PRO Consortium Workshop 2017: Difference between revisions
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'''Date''': | '''Date''': October 11-12, 2017 | ||
'''Venue''': Jackson Lab, Bar Habor, Maine | |||
'''Venue''': | |||
---- | ---- | ||
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:'''IntAct''': Identify points of agreement and discrepancy in curation pipelines and resolve as appropriate. Reach agreements for example on reciprocal links and accession issues | :'''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, | =='''Schedule: Tuesday, October, 10, 2017== | ||
19:00 Informal reception for early arrivals in conference hotel | |||
=='''Schedule: Wednesday, October, 11, 2017== | |||
<u>Chair: Barry Smith</u> | <u>Chair: Barry Smith</u> | ||
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18:00 Working Dinner: Cafe Divan, 1834 Wisconsin Ave | 18:00 Working Dinner: Cafe Divan, 1834 Wisconsin Ave | ||
=='''Schedule: Thursday, | =='''Schedule: Thursday, October 12, 2017'''== | ||
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] | 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] | ||
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:Cecilia Arighi (Delaware / PRO) | :Cecilia Arighi (Delaware / PRO) | ||
: | :Alex Bateman (EBI) | ||
:Judith Blake (JAX) | :Judith Blake (JAX) | ||
: | :? Karen Christie (JAX) | ||
:Alex Diehl (Buffalo) | :Alex Diehl (Buffalo) | ||
:Harold Drabkin (JAX) | :Harold Drabkin (JAX) | ||
:Gang Fu (NCBI / NIH) | :? Gang Fu (NCBI / NIH) | ||
:John S. Garavelli (Delaware) | :? John S. Garavelli (Delaware) | ||
:Donna Maglott (NIH / NLM / NCBI | :? Donna Maglott (NIH / NLM / NCBI) | ||
:Darren Natale (Georgetown) | :Darren Natale (Georgetown) | ||
: | :? Veerasamy “Ravi” Ravichandran (NIH / NIGMS) | ||
:? Karen Ross (Delaware) | |||
:Karen Ross (Delaware) | |||
:Alan Ruttenberg (Buffalo) | :Alan Ruttenberg (Buffalo) | ||
:Barry Smith (Buffalo) | :Barry Smith (Buffalo) | ||
: | :Kimberley VanAuken (CalState) | ||
:Cathy Wu (Delaware / PRO) | :Cathy Wu (Delaware / PRO) | ||
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:[http://pir.georgetown.edu/pro/ The Protein Ontology Consortium] | :[http://pir.georgetown.edu/pro/ The Protein Ontology Consortium] | ||
:[http://ncor.buffalo.edu National Center for Ontological Research] | :[http://ncor.buffalo.edu National Center for Ontological Research] |
Revision as of 21:25, 17 May 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
- 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: Tuesday, October, 10, 2017
19:00 Informal reception for early arrivals in conference hotel
Schedule: Wednesday, October, 11, 2017
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, October 12, 2017
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
Participants
- Cecilia Arighi (Delaware / PRO)
- Alex Bateman (EBI)
- Judith Blake (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)
- Barry Smith (Buffalo)
- Kimberley VanAuken (CalState)
- Cathy Wu (Delaware / PRO)
Please contact Barry Smith for further information.