Relation Ontology 2018
Date: October 24-25, 2018
Venue: SpringHill Suites Denver at Anschutz Medical Campus, Aurora, CO
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
Teleconferences will be scheduled in conjunction with the OBO-Coordinators calls at noon to 1pm Eastern on the following dates:
- July 17
- July 31
- August 14
- August 28
- September 11
- September 25
- October 9
Dial-in details will be provided in due course.
All discussions will be documented here [2]. Email forum is here: [3]
Draft Schedule: Wednesday, October 24, 2018
- 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
- 10:15 Barry Smith: Strategy for improving RO
- 10:45 Break
- 11:00 Alan Ruttenberg: OWL, Relations and Time
- 11:30 Larry Hunter: Relation Ontology 2018: Cross-ontology harmonization and new use cases
- 12:00 Mike Bada: RO and the CRAFT Corpus
- 12:30 Lunch
- 13:30 Jim Ballhof: RO and GO
- 14:00 Cecilia Arighi: PRO/NLP and need for relations
- 14:30 Darren Natale: Relations in PRO
- 15:00 Break
- 15:15 Bjoern Peters: RO, RO Core, and RO Extended Core
- 16:00 Dividing into workgroups / sessions on different subtopics
- 18:00 Working dinner
Draft Schedule: Thursday, October 25, 2018
Thursday topics will be scheduled in the course of Wednesday discussions
- 9:00 TBD
- 10:30 Break
- 10:45 TBD
- 12:15 Lunch
- 13:00 TBD
- 16:00 Close
Participants will include:
- Cecilia Arighi (Delaware / PRO)
- Mike Bada (Denver)
- William Baumgartner (Denver)
- Judith Blake (JAX)
- Mayla Boguslav (Denver)
- Jonathan Bona (Arkansas)
- Matt Brush (Oregon)
- Peter d'Eustachio (NYU)
- Alexander Diehl (Buffalo)
- Robert Hoehndorf (KAUST)
- William Hogan (Florida)
- Larry Hunter (Denver)
- Suzanna Lewis (LBNL)
- Nicolas Matentzoglu (EBI)
- Chris Mungall (LBNL)
- Darren Natale (Georgetown)
- David Osumi-Sutherland (EBI / Cambridge)
- Alan Ruttenberg (Buffalo)
- Michael Sinclair (Utah)
- Barry Smith (Buffalo)
- Christian Stoeckert (Penn)
- Anne Thessen (Oregon)
- Cathy Wu (Delaware / PRO)
Please contact Barry Smith for further information.
Sponsors
- The Protein Ontology Consortium
- University of Colorado Knowledge-Based Biomedical Data Science Program
- National Center for Ontological Research
