PRO Consortium Workshop 2017: Difference between revisions
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=='''Schedule: Wednesday, October, 11, 2017== | =='''Schedule: Wednesday, October, 11, 2017== | ||
8:45 | 8:45 '''Introductory Session: The Landscape of the Protein Ontology''' | ||
:Cathy Wu: Protein Ontology: Its current state and future development | |||
::Sites, PTMs | |||
TBD: | :TBD: ProKinO: Protein Kinase Ontology Browser (action item) | ||
:TBD: NeXtProt | |||
Cindy Smith: The Alliance of Genome Resources | :Pamela VanAuken: Noctua | ||
:Cindy Smith: The Alliance of Genome Resources | |||
10:30 Break | 10:30 Break | ||
10:45 '''PRO and | 10:45 '''PRO and SPARQL / PRO and NLP''' | ||
Chair: TBD | |||
:Chuming Chen: Writing SPARQL queries for PRO | |||
:Alan Ruttenberg: Enhanced SPARQL queries for PRO | |||
PRO curation | :Cecilia Arighi: The role of NLP in PRO curation | ||
12:30 Lunch | 12:30 Lunch | ||
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Chair: Barry Smith | Chair: Barry Smith | ||
Judith Blake | :Judith Blake: Disease Ontology -- overview of available resources | ||
Elissa Chesler | :Elissa Chesler: MGI effort to combine variant data with disease forms; Genereader resource, PRO IDs for variants | ||
Barry Smith Protein-Disease Relations | :Barry Smith: Protein-Disease Relations | ||
Other large-scale frameworks working with protein variants | :Other large-scale frameworks working with protein variants | ||
14:30 Break | 14:30 Break | ||
Line 83: | Line 84: | ||
Chair: Darren Natale | Chair: Darren Natale | ||
Alex Diehl: PRO and the Antibody | :Alex Diehl: PRO and the Antibody Ontology | ||
: | :Alex Diehl: PRO the Cell Ontology | ||
::HIPC, cell populations, the Antibody Panel Ontology, Cell types vs. cell states -- when do combinations of protein markers | |||
16:00 Close | 16:00 Close | ||
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8:00 Continental breakfast | 8:00 Continental breakfast | ||
'''GO, PRO and UniProt: How they should work together''' | 9:00 '''GO, PRO and UniProt: How they should work together''' | ||
Chair: | Chair: Cathy Wu | ||
:Alex Bateman (EBI) | |||
10:30 Break | 10:30 Break | ||
10:45 | :10:45 Alan Ruttenberg: Proposal regarding representation of PRO annotations | ||
:Responses by Chris Mungall, David Hill, Darren Natale | |||
12:00 Lunch | 12:00 Lunch | ||
12:45 ''' | 12:45 '''Debate: How genes are referenced in OBO Foundry and in PRO: why do they differ?''' | ||
Chair: TBD | Chair: TBD | ||
:Participants: Chris Mungall, Darren Natale, Alan Ruttenberg (could be moved to working dinner if space needed) | |||
Participants: Chris Mungall, Darren Natale | |||
14:00 Close of Plenary Sessions | 14:00 Close of Plenary Sessions | ||
14:00 Working group meetings | 14:00 Working group meetings |
Revision as of 19:07, 18 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 -- focus on PTMs, sites
- Relating to PRO's interactions with external resources:
- UniProt: Draft of policies/recommendations regarding accession/site tracking for UniProt and PRO
Benefits and limitations of PRO
PRO and PTM knowledge networks
Developing PROs scope for annotating diseases
Schedule: Tuesday, October, 10, 2017
19:00 Informal reception for early arrivals in conference hotel
Schedule: Wednesday, October, 11, 2017
8:45 Introductory Session: The Landscape of the Protein Ontology
- Cathy Wu: Protein Ontology: Its current state and future development
- Sites, PTMs
- TBD: ProKinO: Protein Kinase Ontology Browser (action item)
- TBD: NeXtProt
- Pamela VanAuken: Noctua
- Cindy Smith: The Alliance of Genome Resources
10:30 Break
10:45 PRO and SPARQL / PRO and NLP
Chair: TBD
- Chuming Chen: Writing SPARQL queries for PRO
- Alan Ruttenberg: Enhanced SPARQL queries for PRO
- Cecilia Arighi: The role of NLP in PRO curation
12:30 Lunch
13:30 PRO and Disease
Chair: Barry Smith
- Judith Blake: Disease Ontology -- overview of available resources
- Elissa Chesler: MGI effort to combine variant data with disease forms; Genereader resource, PRO IDs for variants
- Barry Smith: Protein-Disease Relations
- Other large-scale frameworks working with protein variants
14:30 Break
14:45 PRO and Immunology
Chair: Darren Natale
- Alex Diehl: PRO and the Antibody Ontology
- Alex Diehl: PRO the Cell Ontology
- HIPC, cell populations, the Antibody Panel Ontology, Cell types vs. cell states -- when do combinations of protein markers
16:00 Close
Schedule: Thursday, October 12, 2017
Venue: JAX
8:00 Continental breakfast
9:00 GO, PRO and UniProt: How they should work together
Chair: Cathy Wu
- Alex Bateman (EBI)
10:30 Break
- 10:45 Alan Ruttenberg: Proposal regarding representation of PRO annotations
- Responses by Chris Mungall, David Hill, Darren Natale
12:00 Lunch
12:45 Debate: How genes are referenced in OBO Foundry and in PRO: why do they differ?
Chair: TBD
- Participants: Chris Mungall, Darren Natale, Alan Ruttenberg (could be moved to working dinner if space needed)
14:00 Close of Plenary Sessions
14:00 Working group meetings
17:00 Close
Participants
- Cecilia Arighi (Delaware / PRO)
- Erich Baker (Baylor))
- Alex Bateman (EBI)
- Judith Blake (JAX)
- Elissa Chesler (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)
- Cynthia Smith (JAX)
- Barry Smith (Buffalo)
- Kimberley VanAuken (CalTech)
- Laurens Wilming (JAX)
- Cathy Wu (Delaware / PRO)
Please contact Barry Smith for further information.