Protein Ontology Workshop

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Date: June (17)-18-19, 2014. The meeting will begin with an informal reception in the Holiday Inn, Georgetown, on Tuesday, June 17 and conclude at 4pm on June 19.

Venue: Georgetown University's Harris Building is about 3 miles from Union Station, and 1.5 miles from the Woodley Park subway station. The Circulator Bus Line has pickups at the Union Station and Woodley Park, and the Holiday Inn Georgetown is on the route. The cost is just $1. The Holiday Inn is 1/2 a block from Georgetown University's Harris Building.


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

Schedule: Wednesday, June 18, 2014

Venue: Conference Room #1300, Harris Building, Georgetown University, 3300 Whitehaven Street NW

8:00 Continental Breakfast

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

12:00 Lunch

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

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

17:05 Alexander Cox (Buffalo): Neurofibrillary Tangles and Amyloid Plaques: The Treatment of Protein Aggregates in the Protein Ontology

17:30 Close

18:00 Working Dinner

Schedule: Thursday, June 19th, 2014

Venue: Conference Room #1300, Harris Building, Georgetown University, 3300 Whitehaven Street NW

8:00 Continental breakfast

9:00 Donna Maglott (NIH): PRO and Medical Genetics resources at NCBI

9:45 Claire Donovan (EBI): Ontologies at the EBI

10:30 Break

10:45 Paul Martin Thomas (Northwestern): Descriptive and Quantitative Top Down Proteomics

11:30 Jonathan Bona and Alan Ruttenberg (Buffalo): UniProt Accessions - Issues of Tracking and Stability

12:30 Lunch

13:30 Judith Blake (Jackson Lab) and Barry Smith (Buffalo):

  • 1. Ontologies, Databases, Knowledgebases: How Should They Interoperate?
  • 2. Relations linking Proteins to Diseases

14:30 Break

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

16:00 Close


Participants

Cecilia Arighi (Georgetown)
Carol Bean (NCBO / Stanford)
Judith Blake (JAX)
Olivier Bodenreider (NIH / NLM / LHC)
Evan Bolton (NIH / NCBI)
Jonathan Bona (Buffalo)
Karen Christie (JAX)
Alexander Cox (Buffalo)
Peter d'Eustachio (NYU / Reactome)
Alex Diehl (Buffalo)
Harold Drabkin (JAX)
Gang Fu (NCBI / NIH)
John S. Garavelli (Delaware)
Donna Maglott (NIH / NLM / NCBI)
John Mattison (Global Alliance for Genomics and Health)
Darren Natale (Georgetown)
Claire O'Donovan (EBI / UniProt)
Gilbert S. Omenn (Michigan)
Sandra Orchard (EBI / IntAct)
Veerasamy “Ravi” Ravichandran (NIH / NIGMS)
Karen Ross (Delaware)
Alan Ruttenberg (Buffalo)
Sirarat Sarntivijai (FDA)
Selja Seppälä (Buffalo)
Lynn Schriml (Baltimore)
Barry Smith (Buffalo)
Paul Martin Thomas (Top Down Proteomics / Northwestern)
John Westbrook (PDB / Rutgers)
Cathy Wu (Delaware)

Please contact Barry Smith for further information.

Sponsors

The Protein Ontology Consortium
National Center for Biomedical Ontology
National Center for Ontological Research