PRO Consortium Workshop 2019: Difference between revisions

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'''Venue''':  
'''Venue''':  
:Protein Informatics Resource
:Protein Information Resource
:Georgetown University Medical Center  
:Georgetown University Medical Center  
:3300 Whitehaven Street, NW, Suite 1200
: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


==Goals==
'''Parking''' is available [https://buffalo.app.box.com/v/PRO-parking-map here] ($11 per day)


The goals of this meeting are:
'''Zoom''': https://georgetown.zoom.us/j/3531468363
*1. To review the current state of the Protein Ontology and its relation to other protein-related information resources, especially UniProt and GO and to document these relations with a view to publication.
*2. To evaluate current competing approaches to gene annotation in PRO and in other OBO Foundry ontologies and to document the implications of this evaluation with a view to publication.
*3. To assess progress in the use of advanced computational techniques, including Natural Language Processing, in the development of the PRO.
*4. To examine the actual and potential contribution of PRO to the understanding of disease across organisms.
*5. To advance the treatment of protein-related clinical and translational data from the perspective of consistency, discoverability and support for diagnosis.




==Schedule: Wednesday, October 23, 2019==


'''Introductory Session: The Landscape of the Protein Ontology'''
==Goals==


:8:45 Cathy Wu: Protein Ontology: Its current state and future development [https://buffalo.box.com/s/ahra2it1glmtsqm2e96yhgsp20u9jou3 Slides]
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.


:9:30 Susan Gregurick: NIH 2018 Priorities in Data Science and Computational Science [https://buffalo.box.com/s/8002lr7syg8gf2blt6hyjg7q69ka63b7 Slides]
*2. To describe PRO's collaborating projects and how they fit into PRO.


'''PRO and Related Resources'''
*3. To discuss implementation plans, especially with respect to collaborations.


:9:45 Darren Natale: Implementation of the  PRO Sites Ontology [https://buffalo.box.com/s/2an2i0wcfn7r3m5dld2q6tilr03oy0gg Slides]
==Schedule: Wednesday, October 23, 2019==


:10:25 Karen Ross: PRO Collaborations (ProKinO, NeXtProt ...) [https://buffalo.box.com/s/zpicxbl4qj4b5y1o69bq3te8gkd8bakq Slides]
:8:15 Breakfast


:10:45 Break
'''Advancing disease understanding with site information: PRO and UniProtKB'''


:11:00 Erich Baker and Elissa Chesler: GeneWeaver [https://buffalo.box.com/s/lglbejd3men722onm6m5xs1a5nsxmar4 Slides]
''Chair: Darren Natale''


:11:30 Cindy Smith: Disease Ontology at MGI [https://buffalo.box.com/s/mc67ue7h306aimgdipf0l16yok4t2u5h Slides]
: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)


:12:00 Kimberley VanAuken: Noctua and GO-CAM
:10:15-10:30 Break
[https://buffalo.box.com/s/c855q50pges44czj6v6hro7rf2c8r6u1 Slides]


:12:30 Lunch
'''Uncovering disease mechanisms: connecting site annotations to ontologies'''
''Chair: Judith Blake''


'''PRO and Disease'''
: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


Chair: Darren Natale
'''Uncovering disease mechanisms: connecting variants to diseases'''


:13:30 Judith Blake: Alliance of Genome Resources [https://buffalo.box.com/s/gu31c0z6vkgbd950tf4uft47zdd4ij6p Slides]
''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


:14:00 Chris Mungall: An Update on OBO / MONARCH [https://buffalo.box.com/s/uppgc4r87jn80xcpn4etiu2th19wfyax Slides]
:15:00-15:30 Break


:14:30 Barry Smith: How to define 'causally upstream of'
: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)
:15:00 Break
:16:30 Close of Day 1
 
:15:15 Peter McGarvey: Genome Annotation, ClinGen and PRO [https://buffalo.box.com/s/gu31c0z6vkgbd950tf4uft47zdd4ij6p Slides]
 
:15:45 Peter d'Eustachio: Reactome, PRO, GO, Phenotypes,
Complexes [https://buffalo.box.com/s/bo5yiutb082sp8qlc6egyh3o3aed6xwr Slides]
 
:16:15 Alexander Diehl: Cells, Proteins, Antibodies and Diseases [https://buffalo.box.com/s/xpjpn5kilahkvtt69gp4p7f28axewitm Slides]
 
17:00 '''Discussion of the representation of PRO annotations'''
:Chair: Barry Smith
:Participants: Alan Ruttenberg and Darren Natale


:18:00 Working dinner
:18:00 Working dinner
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==Schedule: Thursday, October 24, 2019==
==Schedule: Thursday, October 24, 2019==


'''GO, PRO and UniProt'''
[https://docs.google.com/document/d/1PiVxUQcEjsMlbudSGbxkVKwg3ib7KFnRyvHgv-CpUa4/edit?ts=5db0bc19 Googledocs discussion page from Day 1]


Chair: Cathy Wu
:8:15 Breakfast


:8:45 Maria Martin: Representing UniProt
'''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)


:9:30 Chris Mungall: Representing GO
:10:30-10:45 Break


:9:45 GO, PRO and UniProt: How will they work together
'''Cell type discovery: proteoform expression and clinically-relevant cell types'''


:10:30 Break
''Chair: Alexander Diehl''


:10:45 Julie Cowart: Data Access and Writing SPARQL Queries [https://buffalo.box.com/s/6u4ef8l0gjylwgsdbv5eb9ww4yhmkja2 Slides]
: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


:11:15 Alan Ruttenberg: Discussion of how genes are referenced in OBO Foundry and in PRO: why do they differ?
: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


:11:45 Cecilia Arighi: The role of NLP in PRO curation [https://buffalo.box.com/s/ykzpfu5quyx44qr3fenoqqi45o084x3b Slides]
:15:00 Close of meeting
 
:12:15 Lunch
 
13:00 '''Discussion of how genes are referenced in OBO Foundry and in PRO: why do they differ?'''
:Chair: Barry Smith
:Participants: David Hill, Chris Mungall, Darren Natale, Alan Ruttenberg.
 
:14:00 '''Roundtable on killer apps for PRO'''
 
:16:00 Close


----
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Line 102: Line 110:
== '''Participants''' ==
== '''Participants''' ==


:Cecilia Arighi (Delaware / PRO)
:Alexander Bateman (EBI)*
:Alexander Bateman (EBI)*
:Alexander Diehl (Buffalo)
:Cecilia Arighi (Delaware / PRO)
:Judith Blake (JAX)
:Judith Blake (JAX)
:Peter d'Eustachio (NYU)*
:Peter d'Eustachio (NYU)
:Alexander Diehl (Buffalo)
:Alexander Diehl (Buffalo)
:? Harold Drabkin (JAX)
:Harold Drabkin (JAX)
:Michelle Giglio (Baltimore)
:Patrick Dunn (ImmPort)
:Yongqun (Oliver) He (Michigan)
:Natarajan Kannan (Georgia)
:? Neil Kelleher
: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)
:Li Ni (JAX)
:? Bjoern Peters (San Diego)
:Karen Ross (Georgetown/PRO)  
:? Karen Ross (Delaware)  
:Alan Ruttenberg (Buffalo)
:Alan Ruttenberg (Buffalo)
:?Stephan Schürer (Miami)
: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.

Sponsors

The Protein Ontology Consortium
National Center for Ontological Research