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 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

• Relating to PRO's interactions with external resources:

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

IntAct: Identify points of agreement and discrepancy in curation pipelines and resolve as appropriate. Reach agreements for example on reciprocal links and accession issues

Relations between GO, UniProt, PRO The future development of PRO and of PRO’s role in the Alliance of Genome Resources Use of Noctua for GO annotation, use of PRO in Noctua 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

Chair: Barry Smith

8:45 Cathy Wu (Delaware/Georgetown): ​Current Status and Future Goals of the Protein Ontology

9:45 Peter d'Eustachio (NYU): PRO, Reactome and Disease Pathways

10:30 Break

10:45 Olivier Bodenreider (NLM): Ontologies in the NLM

11:25 Sirarat Sarntivijai (FDA): Using the Protein Ontology: The View from the Outside

11:55 Carol Bean (Stanford / NCBO): The Future of the Bioportal

12:15 Lunch

Chair: Peter d'Eustachio

13:00 Sandra Orchard (EBI): PRO and IntAct

14:00 Evan Bolton (NCBI): PubChemRDF: Towards a Semantic Description of PubChem

14:40 Lynn Schriml (Baltimore): Collaboration of PRO and PubChem with the Disease Ontology

15:20 Break

Chair: Darren Natale

15:40 Veerasamy “Ravi” Ravichandran (NIGMS): NIGMS and the Protein Ontology

16:00 John Westbrook (PDB): PRO Represention of Proteins Observed in 3D Experimental Structure Data

16:40 Alexander Diehl (Buffalo): PRO and the NIF / ImmPort Antibody Registries

17:20 Close

18:00 Working Dinner: Cafe Divan, 1834 Wisconsin Ave

Schedule: Thursday, October 12, 2017

Venue: JAX

8:00 Continental breakfast

Chair: TBD PRO and UniProt

9:00 Alex Bateman (EBI)

10:30 Break

10:45

12:30 Lunch

Chair: Cecilia Arrighi

13:30 Judith Blake (Jackson Lab): Ontologies, Databases, Knowledgebases: How Should They Interoperate?

14:00 Barry Smith (Buffalo): Introduction to the Relation Ontology

14:15 Darren Natale: Relations linking Proteins to Diseases

14:30 Break

14:45 Gilbert S. Omenn (Michigan): The Human Proteome Project

16:00 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)

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