Protein Ontology Workshop

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Date: June 18-19, 2014

Venue: Georgetown University

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

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, June 19th, 2014

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

8:00 Continental breakfast

Chair: Alexander Diehl

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

9:40 Paul Martin Thomas (Northwestern): Descriptive and Quantitative Top Down Proteomics

10:20 John Garavelli (Delaware): Use Cases for Modified Protein Interactions (for UniProt, PRO and proteomics)

10:30 Break

10:45 Alexander Cox (Buffalo): Neurofibrillary Tangles and Amyloid Plaques: The Treatment of Protein Aggregates in the Protein Ontology

11.15 Alan Ruttenberg and Jonathan Bona (Buffalo): Issues surrounding coordination of UniProtKB and the Protein Ontology

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


Cecilia Arighi (Delaware / PRO)
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 / PRO)

Please contact Barry Smith for further information.


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