Relation Ontology 2018: Difference between revisions

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'''Date''': October 24-25, 2018
'''Date''': October 24-25, 2018


'''Venue''': SpringHill Suites Denver at Anschutz Medical Campus, Aurora, CO
'''Venue''': [https://www.google.com/maps?q=nighthorse+campbell+building&rlz=1C1CHBF_enUS799US799&um=1&ie=UTF-8&sa=X&ved=0ahUKEwjjo6W2sZreAhULWqwKHQ2UBxIQ_AUIDigB Nighthorse Campbell Building] (Wednesday), [https://goo.gl/maps/9wgNyaeezav Health Sciences Library] (Thursday)
 
'''Map''' [https://www1.ucdenver.edu/maps/cu-anschutz-map Anschutz Campus Map]
 
'''Hotel: SpringHill Suites Denver at Anschutz Medical Campus, Aurora, CO [https://www.marriott.com/meeting-event-hotels/group-corporate-travel/groupCorp.mi?resLinkData=Relation%20Ontology%5EDENAF%60REOREOA%60154.00%60USD%60false%604%6010/23/18%6010/25/18%609/23/18&app=resvlink&stop_mobi=yes Link for SPECIAL HOTEL ROOM RATE]


==Background==
==Background==


The first [https://www.bioontology.org/wiki/index.php/OntologyRelations Relation Ontology meeting], organized by Mike Bada, Chris Mungall and Barry Smith, was held in Denver in 2008. Since then the Relation Ontology has languished. Different ontology developers and users employ locally curated relations that are not harmonized across ontologies. The result is inconsistency and failure of comparability, causing serious problems for example in the logical definitions of terms. There are differences of opinion about whether relations (or some relations, especially parthood) should be temporally scoped. There are other issues that arise in various communities of use (e.g. PRO, Monarch, text miners). 
The first [https://www.bioontology.org/wiki/index.php/OntologyRelations 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.
 
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 create a core Relation Ontology with a firm logical foundation that will enjoy widespread acceptance. The meeting, organized by Larry Hunter 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. Those wishing to participate in these pre-meetings and/or in the face-to-face meeting in Denver should contact [mailto:phismith@buffalo.edu Barry Smith].
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 [http://www.obofoundry.org/ontology/ro.html 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==
==Goals==


The goals of this meeting are:
The goals of this meeting are:
*1. To review the current treatment of relations in the OBO Foundry and 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 the technology of short-cut relations.
*1. To review the current treatment of relations in the OBO Foundry: [https://raw.githubusercontent.com/oborel/obo-relations/v2018-09-25-PRELEASE/src/ontology/ro.owl]
*2. To explore use cases for the Relation Ontology, with special attention to relations within the PRO and between PRO and other ontologies.
 
*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 [http://purl.obolibrary.org/obo/ro/core.owl 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 [https://docs.google.com/document/d/19dhzj5QoliQZQgDJRczI878rLtexzMDo1g0K9_LRUWk/edit]. Email forum is here: [http://groups.google.com/group/obo-relations]
 
==Wednesday, October 24, 2018 - Nighthorse Campbell Building Room 204==
 
:9:00 Cathy Wu: '''Introduction'''
 
:9:15 [https://buffalo.box.com/s/6w7ez4t2pghrke3xmc2cgw5jnfm7b2ni 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


==Schedule: Wednesday, October 24, 2018==
:10:30 Break


'''Introductory Session'''
:10:45 Barry Smith: '''[https://buffalo.box.com/s/2vqdjucvw1tqiyfx32313ah5snxshati BFO-ISO and RO]'''


:9:00 TBD
:11:15 Bjoern Peters: '''[https://buffalo.box.com/s/onmaxovv3ttvt1xbxvy3ebuq8m2kqi2p RO, RO Core, and RO Extended Core]'''


:10:45 Break
:11:45 Larry Hunter: '''[https://buffalo.box.com/s/299cjccbrpgoxfhpas92fod5qzfxzciz RO grant ideas: NLP, Graph Learning and cross-ontology harmonization]'''


:11:00 TBD
:12:00 Lunch. Informal discussions


:12:30 Lunch
:13:00 Jim Ballhof: '''[https://buffalo.box.com/s/spp9iam2zjoe0hmxjur5fvlyssvp56vl RO and GO]''' (via [https://georgetown.zoom.us/j/977844453 Zoom], set up at 12:45)


'''TBD'''
:13:30 '''RO and PRO'''
::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]'''
::Alex Diehl: '''[https://buffalo.box.com/s/2q4z2odyarnowgrzeeli5kw8mu6prxeb Relations used in Antibody Ontology (AntiO)]'''  


Chair:  
:14:30 Break


:13:30 TBD
:14:45 Alan Ruttenberg: '''[https://buffalo.box.com/s/ihcdleu3vzxm6x5vmx6eyrexhh7ysxbn OWL, Relations and Time]'''


:15:00 Break
:15:15 Mike Bada: '''[https://buffalo.box.com/s/wkudhab787wzyrk4bgad19ioslj6hefz RO and CRAFT]'''


:15:15 TBD
: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
:18:00 Working dinner at [https://www.eatlasandia.com/denver/ La Sandia Cantina]


==Schedule: Thursday, October 25, 2018==
==Thursday, October 25, 2018 - 3rd Floor Reading Room, [https://goo.gl/maps/9wgNyaeezav Health Science Library] ==


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


Chair:  
:9:15 Breakout groups
::Funding for RO
::Site Ontology [https://buffalo.box.com/s/ns3f1vj3aebuq39h28e2a4b5xrbv6cj3 Summary of discussion]


:9:00 TBD
:10:15 Break


:10:30 Break
:10:30 Breakout groups
::FOL and time
::PATO ''Quality'' [https://docs.google.com/document/d/1bEsj4lmZ_iAonH3JeNMG9iRSLtgeXEmR0s5SrYv1muY/edit Summary of discussion]


:10:45 TBD
:11:30 Report out and discussion


:12:15 Lunch
:12:00 Lunch


13:00 TBD
:13:00 OBO Core


:16:00 Close
:14:00 Governance


----
:14:45 Discussion and follow-up planning


== '''Participants''' ==
== Participants ==


:Cecilia Arighi (Delaware / PRO)
:Cecilia Arighi (Delaware / PRO)
:Mike Bada (Denver)
:William Baumgartner (Denver)
:Judith Blake (JAX)
:Judith Blake (JAX)
:Chuming Chen (Delaware)?
:Mayla Boguslav (Denver)
:Julie Cowart (Delaware)?
:Jonathan Bona (Arkansas)
:Dahdul Wasila (USD)
:Peter d'Eustachio (NYU)
:Peter d'Eustachio (NYU)?
:Alexander Diehl (Buffalo)
:Alexander Diehl (Buffalo)
:Harold Drabkin (JAX)?
:David Hill (JAX)?
:William Hogan (Gainesville)
:Robert Hoehndorf (KAUST)
:Robert Hoehndorf (KAUST)
:William Hogan (Florida)
:Larry Hunter (Denver)
:Larry Hunter (Denver)
:Suzanna Lewis (LBNL)
:Chris Mungall (LBNL)
:Chris Mungall (LBNL)
:Darren Natale (Georgetown)
:Darren Natale (Georgetown)
:Li Ni (JAX)?
:James Overton (Knocean)
:Karen Ross (Delaware)?
:David Osumi-Sutherland (EBI / Cambridge)
:Alan Ruttenberg (Buffalo)
:Bjoern Peters (San Diego)
:Cynthia Smith (JAX)
:Alan Ruttenberg (Buffalo)  
:Barry Smith (Buffalo)  
:Barry Smith (Buffalo)  
:Kimberley VanAuken (CalTech)?
:Christian Stoeckert (Penn)
:Laurens Wilming (JAX)?
:Anne Thessen (Oregon)
:Ramona Walls (Utah)
:Elizabeth White (Denver)
:Cathy Wu (Delaware / PRO)
:Cathy Wu (Delaware / PRO)


Please contact [mailto:phismith@buffalo.edu Barry Smith] for further information.
Remotely:
:Jim Ballhoff (Chapel Hill)
:Nicolas Matentzoglu (EBI)
:Fabian Neuhaus (Magdeburg)
:Philippe Rocca-Sera (Oxford)


== '''Sponsors''' ==
== Sponsors ==
   
   
:[http://pir.georgetown.edu/pro/ The Protein Ontology Consortium]
:[http://pir.georgetown.edu/pro/ The Protein Ontology Consortium]
:University of Colorado Knowledge-Based Biomedical Data Science Program
:[http://ncor.buffalo.edu National Center for Ontological Research]
:[http://ncor.buffalo.edu National Center for Ontological Research]

Latest revision as of 19:24, 25 October 2018

Date: October 24-25, 2018

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

Map Anschutz Campus Map

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: 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
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
Retrieved from "https://ncorwiki.buffalo.edu/index.php?title=Relation_Ontology_2018&oldid=70488"