PRO Consortium Workshop 2019

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Date: October 11-12, 2017

Venue: Atlantic Oceanside Hotel, Bar Harbor, MN


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

PRO Family Relations

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
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


Alexander Bateman*
Alexander Diehl
Cecilia Arighi (Delaware / PRO)
Judith Blake (JAX)
? Peter d'Eustachio (NYU)*
Alexander Diehl (Buffalo)
? Harold Drabkin (JAX)
Yongqun (Oliver) He (Michigan)
Darren Natale (Georgetown)
Alan Ruttenberg (Buffalo)
Barry Smith (Buffalo)
Cathy Wu (Delaware / PRO)
  • =online

Please contact Barry Smith for further information.


The Protein Ontology Consortium
National Center for Ontological Research