Protein Ontology Workshop

Venue: Georgetown University

Date: June (17)-18-19, 2014. The meeting will start with dinner on Tuesday, June 17 and conclude at 4pm on June 19.

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Goals

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 resources, including the UniProtKB and the Protein Data Bank

Themes:

Neurological disease, immunology, cancer

Protein-based disease/phenotype representation

PRO and UniProt

Persons interested in participating should contact Barry Smith as soon as possible.

Draft Schedule

Wednesday, June 18, 2014

8:00 Continental Breakfast

9:00 Cathy Wu (Delaware/Georgetown): ​Current Status and Future Goals of the Protein Ontology

10:00 Peter d'Eustachio (NYU): PRO, Reactome and Disease Pathways

10:45 Break

11:00 Sirarat Sarntivijai (FDA): Using the Protein Ontology: The View from the Outside

12:00 Lunch

13:00 Evan Bolton (NCBI) PubChemRDF: Towards a Semantic Description of PubChem

13:40 Lynn Schriml (Baltimore): Collaboration of PRO and PubChem with the Disease Ontology

14:20 John Westbrook (PDB): PRO Represention of Proteins Observed in 3D Experimental Structure Data

15:00 Break

15:20 Alexander Diehl (Buffalo): PRO and the NIF / ImmPort Antibody Registries

16:00 Neurofibrillary Tangles and Amyloid Plaques: The Treatment of Protein Aggregates in the Protein Ontology: Discussion introduced by Alexander Cox (Buffalo)

17:30 Close

18:00 Working Dinner

Thursday, June 19th, 2014

8:00 Continental breakfast

9:00 Ioannis Xenarios (SIB): Ontologies in UniProtKB/Swiss-Prot

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

10:30 Break

10:45 Judith Blake (Jackson Lab) and Barry Smith (Buffalo): Ontologies, Databases, Knowledgebases: How Should They Interoperate?

12:30 Lunch

13:30 Jonathan Bona and Alan Ruttenberg (Buffalo): UniProt Accessions - Issues of Tracking and Stability

14:15 TBD

16:00 Close

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Participants

Cecilia Arighi (Georgetown)

Carol Bean (NCBO / Stanford)

Judith Blake (JAX)

Evan Bolton (NCBI / NIH)

Jonathan Bona (Buffalo)

Karen Christie (JAX)

Alexander Cox (Buffalo)

Peter d'Eustachio (NYU / Reactome)

Alex Diehl (Buffalo)

Harold Drabkin (JAX)

Gang Fu (NCBI / NIH)

Darren Natale (Georgetown)

Claire O'Donovan (EBI / UniProt)

Karen Ross (Delaware)

Sirarat Sarntivijai (FDA)

Selja Seppälä (Buffalo)

Lynn Schriml (Baltimore)

Barry Smith (Buffalo)

John Westbrook (PDB / Rutgers)

Cathy Wu (Delaware)

Ioannis Xenarios (Geneva / UniProt)

Please contact Barry Smith for further information.

Sponsors

The Protein Ontology Consortium

Co-Sponsors

National Center for Biomedical Ontology

National Center for Ontological Research