PRO Consortium Workshop 2017: Difference between revisions
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'''Date''': October 11-12, 2017 | '''Date''': October 11-12, 2017 | ||
[[PRO Consortium Workshop 2019]] | |||
'''Venue''': [https://barharbormainehotel.com/ Atlantic Oceanside Hotel], Bar Harbor, MN | |||
==Goals== | |||
The goals of this meeting are: | 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 | *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 assess progress in the use of advanced computational techniques, including Natural Language Processing, in the development of the PRO | *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 | *5. To advance the treatment of protein-related clinical and translational data from the perspective of consistency, discoverability and support for diagnosis. | ||
== | ==White Papers== | ||
[https://buffalo.box.com/s/i1saod7olqdxc3c5n4vgikbpwxmk7qx7 PRO Family Relations] | |||
[https://buffalo.box.com/s/hx6wd7eeyg6iw6q1kn7h956zyzpqs62w Functional Annotation of Proteins] | |||
==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 [https://buffalo.box.com/s/ahra2it1glmtsqm2e96yhgsp20u9jou3 Slides] | ||
: | :9:30 Susan Gregurick: NIH 2018 Priorities in Data Science and Computational Science [https://buffalo.box.com/s/8002lr7syg8gf2blt6hyjg7q69ka63b7 Slides] | ||
'''PRO and Related Resources''' | |||
: | :9:45 Darren Natale: Implementation of the PRO Sites Ontology [https://buffalo.box.com/s/2an2i0wcfn7r3m5dld2q6tilr03oy0gg Slides] | ||
: | :10:25 Karen Ross: PRO Collaborations (ProKinO, NeXtProt ...) [https://buffalo.box.com/s/zpicxbl4qj4b5y1o69bq3te8gkd8bakq Slides] | ||
10: | :10:45 Break | ||
:11:00 Erich Baker and Elissa Chesler: GeneWeaver [https://buffalo.box.com/s/lglbejd3men722onm6m5xs1a5nsxmar4 Slides] | |||
:11:30 Cindy Smith: Disease Ontology at MGI [https://buffalo.box.com/s/mc67ue7h306aimgdipf0l16yok4t2u5h Slides] | |||
: | :12:00 Kimberley VanAuken: Noctua and GO-CAM | ||
[https://buffalo.box.com/s/c855q50pges44czj6v6hro7rf2c8r6u1 Slides] | |||
: | :12:30 Lunch | ||
'''PRO and Disease''' | |||
Chair: Darren Natale | |||
Chair: | |||
: | :13:30 Judith Blake: Alliance of Genome Resources [https://buffalo.box.com/s/gu31c0z6vkgbd950tf4uft47zdd4ij6p Slides] | ||
: | :14:00 Chris Mungall: An Update on OBO / MONARCH [https://buffalo.box.com/s/uppgc4r87jn80xcpn4etiu2th19wfyax Slides] | ||
: | :14:30 Barry Smith: How to define 'causally upstream of' | ||
14:30 | |||
: | :15:00 Break | ||
: | :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: | :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 | |||
==Schedule: Thursday, October 12, 2017== | |||
'''GO, PRO and UniProt''' | |||
Chair: Cathy Wu | Chair: Cathy Wu | ||
: | :8:45 Maria Martin: Representing UniProt | ||
:9:30 Chris Mungall: Representing GO | |||
: | :9:45 GO, PRO and UniProt: How will they work together | ||
: | :10:30 Break | ||
:10:45 Julie Cowart: Data Access and Writing SPARQL Queries [https://buffalo.box.com/s/6u4ef8l0gjylwgsdbv5eb9ww4yhmkja2 Slides] | |||
:11:15 Alan Ruttenberg: Discussion of how genes are referenced in OBO Foundry and in PRO: why do they differ? | |||
:11:45 Cecilia Arighi: The role of NLP in PRO curation [https://buffalo.box.com/s/ykzpfu5quyx44qr3fenoqqi45o084x3b Slides] | |||
: | :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 | :14:00 '''Roundtable on killer apps for PRO''' | ||
:16:00 Close | |||
---- | ---- | ||
| Line 111: | Line 104: | ||
== '''Participants''' == | == '''Participants''' == | ||
:Cecilia Arighi (Delaware / PRO) | *=online | ||
:Erich Baker (Baylor | :Cecilia Arighi (Delaware / PRO)* | ||
:Erich Baker (Baylor) | |||
:Judith Blake (JAX) | :Judith Blake (JAX) | ||
:Chuming Chen (Delaware)* | |||
:Elissa Chesler (JAX) | :Elissa Chesler (JAX) | ||
: | :Julie Cowart (Delaware)* | ||
: | :Mary Dolan (JAX) | ||
:Peter d'Eustachio (NYU)* | |||
:Alexander Diehl (Buffalo) | |||
:Harold Drabkin (JAX) | :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) | :Darren Natale (Georgetown) | ||
: | :Li Ni (JAX) | ||
: | :Karen Ross (Delaware)* | ||
:Alan Ruttenberg (Buffalo) | :Alan Ruttenberg (Buffalo) | ||
:Cynthia Smith (JAX) | :Cynthia Smith (JAX) | ||
Latest revision as of 19:49, 13 June 2019
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 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.
White Papers
Functional Annotation of Proteins
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 Slides
- 9:30 Susan Gregurick: NIH 2018 Priorities in Data Science and Computational Science Slides
PRO and Related Resources
- 9:45 Darren Natale: Implementation of the PRO Sites Ontology Slides
- 10:25 Karen Ross: PRO Collaborations (ProKinO, NeXtProt ...) Slides
- 10:45 Break
- 11:00 Erich Baker and Elissa Chesler: GeneWeaver Slides
- 11:30 Cindy Smith: Disease Ontology at MGI Slides
- 12:00 Kimberley VanAuken: Noctua and GO-CAM
Slides
- 12:30 Lunch
PRO and Disease
Chair: Darren Natale
- 13:30 Judith Blake: Alliance of Genome Resources Slides
- 14:00 Chris Mungall: An Update on OBO / MONARCH Slides
- 14:30 Barry Smith: How to define 'causally upstream of'
- 15:00 Break
- 15:15 Peter McGarvey: Genome Annotation, ClinGen and PRO Slides
- 15:45 Peter d'Eustachio: Reactome, PRO, GO, Phenotypes,
Complexes Slides
- 16:15 Alexander Diehl: Cells, Proteins, Antibodies and Diseases Slides
17:00 Discussion of the representation of PRO annotations
- Chair: Barry Smith
- Participants: Alan Ruttenberg and Darren Natale
- 18:00 Working dinner
Schedule: Thursday, October 12, 2017
GO, PRO and UniProt
Chair: Cathy Wu
- 8:45 Maria Martin: Representing UniProt
- 9:30 Chris Mungall: Representing GO
- 9:45 GO, PRO and UniProt: How will they work together
- 10:30 Break
- 10:45 Julie Cowart: Data Access and Writing SPARQL Queries Slides
- 11:15 Alan Ruttenberg: Discussion of how genes are referenced in OBO Foundry and in PRO: why do they differ?
- 11:45 Cecilia Arighi: The role of NLP in PRO curation Slides
- 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
Participants
*=online
- Cecilia Arighi (Delaware / PRO)*
- Erich Baker (Baylor)
- 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.
