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 -- 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
Chair: TBD The future of the PRO
Sites PTMs
8:45 Cathy Wu: Protein Ontology: Its current state and future development
TBD: ProKinO: Protein Kinase Ontology Browser
TBD: NeXtProt
Pamela VanAuken: Noctua
Cindy Smith: The Alliance of Genome Resources
10:30 Break
10:45 PRO and software / NLP / SPARQL
ChuMing: Writing SPARQL queries for PRO
PRO and its relations to the experimental community
Chair: Alan Ruttenberg
12:30 Lunch
13:30
PRO and Disease
Chair: Barry Smith
Judith Blake (MGI): Disease Ontology -- overview of available resources
Elissa Chesler (MGI): 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
16:00 Close
Schedule: Thursday, October 12, 2017
Venue: JAX
8:00 Continental breakfast
GO, PRO and UniProt: How they should work together
Chair: TBD
9:00 Alex Bateman (EBI)
10:30 Break
10:45
12:00 Lunch
12:45 PRO and OBO Foundry
Chair: TBD
Scope of PRO
Treatment of protein complexes
Alan Ruttenberg: How genes are referenced in OBO Foundry? in PRO?
Participants: Chris Mungall, Darren Natale
Proper treatment of functions in PRO
14:00 Close of Plenary Sessions
14:00 Working group meetings
17:00 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.
