PRO Consortium Workshop 2017

Date: October 11-12, 2017

Venue: Atlantic Oceanside Hotel, Bar Harbor, MN

Dial-in

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

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

11:30 Cindy Smith: The Alliance of Genome Resources

12:00 Kimberley VanAuken: Noctua

12:30 Lunch

PRO and Disease

Chair: Darren Natale

13:30 Judith Blake: Disease Ontology -- overview of available resources

14:00 Chris Mungall: An Update on OBO / MONARCH Slides

14:30 Elissa Chesler: MGI effort to combine variant data with disease forms; Genereader resource, PRO IDs for variants

15:00 Break

15:15 Peter McGarvey: Genome Annotation, ClinGen and PRO

15:45 Peter d'Eustachio: PRO and Reactome

16:15 Alexander Diehl: PRO, the Antibody Ontology and the Cell Ontology

• HIPC, cell populations, the Antibody Panel Ontology, Cell types vs. cell states -- when do combinations of protein markers

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: Enhanced SPARQL queries for PRO

11:45 Cecilia Arighi: The role of NLP in PRO curation

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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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.

Sponsors

The Protein Ontology Consortium

National Center for Ontological Research