'''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 [http://obofoundry.org/ontology/ro.html 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): [http://ncor.buffalo.edu/2014/PRO/Wu.pdf Current Status and Future Goals of the Protein Ontology]
9:45 Peter d'Eustachio (NYU): [http://ncor.buffalo.edu/2014/PRO/d'Eustachio.pptx PRO, Reactome and Disease Pathways]
10:30 Break
10:45 Olivier Bodenreider (NLM): [http://ncor.buffalo.edu/2014/PRO/Bodenreider.pdf Ontologies in the NLM]
11:25 Sirarat Sarntivijai (FDA): [http://ncor.buffalo.edu/2014/PRO/Sarntivijai.ppt Using the Protein Ontology: The View from the Outside]
11:55 Carol Bean (Stanford / NCBO): The Future of the [http://bioportal.bioontology.org/ Bioportal]
12:15 Lunch
Chair: Peter d'Eustachio
13:00 Sandra Orchard (EBI): [http://ncor.buffalo.edu/2014/PRO/Orchard.pptx PRO and IntAct]
14:00 Evan Bolton (NCBI): [http://ncor.buffalo.edu/2014/PRO/Bolton.pdf PubChemRDF: Towards a Semantic Description of PubChem]
14:40 Lynn Schriml (Baltimore): [http://ncor.buffalo.edu/2014/PRO/Schriml.pdf Collaboration of PRO and PubChem with the Disease Ontology]
15:20 Break
Chair: Darren Natale
15:40 Veerasamy “Ravi” Ravichandran (NIGMS): [http://ncor.buffalo.edu/2014/PRO/Ravichandran.pptx NIGMS and the Protein Ontology]
16:00 John Westbrook (PDB): [http://ncor.buffalo.edu/2014/PRO/Westbrook.pdf PRO Represention of Proteins Observed in 3D Experimental Structure Data]
16:40 Alexander Diehl (Buffalo): [http://ncor.buffalo.edu/2014/PRO/Diehl.pptx 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, [https://www.google.com/maps/place/3300+Whitehaven+St+NW/@38.917007,-77.06752,17z/data=!3m1!4b1!4m2!3m1!1s0x89b7b630848d084f:0x22bd0eb5dab5a2ff 3300 Whitehaven Street NW]
8:00 Continental breakfast
Chair: Alexander Diehl
9:00 Donna Maglott (NIH): [http://ncor.buffalo.edu/2014/PRO/Maglott.pptx PRO and Medical Genetics resources at NCBI]
9:40 Paul Martin Thomas (Northwestern): [http://ncor.buffalo.edu/2014/PRO/Thomas.pdf Descriptive and Quantitative Top Down Proteomics]
10:20 John Garavelli (Delaware): [http://ncor.buffalo.edu/2014/PRO/Garavelli.ppt Use Cases for Modified Protein Interactions (for UniProt, PRO and proteomics)]
10:30 Break
10:45 Alexander Cox (Buffalo): [http://ncor.buffalo.edu/2014/PRO/Cox.pptx Neurofibrillary Tangles and Amyloid Plaques: The Treatment of Protein Aggregates in the Protein Ontology]
11.15 Alan Ruttenberg and Jonathan Bona (Buffalo): [http://goo.gl/i1bMRo Issues surrounding coordination of UniProtKB and the Protein Ontology]
12:30 Lunch
Chair: Cecilia Arrighi
13:30 Judith Blake (Jackson Lab): [http://ncor.buffalo.edu/2014/PRO/Blake.pptx Ontologies, Databases, Knowledgebases: How Should They Interoperate?]
14:00 Barry Smith (Buffalo): [http://ncor.buffalo.edu/2014/PRO/Smith.ppt Introduction to the Relation Ontology]
14:15 Darren Natale: [http://ncor.buffalo.edu/2014/PRO/Natale.pptx Relations linking Proteins to Diseases]
14:30 Break
14:45 Gilbert S. Omenn (Michigan): [http://ncor.buffalo.edu/2014/PRO/Omenn.pptx The Human Proteome Project]
16:00 Close
----
== '''Participants''' ==
: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 ([http://www.kelleher.northwestern.edu/research/top-down-proteomics Top Down Proteomics] / Northwestern)
:John Westbrook (PDB / Rutgers)
:Cathy Wu (Delaware / PRO)
Please contact [mailto:phismith@buffalo.edu Barry Smith] for further information.
== '''Sponsors''' ==
:[http://pir.georgetown.edu/pro/ The Protein Ontology Consortium]
:[http://bioontologies.org National Center for Biomedical Ontology]
:[http://ncor.buffalo.edu National Center for Ontological Research]