PRO Consortium Workshop 2019: Difference between revisions
(113 intermediate revisions by the same user not shown) | |||
Line 2: | Line 2: | ||
'''Venue''': | '''Venue''': | ||
:Protein | :Protein Information Resource | ||
:Georgetown University Medical Center | :Georgetown University Medical Center | ||
:3300 Whitehaven Street | :Suite 1300 | ||
:3300 Whitehaven Street NW (Milton Harris Building), | |||
:Washington, DC 20007, USA | :Washington, DC 20007, USA | ||
For '''logistic questions''' please call BS at (716) 361-5100 | |||
'''Parking''' is available [https://buffalo.app.box.com/v/PRO-parking-map here] ($11 per day) | |||
'''Zoom''': https://georgetown.zoom.us/j/3531468363 | |||
Line 11: | Line 19: | ||
The goals of this meeting are: | The goals of this meeting are: | ||
*1. To | *1. To describe the future of PRO in light of the aims of the upcoming grant proposal: | ||
::(a) represent proteoforms of clinical interest | |||
::(b) connect sequence variations with molecular mechanisms using semantic web technologies | |||
::(c) link disease biomarker, antibody, and drug target information to appropriate proteoforms | |||
::(d) connect proteoform expression profiles to cell types | |||
::(e) enhance PRO quality control and distribution mechanisms. | |||
*2. To describe PRO's collaborating projects and how they fit into PRO. | |||
*3. To discuss implementation plans, especially with respect to collaborations. | |||
==Schedule: Wednesday, October 23, 2019== | ==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 [https://buffalo.box.com/s/9k3mnsy2ddodun7wje10ud9fe1dzuepg Meeting objectives] (Darren Natale) | |||
:9:20 [https://buffalo.box.com/s/2ge3p0ae5x6dd8oidks6vh4xgms9ichu General introduction to PRO] (Darren Natale) | |||
:9:35 [https://buffalo.box.com/v/Ruttenberg-PRO-Sites PRO sites] (Alan Ruttenberg) | |||
:9:45 [https://buffalo.box.com/s/og1tusat1l4ucbbhm51wd6zh539dxfyk PRO Sites] (Darren Natale) | |||
:10:15-10:30 Break | |||
'''Uncovering disease mechanisms: connecting site annotations to ontologies''' | |||
''Chair: Judith Blake'' | |||
:10:30 [https://buffalo.box.com/s/d93kobo8dh0alyb5ykkina6e1nw81s5p UniProtKB Feature Viewer] (Alexander Bateman) | |||
:11:00 [https://buffalo.box.com/s/ylbpwqz19y7cvxuwhg2eqg40yzxq7mr5 UniProtKB's molecular impact information] (Harold Drabkin) - connecting feature line information to ontologies | |||
:11:30 [https://buffalo.box.com/s/42fky2o87di08dk4q943t52l4ktpovi0 Disease Ontology] (Melody Swen) - introduction to DO and how it can be used to go from UniProtKB variants to disease identifiers | |||
:12:00 [https://buffalo.box.com/v/PRO-meeting-BFO-OGMS Basic Formal Ontology and Ontology for General Medical Science] (Barry Smith) - introduction to OGMS and to the new ISO/IEC 21838 top-level ontology standard | |||
:12:30-13:30 Lunch | |||
'''Uncovering disease mechanisms: connecting variants to diseases''' | |||
''Chair: Judith Blake'' | |||
:13:30 [https://buffalo.box.com/s/p640nyu246h7736k7xt8sbkak6twffoz Mouse models of human disease] (Li Ni) | |||
:14:00 [https://buffalo.box.com/s/jo07sdssyn52fj89j3stn63aucx6a5yv Extracting variant / disease associations from text] (Cecilia Arighi) | |||
:14:30 [https://buffalo.box.com/s/d1qbf10l14lv31bnnpg2i17oi1re49r6 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 [https://buffalo.box.com/s/6kdes4lhv1s0rz89fn6tm943jxb3ajca Leveraging PRO in EuPathDB, OrthoMCL, and NIAGADS Genomics] (Chris Stoeckert) | |||
:16:00 [https://buffalo.box.com/s/ygac6ictkvsfqvx79snsl8jxgejewyiz Protein aggregates] (Lauren Wishnie) | |||
:16:30 Close of Day 1 | |||
:18:00 Working dinner | :18:00 Working dinner | ||
==Schedule: Thursday, October 24, 2019== | ==Schedule: Thursday, October 24, 2019== | ||
''' | [https://docs.google.com/document/d/1PiVxUQcEjsMlbudSGbxkVKwg3ib7KFnRyvHgv-CpUa4/edit?ts=5db0bc19 Googledocs discussion page from Day 1] | ||
:8:15 Breakfast | |||
'''Clinical discovery: connecting clinically-relevant information to proteoforms and complexes''' | |||
''Chair: Peter d'Eustachio'' | |||
:8:45 Introduction to Day 2 theme (Darren Natale) / Logistics (Barry Smith) | |||
:9:00 [https://buffalo.box.com/s/x66k2vdtw0cjnqvl2npklofj92pi08bm Reactome's disease pathways] (Peter d'Eustachio) - how they can be used with PRO to make new proteoform/disease associations | |||
:9:30 [https://buffalo.box.com/s/pptezlimqnxqd7maxamw2aa9ke33nla3 Using DTO and PRO for Drug target discovery] (Stephan Schürer) | |||
:10:00 [https://buffalo.box.com/s/xvaekv096s5pmwhium9c73jwmc2xn45x Connecting diseases to epitopes and proteins] (Randi Vita) | |||
:10:30-10:45 Break | |||
'''Cell type discovery: proteoform expression and clinically-relevant cell types''' | |||
Chair: | ''Chair: Alexander Diehl'' | ||
: | :10:45 [https://buffalo.box.com/s/0sexse2ofjo7nl96d0dy4qahtvkgbhic Cell Ontology and its use of PRO] (Alexander Diehl) | ||
:11:05 Proteoform-based cell type dictionary (Alexander Diehl) | |||
:11:30 [https://buffalo.box.com/s/q5qpc7v0dsfi0kiksc6id4r5k89yysdz ImmPort and its use of PRO] (Patrick Dunn) | |||
:12:00 [https://buffalo.box.com/s/y2lcjgvha37ls6xmxx829qah4x6enbwy Communicating and cataloging proteoforms within the Blood Proteoform Atlas] (Paul Martin Thomas and Richard Dann LeDuc) | |||
:12:30-13:00 Lunch | |||
:15:00 Close | :13:00 [https://buffalo.box.com/s/gvmwx3nzb24p30kz1xrqaqvot8wlnm00 Sequences beyond the Central Dogma: describing, quality controlling, exchanging, and visualizing proteoforms with concrete chemical semantics using BpForms/BcForms] (Jonathan Karr) | ||
:13:30 TBD | |||
:13:45 PRO grant working session | |||
:15:00 Close of meeting | |||
---- | ---- | ||
Line 39: | Line 110: | ||
== '''Participants''' == | == '''Participants''' == | ||
:Cecilia Arighi (Delaware / PRO) | |||
:Alexander Bateman (EBI)* | :Alexander Bateman (EBI)* | ||
:Judith Blake (JAX) | :Judith Blake (JAX) | ||
:Peter d'Eustachio (NYU) | :Peter d'Eustachio (NYU) | ||
:Alexander Diehl (Buffalo) | :Alexander Diehl (Buffalo) | ||
: | :Harold Drabkin (JAX) | ||
: | :Patrick Dunn (ImmPort) | ||
:Natarajan Kannan (Georgia) | :Natarajan Kannan (Georgia) | ||
: | :Jonathan Karr (MSSM) | ||
:Richard LeDuc (Northwestern) | |||
:Yu Lin (FDA) | |||
:Birgit Meldal (EBI)* | :Birgit Meldal (EBI)* | ||
:Darren Natale (Georgetown) | :Darren Natale (Georgetown/PRO) | ||
: | :Li Ni (JAX) | ||
:Karen Ross (Georgetown/PRO) | |||
:Karen Ross ( | |||
:Alan Ruttenberg (Buffalo) | :Alan Ruttenberg (Buffalo) | ||
: | :Stephan Schürer (Miami) | ||
:Henry Schaefer (ImmPort) | |||
:Barry Smith (Buffalo) | :Barry Smith (Buffalo) | ||
:Christian Stoeckert (Penn) | |||
:Melody Swen (Baltimore) | |||
:Paul Martin Thomas (Northwestern) | |||
:Randi Vita (San Diego) | |||
:Lauren Wishnie (Buffalo) | |||
:Cathy Wu (Delaware / PRO) | :Cathy Wu (Delaware / PRO) | ||
:Sara Yang (NIST) | |||
*=online | *=online | ||
Please contact [mailto:phismith@buffalo.edu Barry Smith] for further information. | Please contact [mailto:phismith@buffalo.edu Barry Smith] for further information. |
Latest revision as of 14:59, 24 October 2019
Date: October 23-24, 2019
Venue:
- Protein Information Resource
- Georgetown University Medical Center
- Suite 1300
- 3300 Whitehaven Street NW (Milton Harris Building),
- Washington, DC 20007, USA
For logistic questions please call BS at (716) 361-5100
Parking is available here ($11 per day)
Zoom: https://georgetown.zoom.us/j/3531468363
Goals
The goals of this meeting are:
- 1. To describe the future of PRO in light of the aims of the upcoming grant proposal:
- (a) represent proteoforms of clinical interest
- (b) connect sequence variations with molecular mechanisms using semantic web technologies
- (c) link disease biomarker, antibody, and drug target information to appropriate proteoforms
- (d) connect proteoform expression profiles to cell types
- (e) enhance PRO quality control and distribution mechanisms.
- 2. To describe PRO's collaborating projects and how they fit into PRO.
- 3. To discuss implementation plans, especially with respect to collaborations.
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)
- 9:35 PRO sites (Alan Ruttenberg)
- 9:45 PRO Sites (Darren Natale)
- 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 Swen) - introduction to DO and how it can be used to go from UniProtKB variants to disease identifiers
- 12:00 Basic Formal Ontology and Ontology for General Medical Science (Barry Smith) - introduction to OGMS and to the new ISO/IEC 21838 top-level ontology standard
- 12:30-13:30 Lunch
Uncovering disease mechanisms: connecting variants to diseases
Chair: Judith Blake
- 13:30 Mouse models of human disease (Li Ni)
- 14:00 Extracting variant / disease associations from text (Cecilia Arighi)
- 14:30 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 Leveraging PRO in EuPathDB, OrthoMCL, and NIAGADS Genomics (Chris Stoeckert)
- 16:00 Protein aggregates (Lauren Wishnie)
- 16:30 Close of Day 1
- 18:00 Working dinner
Schedule: Thursday, October 24, 2019
Googledocs discussion page from Day 1
- 8:15 Breakfast
Clinical discovery: connecting clinically-relevant information to proteoforms and complexes
Chair: Peter d'Eustachio
- 8:45 Introduction to Day 2 theme (Darren Natale) / 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 diseases 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)
- 11:05 Proteoform-based cell type dictionary (Alexander Diehl)
- 11:30 ImmPort and its use of PRO (Patrick Dunn)
- 12:00 Communicating and cataloging proteoforms within the Blood Proteoform Atlas (Paul Martin Thomas and Richard Dann LeDuc)
- 12:30-13:00 Lunch
- 13:00 Sequences beyond the Central Dogma: describing, quality controlling, exchanging, and visualizing proteoforms with concrete chemical semantics using BpForms/BcForms (Jonathan Karr)
- 13:30 TBD
- 13:45 PRO grant working session
- 15:00 Close of meeting
Participants
- Cecilia Arighi (Delaware / PRO)
- Alexander Bateman (EBI)*
- Judith Blake (JAX)
- Peter d'Eustachio (NYU)
- Alexander Diehl (Buffalo)
- Harold Drabkin (JAX)
- Patrick Dunn (ImmPort)
- Natarajan Kannan (Georgia)
- Jonathan Karr (MSSM)
- Richard LeDuc (Northwestern)
- Yu Lin (FDA)
- Birgit Meldal (EBI)*
- Darren Natale (Georgetown/PRO)
- Li Ni (JAX)
- Karen Ross (Georgetown/PRO)
- Alan Ruttenberg (Buffalo)
- Stephan Schürer (Miami)
- Henry Schaefer (ImmPort)
- Barry Smith (Buffalo)
- Christian Stoeckert (Penn)
- Melody Swen (Baltimore)
- Paul Martin Thomas (Northwestern)
- Randi Vita (San Diego)
- Lauren Wishnie (Buffalo)
- Cathy Wu (Delaware / PRO)
- Sara Yang (NIST)
- =online
Please contact Barry Smith for further information.