Relation Ontology 2018

Date: October 24-25, 2018

Venue: Nighthorse Campbell Building (Wednesday), Health Sciences Library (Thursday)

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Hotel: SpringHill Suites Denver at Anschutz Medical Campus, Aurora, CO Link for SPECIAL HOTEL ROOM RATE

Background

The first Relation Ontology meeting, organized by Mike Bada, Larry Hunter, Chris Mungall and Barry Smith, was held in Denver in 2008. Through a series of preparatory phone calls and then the two day meeting in October, we propose to make progress on these issues. Your participation, including in defining the goals and tasks of the group, would be welcome.

This ten-year anniversary meeting is designed to draw on the lessons learned in the intervening years in order to review progress on the current RO and suggest a plan for the future. The meeting, organized by Larry Hunter, Chris Mungall and Barry Smith, is part of the series of meetings organized by the Protein Ontology Consortium. Groundwork for the meeting will be laid in a series of pre-meetings, both online and in the form of teleconferences.

Goals

The goals of this meeting are:

• 1. To review the current treatment of relations in the OBO Foundry: [1]

• 2. To establish a strategy to establish the Relation Ontology on a firmer footing, with a core, consisting of the relations used in a wide range of ontologies, and a well-curated collection of modules extending the core, wherever possible using standard ontology engineering techniques so that more complex relations are defined in terms of more primitive relations in the RO Core.

• 3. To harmonize the many alternative sets of relations used by various OBO ontologies.

• 4. To provide a set of paradigm RO use cases, for example:

providing a set of relations sufficient for expressing the relations among OBO terms denoted by statements in biomedical journal articles.

providing a set of relations sufficient for capturing the relations between PRO terms and terms in other OBO ontologies.

• 5. To clarify the procedures to be used when requesting a new relation to be added to RO, specifically as concerns use of definitions.

Pre-Meetings

Teleconference discussions held in advance of the meeting are documented here [2]. Email forum is here: [3]

Wednesday, October 24, 2018 - Nighthorse Campbell Building Room 204

9:00 Cathy Wu: Introduction

9:15 Chris Mungall, David Osumi Sutherland, James Overton: A basic introduction to RO

Underlying principles and organization

OWL axiomatization

Design Patterns

Overview of main areas

How to contribute

10:30 Break

10:45 Barry Smith: BFO-ISO and RO

11:15 Bjoern Peters: RO, RO Core, and RO Extended Core

11:45 Larry Hunter: RO grant ideas: NLP, Graph Learning and cross-ontology harmonization

12:00 Lunch. Informal discussions

13:00 Jim Ballhof: RO and GO (via Zoom, set up at 12:45)

13:30 RO and PRO

Darren Natale: Relations needed for sites Supporting Document

Cecilia Arighi: Relations used in PRO annotations

Alex Diehl: [4] Relations used in Antibody Ontology (AntiO)]

14:30 Break

14:45 Alan Ruttenberg: OWL, Relations and Time

15:15 Mike Bada: RO and Craft/text

15:30 Group Discussion (Larry Hunter, facilitator). Topics:

Organizational plan for two working breakout groups:

Immediate action

Longer term goals, governance and grant-writing

Self-selection into groups & balancing

Identifying dependencies (coordination planning)

Priority setting for groups on Thursday

17:00 Break and transportation to dinner

18:00 Working dinner at La Sandia Cantina

Thursday, October 25, 2018 - 3rd Floor Reading Room, Health Science Library

9:00 Larry Hunter: Summary of Day 1 discussion, charge to breakout groups

9:15 Breakout group meetings in Study Rooms, 3301 and 3302, in the Library (3rd floor)

10:30 Break

10:45 Breakout groups

11:45 Report on progress and issues (all together)

12:15 Lunch

13:00 Breakout groups

14:30 Break

14:45 Discussion and follow-up planning

17:00 (or earlier) Closing

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Participants

Cecilia Arighi (Delaware / PRO)

Mike Bada (Denver)

William Baumgartner (Denver)

Judith Blake (JAX)

Mayla Boguslav (Denver)

Jonathan Bona (Arkansas)

Peter d'Eustachio (NYU)

Alexander Diehl (Buffalo)

Robert Hoehndorf (KAUST)

William Hogan (Florida)

Larry Hunter (Denver)

Suzanna Lewis (LBNL)

Chris Mungall (LBNL)

Darren Natale (Georgetown)

James Overton (Knocean)

David Osumi-Sutherland (EBI / Cambridge)

Bjoern Peters (San Diego)

Alan Ruttenberg (Buffalo)

Barry Smith (Buffalo)

Christian Stoeckert (Penn)

Anne Thessen (Oregon)

Ramona Walls (Utah)

Elizabeth White (Denver)

Cathy Wu (Delaware / PRO)

Remotely:

Jim Ballhoff (Chapel Hill)

Nicolas Matentzoglu (EBI)

Fabian Neuhaus (Magdeburg)

Philippe Rocca-Sera (Oxford)

Sponsors

The Protein Ontology Consortium

University of Colorado Knowledge-Based Biomedical Data Science Program

National Center for Ontological Research