TBD

Participants: Chris Mungall, Darren Natale, Alan Ruttenberg (could be moved to working dinner if space needed)

14:00 Close of Plenary Sessions

14:00 Working group meetings

17:00 Close

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Participants

Cecilia Arighi (Delaware / PRO)

Erich Baker (Baylor))

Alex Bateman (EBI)

Judith Blake (JAX)

Elissa Chesler (JAX)

? Karen Christie (JAX)

Alex Diehl (Buffalo)

Harold Drabkin (JAX)

? Gang Fu (NCBI / NIH)

? John S. Garavelli (Delaware)

? Donna Maglott (NIH / NLM / NCBI)

? Chris Mungall (LBNL)

Darren Natale (Georgetown)

? Veerasamy “Ravi” Ravichandran (NIH / NIGMS)

? 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