PRO Consortium Workshop 2019: Difference between revisions
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==Schedule: Wednesday, October 23, 2019== | ==Schedule: Wednesday, October 23, 2019== | ||
:8: | :8:15 Breakfast | ||
''' | '''Advancing disease understanding with site information: PRO and UniProtKB''' | ||
''Chair: Darren Natale'' | ''Chair: Darren Natale'' | ||
:9:00 | :8:45 Logistics and introductions (Barry Smith) | ||
:: | :9:00 Meeting objectives (Darren Natale) | ||
::PRO sites (Alan Ruttenberg) | :9:20 General introduction to PRO (Darren Natale) | ||
:9:45 PRO sites (Alan Ruttenberg) | |||
:10: | :10:15-10:30 Break | ||
''' | '''Uncovering disease mechanisms: connecting site annotations to ontologies''' | ||
''Chair: Judith Blake'' | ''Chair: Judith Blake'' | ||
:10: | :10:30 UniProtKB Feature Viewer (Alexander Bateman) | ||
:11:00 UniProtKB's molecular impact information (Harold Drabkin) - connecting feature line information to ontologies | |||
:11:30 Disease Ontology (Melody Swan) - introduction to DO and how it can be used to go from UniProtKB variants to disease identifiers | |||
::UniProtKB's molecular impact information (Harold Drabkin | :12:00 Ontology for General Medical Science (Barry Smith) - introduction to OGMS and how it can be used to standardize UniProt Feature Table (FT) information | ||
::: | |||
:12:30-13:30 Lunch | :12:30-13:30 Lunch | ||
''' | '''Uncovering disease mechanisms: connecting variants to diseases''' | ||
::Chair: Judith Blake'' | |||
:13:30 | :13:30 Mouse models of human disease (TBD) | ||
:14:00 Extracting variant / disease associations from text (Cecilia Arighi) | |||
:: | :14:00 Discovering molecular mechanisms underlying disease (Karen Ross, Natarajan Kannan) - the PRO/ProKinO/NeXtProt work as a model for what's to come | ||
::Discovering molecular mechanisms underlying disease (Karen Ross, Natarajan Kannan) | |||
:15:00-15:30 Break | |||
:15:30 | :15:30 TBD | ||
:TBD Protein aggregates (Lauren Wishnie) | |||
:17: | :17:00 Close of Day 1 | ||
:18:00 Working dinner | :18:00 Working dinner | ||
Line 61: | Line 66: | ||
''Chair: Peter d'Eustachio'' | ''Chair: Peter d'Eustachio'' | ||
:8:45 | :8:45 Introduction to Day 2 theme / Logistics (Barry Smith) | ||
:9:00 Reactome's disease pathways (Peter d'Eustachio) - how they can be used with PRO to make new proteoform/disease associations | |||
::Drug | :9:30 Using DTO and PRO for Drug target discovery (Stephan Schürer) | ||
: | 10:00 Connecting antibodies to epitopes and proteins (Randi Vita) | ||
:10:30- | :10:30-10:45 Break | ||
'''Cell type discovery: | '''Cell type discovery: proteoform expression and clinically-relevant cell types''' | ||
''Chair: Alexander Diehl'' | ''Chair: Alexander Diehl'' | ||
: | :10:45 Cell Ontology and its use of PRO (Alexander Diehl) | ||
:11:10 ImmPort and its use of PRO (Patrick Dunn) | |||
:: | :11:40 The Kidney Precision Medicine Project (Oliver He) - with an emphasis on how scRNA can detect new isomoforms | ||
::Proteoform-based cell type dictionary (Alex Diehl) | :12:05 Proteoform-based cell type dictionary (Alex Diehl) | ||
:12:30-1:30 Lunch | :12:30-1:30 Lunch | ||
:13:30 | :13:30 TBD - includes PRO grant working session | ||
: | :16:00 Close of meeting | ||
---- | ---- |
Revision as of 16:02, 20 August 2019
Date: October 23-24, 2019
Venue:
- Protein Informatics Resource
- Georgetown University Medical Center
- 3300 Whitehaven Street, NW, Suite 1200
- Washington, DC 20007, USA
Goals
The goals of this meeting are:
- 1. To plan the future of the PRO
- 2. To foster PRO's collaborations with other initiatives
Schedule: Wednesday, October 23, 2019
- 8:15 Breakfast
Advancing disease understanding with site information: PRO and UniProtKB
Chair: Darren Natale
- 8:45 Logistics and introductions (Barry Smith)
- 9:00 Meeting objectives (Darren Natale)
- 9:20 General introduction to PRO (Darren Natale)
- 9:45 PRO sites (Alan Ruttenberg)
- 10:15-10:30 Break
Uncovering disease mechanisms: connecting site annotations to ontologies
Chair: Judith Blake
- 10:30 UniProtKB Feature Viewer (Alexander Bateman)
- 11:00 UniProtKB's molecular impact information (Harold Drabkin) - connecting feature line information to ontologies
- 11:30 Disease Ontology (Melody Swan) - introduction to DO and how it can be used to go from UniProtKB variants to disease identifiers
- 12:00 Ontology for General Medical Science (Barry Smith) - introduction to OGMS and how it can be used to standardize UniProt Feature Table (FT) information
- 12:30-13:30 Lunch
Uncovering disease mechanisms: connecting variants to diseases
- Chair: Judith Blake
- 13:30 Mouse models of human disease (TBD)
- 14:00 Extracting variant / disease associations from text (Cecilia Arighi)
- 14:00 Discovering molecular mechanisms underlying disease (Karen Ross, Natarajan Kannan) - the PRO/ProKinO/NeXtProt work as a model for what's to come
- 15:00-15:30 Break
- 15:30 TBD
- TBD Protein aggregates (Lauren Wishnie)
- 17:00 Close of Day 1
- 18:00 Working dinner
Schedule: Thursday, October 24, 2019
- 8:15 Breakfast
Clinical discovery: connecting clinically-relevant information to proteoforms and complexes
Chair: Peter d'Eustachio
- 8:45 Introduction to Day 2 theme / Logistics (Barry Smith)
- 9:00 Reactome's disease pathways (Peter d'Eustachio) - how they can be used with PRO to make new proteoform/disease associations
- 9:30 Using DTO and PRO for Drug target discovery (Stephan Schürer)
10:00 Connecting antibodies to epitopes and proteins (Randi Vita)
- 10:30-10:45 Break
Cell type discovery: proteoform expression and clinically-relevant cell types
Chair: Alexander Diehl
- 10:45 Cell Ontology and its use of PRO (Alexander Diehl)
- 11:10 ImmPort and its use of PRO (Patrick Dunn)
- 11:40 The Kidney Precision Medicine Project (Oliver He) - with an emphasis on how scRNA can detect new isomoforms
- 12:05 Proteoform-based cell type dictionary (Alex Diehl)
- 12:30-1:30 Lunch
- 13:30 TBD - includes PRO grant working session
- 16:00 Close of meeting
Participants
- Alexander Bateman (EBI)*
- Alexander Diehl (Buffalo)
- Cecilia Arighi (Delaware / PRO)
- Judith Blake (JAX)
- Peter d'Eustachio (NYU)
- Alexander Diehl (Buffalo)
- Harold Drabkin (JAX)
- Patrick Dunn (ImmPort)
- Yongqun (Oliver) He (Michigan)
- Natarajan Kannan (Georgia)
- Richard LeDuc (Northwestern)
- Birgit Meldal (EBI)*
- Darren Natale (Georgetown)
- Li Ni (JAX)
- Karen Ross (Georgetown)
- Alan Ruttenberg (Buffalo)
- Stephan Schürer (Miami)
- Henry Schaefer (ImmPort)
- Barry Smith (Buffalo)
- Christian Stoeckert (Penn)
- Melogy Swan (Baltimore)
- Paul Martin Thomas (Northwestern)
- Randi Vita (San Diego)
- Lauren Wishnie )
- Cathy Wu (Delaware / PRO)
- =online
Please contact Barry Smith for further information.