Relation Ontology 2018: Difference between revisions
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::Darren Natale: '''[https://buffalo.box.com/s/8v6ja6uvxwtgflzkldeno4pdmv750vuq Relations needed for sites]''' [https://buffalo.box.com/s/mlqnm58pks4jlf7pduapl1c68modu4sv Supporting Document] | ::Darren Natale: '''[https://buffalo.box.com/s/8v6ja6uvxwtgflzkldeno4pdmv750vuq Relations needed for sites]''' [https://buffalo.box.com/s/mlqnm58pks4jlf7pduapl1c68modu4sv Supporting Document] | ||
::Cecilia Arighi: '''[https://buffalo.box.com/s/qa87d1ixds4on4smids4e2z22eedk2of Relations used in PRO annotations]''' | ::Cecilia Arighi: '''[https://buffalo.box.com/s/qa87d1ixds4on4smids4e2z22eedk2of Relations used in PRO annotations]''' | ||
::Alex Diehl: '''Relations used in Antibody Ontology (AntiO)''' | ::Alex Diehl: '''[https://buffalo.box.com/s/2q4z2odyarnowgrzeeli5kw8mu6prxeb Relations used in Antibody Ontology (AntiO)]''' | ||
:14:30 Break | :14:30 Break | ||
:14:45 Alan Ruttenberg: '''OWL, Relations and Time''' | :14:45 Alan Ruttenberg: '''[https://buffalo.box.com/s/ihcdleu3vzxm6x5vmx6eyrexhh7ysxbn OWL, Relations and Time]''' | ||
:15:15 Mike Bada: '''RO and | :15:15 Mike Bada: '''[https://buffalo.box.com/s/wkudhab787wzyrk4bgad19ioslj6hefz RO and CRAFT]''' | ||
:15:30 Group Discussion (Larry Hunter, facilitator). Topics: | :15:30 Group Discussion (Larry Hunter, facilitator). Topics: | ||
| Line 81: | Line 81: | ||
:9:00 Larry Hunter: Summary of Day 1 discussion, charge to breakout groups | :9:00 Larry Hunter: Summary of Day 1 discussion, charge to breakout groups | ||
:9:15 Breakout | :9:15 Breakout groups | ||
::Funding for RO | |||
::Site Ontology [https://buffalo.box.com/s/ns3f1vj3aebuq39h28e2a4b5xrbv6cj3 Summary of discussion] | |||
:10: | :10:15 Break | ||
:10: | :10:30 Breakout groups | ||
::FOL and time | |||
::PATO ''Quality'' [https://docs.google.com/document/d/1bEsj4lmZ_iAonH3JeNMG9iRSLtgeXEmR0s5SrYv1muY/edit Summary of discussion] | |||
:11: | :11:30 Report out and discussion | ||
:12: | :12:00 Lunch | ||
:13:00 | :13:00 OBO Core | ||
:14: | :14:00 Governance | ||
:14:45 Discussion and follow-up planning | :14:45 Discussion and follow-up planning | ||
== Participants == | == Participants == | ||
| Line 132: | Line 132: | ||
:Nicolas Matentzoglu (EBI) | :Nicolas Matentzoglu (EBI) | ||
:Fabian Neuhaus (Magdeburg) | :Fabian Neuhaus (Magdeburg) | ||
:Philippe Rocca-Sera (Oxford) | |||
== Sponsors == | == Sponsors == | ||
Latest revision as of 19:24, 25 October 2018
Date: October 24-25, 2018
Venue: Nighthorse Campbell Building (Wednesday), Health Sciences Library (Thursday)
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
- 13:30 RO and PRO
- Darren Natale: Relations needed for sites Supporting Document
- Cecilia Arighi: Relations used in PRO annotations
- Alex Diehl: Relations used in Antibody Ontology (AntiO)
- 14:30 Break
- 14:45 Alan Ruttenberg: OWL, Relations and Time
- 15:15 Mike Bada: RO and CRAFT
- 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
- Organizational plan for two working breakout groups:
- 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 groups
- Funding for RO
- Site Ontology Summary of discussion
- 10:15 Break
- 10:30 Breakout groups
- FOL and time
- PATO Quality Summary of discussion
- 11:30 Report out and discussion
- 12:00 Lunch
- 13:00 OBO Core
- 14:00 Governance
- 14:45 Discussion and follow-up planning
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
