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| '''Introductory Session: The Landscape of the Protein Ontology''' | | '''Introductory Session: The Landscape of the Protein Ontology''' |
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| :8:45 Cathy Wu: Protein Ontology: Its current state and future development [https://buffalo.box.com/s/ahra2it1glmtsqm2e96yhgsp20u9jou3 Slides]
| | :9:00 C |
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| :9:30 Susan Gregurick: NIH 2018 Priorities in Data Science and Computational Science [https://buffalo.box.com/s/8002lr7syg8gf2blt6hyjg7q69ka63b7 Slides] | |
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| '''PRO and Related Resources'''
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| :9:45 Darren Natale: Implementation of the PRO Sites Ontology [https://buffalo.box.com/s/2an2i0wcfn7r3m5dld2q6tilr03oy0gg Slides]
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| :10:25 Karen Ross: PRO Collaborations (ProKinO, NeXtProt ...) [https://buffalo.box.com/s/zpicxbl4qj4b5y1o69bq3te8gkd8bakq Slides]
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| :10:45 Break
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| :11:00 Erich Baker and Elissa Chesler: GeneWeaver [https://buffalo.box.com/s/lglbejd3men722onm6m5xs1a5nsxmar4 Slides]
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| :11:30 Cindy Smith: Disease Ontology at MGI [https://buffalo.box.com/s/mc67ue7h306aimgdipf0l16yok4t2u5h Slides]
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| :12:00 Kimberley VanAuken: Noctua and GO-CAM
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| [https://buffalo.box.com/s/c855q50pges44czj6v6hro7rf2c8r6u1 Slides]
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| :12:30 Lunch
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| '''PRO and Disease'''
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| Chair: Darren Natale
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| :13:30 Judith Blake: Alliance of Genome Resources [https://buffalo.box.com/s/gu31c0z6vkgbd950tf4uft47zdd4ij6p Slides]
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| :14:00 Chris Mungall: An Update on OBO / MONARCH [https://buffalo.box.com/s/uppgc4r87jn80xcpn4etiu2th19wfyax Slides]
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| :14:30 Barry Smith: How to define 'causally upstream of'
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| :15:00 Break
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| :15:15 Peter McGarvey: Genome Annotation, ClinGen and PRO [https://buffalo.box.com/s/gu31c0z6vkgbd950tf4uft47zdd4ij6p Slides]
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| :15:45 Peter d'Eustachio: Reactome, PRO, GO, Phenotypes,
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| Complexes [https://buffalo.box.com/s/bo5yiutb082sp8qlc6egyh3o3aed6xwr Slides]
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| :16:15 Alexander Diehl: Cells, Proteins, Antibodies and Diseases [https://buffalo.box.com/s/xpjpn5kilahkvtt69gp4p7f28axewitm Slides]
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| 17:00 '''Discussion of the representation of PRO annotations'''
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| :Chair: Barry Smith
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| :Participants: Alan Ruttenberg and Darren Natale
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| :18:00 Working dinner | | :18:00 Working dinner |
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| Chair: Cathy Wu | | Chair: Cathy Wu |
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| :8:45 Maria Martin: Representing UniProt | | :8:45 |
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| :9:30 Chris Mungall: Representing GO
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| :9:45 GO, PRO and UniProt: How will they work together
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| :10:30 Break
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| :10:45 Julie Cowart: Data Access and Writing SPARQL Queries [https://buffalo.box.com/s/6u4ef8l0gjylwgsdbv5eb9ww4yhmkja2 Slides]
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| :11:15 Alan Ruttenberg: Discussion of how genes are referenced in OBO Foundry and in PRO: why do they differ?
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| :11:45 Cecilia Arighi: The role of NLP in PRO curation [https://buffalo.box.com/s/ykzpfu5quyx44qr3fenoqqi45o084x3b Slides]
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| :12:15 Lunch
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| 13:00 '''Discussion of how genes are referenced in OBO Foundry and in PRO: why do they differ?'''
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| :Chair: Barry Smith
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| :Participants: David Hill, Chris Mungall, Darren Natale, Alan Ruttenberg.
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| :14:00 '''Roundtable on killer apps for PRO'''
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| :16:00 Close | | :15:00 Close |
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| ---- | | ---- |
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 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
- 9:00 C
- 18:00 Working dinner
Schedule: Thursday, October 24, 2019
GO, PRO and UniProt
Chair: Cathy Wu
- 8:45
- 15:00 Close
Participants
- Alexander Bateman (EBI)*
- Alexander Diehl (Buffalo)
- Cecilia Arighi (Delaware / PRO)
- Judith Blake (JAX)
- Peter d'Eustachio (NYU)*
- Alexander Diehl (Buffalo)
- ? Harold Drabkin (JAX)
- Michelle Giglio (Baltimore)
- Yongqun (Oliver) He (Michigan)
- ? Neil Kelleher
- Birgit Meldal (EBI)*
- Darren Natale (Georgetown)
- Li Ni (JAX)
- Bjoern Peters (San Diego)
- ? Karen Ross (Delaware)
- Alan Ruttenberg (Buffalo)
- ?Stephan Schürer (Miami)
- Barry Smith (Buffalo)
- Cathy Wu (Delaware / PRO)
Please contact Barry Smith for further information.
- The Protein Ontology Consortium
- National Center for Ontological Research
