PRO Consortium Workshop 2017
Date: October 11-12, 2017
Venue: Jackson Lab, Bar Habor, Maine
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
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.
