PRO Consortium Workshop 2017: Difference between revisions
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:9:45 Karen Ross: PRO Collaborations (ProKinO, NeXtProt ...) | :9:45 Karen Ross: PRO Collaborations (ProKinO, NeXtProt ...) | ||
:10: | :10:15 Erich Baker and Elissa Chesler: GeneWeaver | ||
:10:45 Break | :10:45 Break | ||
:11:00 Cindy Smith: The Alliance of Genome Resources | |||
:11: | :11:30 Kimberley VanAuken: Noctua | ||
:12:00 Cecilia Arighi: The role of NLP in PRO curation | |||
:12: | |||
:12:30 Lunch | :12:30 Lunch | ||
Line 52: | Line 49: | ||
:13:30 Judith Blake: Disease Ontology -- overview of available resources | :13:30 Judith Blake: Disease Ontology -- overview of available resources | ||
: | :14:00 Chris Mungall: MONARCH | ||
:14:30 Elissa Chesler: MGI effort to combine variant data with disease forms; Genereader resource, PRO IDs for variants | |||
: | :15:00 Break | ||
:15: | :15:15 Peter McGarvey: Genome Annotation, ClinGen and PRO | ||
:15:45 Peter d'Eustachio : PRO and Reactome | |||
:15:45 | |||
:16:15 Alexander Diehl: PRO, the Antibody Ontology and the Cell Ontology | |||
::*HIPC, cell populations, the Antibody Panel Ontology, Cell types vs. cell states -- when do combinations of protein markers | ::*HIPC, cell populations, the Antibody Panel Ontology, Cell types vs. cell states -- when do combinations of protein markers | ||
'''The Value of PRO Annotations in Enabling Interconnection of Biomedical Ontologies and Databases''' | '''The Value of PRO Annotations in Enabling Interconnection of Biomedical Ontologies and Databases''' | ||
: | :17:00 *This session will include a debate between Alan Ruttenberg, Chris Mungall, David Hill and Darren Natale on the proper representation of PRO annotations | ||
:18:00 Working dinner | :18:00 Working dinner |
Revision as of 17:32, 30 September 2017
Date: October 11-12, 2017
Venue: Atlantic Oceanside Hotel, Bar Harbor, MN
Goals
The goals of this meeting are:
- 1. To review the current state of the Protein Ontology and its relation to other protein-related information resources, especially UniProt and GO
- 2. To assess progress in the use of advanced computational techniques, including Natural Language Processing, in the development of the PRO
- 3. To examine the actual and potential contribution of PRO to the understanding of disease across organisms
- 4. To review PRO's role in the field of immunology informatics
- 5. To advance the treatment of protein-related clinical and translational data from the perspective of consistency, discoverability and support for diagnosis
- 6. To evaluate competing approaches to PRO annotation
Schedule: Tuesday, October, 10, 2017
19:00 Informal reception for early arrivals in conference hotel
Schedule: Wednesday, October, 11, 2017
Introductory Session: The Landscape of the Protein Ontology
- 8:45 Cathy Wu: Protein Ontology: Its current state and future development
- Sites, PTMs
- 9:30 Susan Gregurick: NIH 2018 Priorities in Data Science and Computational Science
PRO and Related Resources
- 9:45 Karen Ross: PRO Collaborations (ProKinO, NeXtProt ...)
- 10:15 Erich Baker and Elissa Chesler: GeneWeaver
- 10:45 Break
- 11:00 Cindy Smith: The Alliance of Genome Resources
- 11:30 Kimberley VanAuken: Noctua
- 12:00 Cecilia Arighi: The role of NLP in PRO curation
- 12:30 Lunch
PRO and Disease
Chair: Darren Natale
- 13:30 Judith Blake: Disease Ontology -- overview of available resources
- 14:00 Chris Mungall: MONARCH
- 14:30 Elissa Chesler: MGI effort to combine variant data with disease forms; Genereader resource, PRO IDs for variants
- 15:00 Break
- 15:15 Peter McGarvey: Genome Annotation, ClinGen and PRO
- 15:45 Peter d'Eustachio : PRO and Reactome
- 16:15 Alexander Diehl: PRO, the Antibody Ontology and the Cell Ontology
- HIPC, cell populations, the Antibody Panel Ontology, Cell types vs. cell states -- when do combinations of protein markers
The Value of PRO Annotations in Enabling Interconnection of Biomedical Ontologies and Databases
- 17:00 *This session will include a debate between Alan Ruttenberg, Chris Mungall, David Hill and Darren Natale on the proper representation of PRO annotations
- 18:00 Working dinner
Schedule: Thursday, October 12, 2017
- 8:00 Continental breakfast
GO, PRO and UniProt
Chair: Cathy Wu
- 8:45 Alex Bateman (EBI)
- 9:15 Maria Martin (EBI) TBD
- 9:45 Discussion of GO, PRO and UniProt: How they should work together
- 10:30 Break
- 11:00 Julie Cowart: Writing SPARQL queries for PRO
- 11:30 Alan Ruttenberg: Enhanced SPARQL queries for PRO
- 12:00 Lunch
- 12:45 Debate: How genes are referenced in OBO Foundry and in PRO: why do they differ?
Chair: Barry Smith
- Participants: Chris Mungall, Darren Natale, Alan Ruttenberg (will be moved to working dinner if space needed)
14:00 Close of Plenary Sessions
14:00 Working group meetings
17:00 Close
Participants
*=online
- Cecilia Arighi (Delaware / PRO)*
- Erich Baker (Baylor)
- Alex Bateman (EBI)*
- Judith Blake (JAX)
- Chuming Chen (Delaware)*
- Elissa Chesler (JAX)
- Julie Cowart (Delaware)*
- Mary Dolan (JAX)
- Peter d'Eustachio (NYU)*
- Alexander Diehl (Buffalo)
- Harold Drabkin (JAX)
- Susan Gregurick (NIH / NIGMS)*
- David Hill (JAX)
- Stanley Laulederkind (Medical College of Wisconsin)
- Peter McGarvey (Georgetown)
- Maria Martin (EBI)
- Chris Mungall (LBNL)
- Darren Natale (Georgetown)
- Li Ni (JAX)
- 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.