2013 BFO Meeting: Difference between revisions
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The goal of the meeting is to assess the current state of the BFO 2.0 Specification and to consider proposals regarding BFO 2.0 OWL. As the OWL working group formally decided not to meet at this time, work on BFO 2.0 OWL will contribute to subsequent meetings of this group, but decisions that require vote will not be taken. | The goal of the meeting is to assess the current state of the BFO 2.0 Specification and to consider proposals regarding BFO 2.0 OWL. As the OWL working group formally decided not to meet at this time, work on BFO 2.0 OWL will contribute to subsequent meetings of this group, but decisions that require vote will not be taken. | ||
== | == Schedule == | ||
<u>Monday, May 13, 2013</u> | <u>Monday, May 13, 2013</u> | ||
11:30 Registration | 11:30 Registration and Lunch | ||
[https://ub.webex.com/ub/lsr.php?AT=pb&SP=MC&rID=23137982&rKey=31170c5a9077ab9e Webex recording] | |||
12:30 | 12:30 BFO 2.0 Brief introduction (Smith) [http://ontology.buffalo.edu/bfo/2013/BFO-2-Smith.ppt Slides] | ||
:Examples of new ontologies based on BFO | |||
:[http://ncor.buffalo.edu/ontologies/AIRS_Ontologies.pdf Actionable Intelligence Retrieval System (AIRS)] | |||
:[http://financialreportontology.wikispaces.com/ Financial Report Ontology] (FRO) | |||
:[https://code.google.com/p/mental-functioning-ontology/ Mental Functioning Ontology] (MFO), [http://code.google.com/p/emotion-ontology Emotion Ontology] (MFO-EM) | |||
:[http://wiki.plantontology.org/index.php/The_cROP_(Common_Reference_Ontologies_for_Plants)_Initiative Common Reference Ontologies for Plants] (cROP) | |||
:*BFO under the hood | |||
:*Use case: Tachycardia | |||
: | 13:10 [http://ontology.buffalo.edu/bfo/2013/ Seppälä Making BFO categories explicit for increased user-friendliness] (Seppälä) | ||
: | |||
: | 13:30 Report on semi-automatic conversion of BFO from v1.1 to v2.0 (Zheng) [http://ontology.buffalo.edu/bfo/2013/BFOconverter.pptx Slides] | ||
13:50 CHEBI's experience with BFO 2.0 (Hastings) [http://ontology.buffalo.edu/bfo/2013/chebi-and-bfo.pptx Slides] | |||
14:10 Experiences with BFO 2.0 in developing the [https://code.google.com/p/neurological-disease-ontology/ Neurological Disease Ontology] (Cox, Diehl, Jensen) [http://ontology.buffalo.edu/bfo/2013/ ND-and-BFO.pptx] | |||
14:30 Break | 14:30 Break | ||
: | 15:00 Issues | ||
[https://ub.webex.com/ub/lsr.php?AT=pb&SP=MC&rID=23137992&rKey=e113d98e24615a11 Webex recording] | |||
:* | :Process profiles | ||
:* | :Rigid vs. non-rigid types | ||
:* | :*Can this be applied also to occurrent types? | ||
:* | :Which general terms refer to universals? | ||
:*BFO and range of IAO:aboutness | :*Use case: heavy smoker from Wisconsin | ||
:See also list [http://code.google.com/p/bfo/issues/list here] | :[https://code.google.com/p/bfo/issues/detail?id=1 Qualities with values] | ||
:*1 Logical distinction between determinable and determinate quality types | |||
:*2 Representation of qualities with values in OWL. | |||
:Granularity | |||
:*Grains | |||
:*Aggregates | |||
:Object aggregates vs. sets | |||
:Exists-at-t | |||
:*"blood specimen collected at 4:30 pm on May 1st, 2011" | |||
:*need for frames of reference for spatial regions and temporal intervals | |||
:BFO and range of IAO:aboutness | |||
:Using 'Domain' and 'Range' to describe ternary temporal relations is confusing or wrong | |||
See also list [http://code.google.com/p/bfo/issues/list here] | |||
17:00 Addressing the Ontology Needs of the United States Geological Survey (Dalia Varanka) [http://ontology.buffalo.edu/bfo/2013/BFOandUSGS.pptx] | |||
18:00 Dinner | 18:00 Dinner | ||
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<u>Tuesday, May 14, 2013</u> | <u>Tuesday, May 14, 2013</u> | ||
9:00 [http://ontology.buffalo.edu/bfo/FOL BFO 2.0 FOL] | 9:00 [http://ontology.buffalo.edu/bfo/FOL BFO 2.0 FOL] (Dipert) [http://ontology.buffalo.edu/bfo/2013/Dipert-FOL.pptx Slides] | ||
[https://ub.webex.com/ub/lsr.php?AT=pb&SP=MC&rID=23147007&rKey=1fa9337a26ca70b6 Webex recording] | |||
10:30 Break | 10:30 Break | ||
11:00 BFO 2.0 OWL | 11:00 Issues with the BFO 2.0 OWL version | ||
*1. Temporalized Relations (Ruttenberg) | |||
: | 12:30 Lunch | ||
: | 13:00 Issues with the BFO 2.0 OWL version | ||
: | [https://ub.webex.com/ub/lsr.php?AT=pb&SP=MC&rID=23147017&rKey=9260a30a3fa2a128 Webex recording] | ||
*2. Temporally qualified continuants (Schulz) | |||
:[http://ontology.buffalo.edu/bfo/2013/Schulz.pptx slides] | |||
:[http://ontology.buffalo.edu/bfo/2013/tqc3.owl ontology] | |||
:How I Learned to Stop Worrying and Love Temporally Qualified Continuants (Neuhaus) [http://ontology.buffalo.edu/bfo/2013/Neuhaus.pdf slides] | |||
[[Mungall paper]] | |||
14:30 Break | 14:30 Break | ||
15:00 | 15:00 Spatial Relations | ||
: | :Space, Time and Spacetime (Bittner) [http://ontology.buffalo.edu/bfo/2013/Bittner.pdf slides] | ||
:Relations between site, material entity, and history (Smith) [http://ontology.buffalo.edu/bfo/2013/Space-Time-BFO.pptx Slides] | |||
:BFO and anatomy | |||
::location | ::location | ||
::fiat boundary | ::fiat boundary | ||
| Line 84: | Line 121: | ||
== Participants == | == Participants == | ||
Thomas Bittner (Buffalo) | |||
Judith Blake (Jackson Lab) | Judith Blake (Jackson Lab) | ||
Jonathan Bona (Buffalo) | |||
Mathias Brochhausen (Arkansas) | |||
Werner Ceusters (Buffalo) | Werner Ceusters (Buffalo) | ||
Alexander Cox (Buffalo) | Alexander Cox (Buffalo) | ||
Alex Diehl (Buffalo) | |||
Randall Dipert (Buffalo) | Randall Dipert (Buffalo) | ||
Bill Duncan (Buffalo) | |||
Louis Goldberg (Buffalo) | |||
Janna Hastings (EBI / Geneva) | Janna Hastings (EBI / Geneva) | ||
Amanda Hicks (Arkansas) | |||
William Hogan (Arkansas) | William Hogan (Arkansas) | ||
| Line 108: | Line 157: | ||
Fabian Neuhaus (NIST) | Fabian Neuhaus (NIST) | ||
James Overton (Toronto) | |||
Patrick Ray (Buffalo) | |||
Ron Rudnicki (Buffalo) | |||
Alan Ruttenberg (Buffalo) | Alan Ruttenberg (Buffalo) | ||
| Line 116: | Line 171: | ||
Barry Smith (Buffalo) | Barry Smith (Buffalo) | ||
Dalia Varanka (USGS) | |||
Jie Zheng (Penn) | |||
Latest revision as of 11:53, 16 May 2013
Venue: Ramada Inn, Amherst, NY 14051
Date: May 13-14, 2013.
This meeting is co-located with the PRO-PO-GO meeting, to be held on May 15-16, 2013.
Goal
The goal of the meeting is to assess the current state of the BFO 2.0 Specification and to consider proposals regarding BFO 2.0 OWL. As the OWL working group formally decided not to meet at this time, work on BFO 2.0 OWL will contribute to subsequent meetings of this group, but decisions that require vote will not be taken.
Schedule
Monday, May 13, 2013
11:30 Registration and Lunch
12:30 BFO 2.0 Brief introduction (Smith) Slides
- Examples of new ontologies based on BFO
- Actionable Intelligence Retrieval System (AIRS)
- Financial Report Ontology (FRO)
- Mental Functioning Ontology (MFO), Emotion Ontology (MFO-EM)
- Common Reference Ontologies for Plants (cROP)
- BFO under the hood
- Use case: Tachycardia
13:10 Seppälä Making BFO categories explicit for increased user-friendliness (Seppälä)
13:30 Report on semi-automatic conversion of BFO from v1.1 to v2.0 (Zheng) Slides
13:50 CHEBI's experience with BFO 2.0 (Hastings) Slides
14:10 Experiences with BFO 2.0 in developing the Neurological Disease Ontology (Cox, Diehl, Jensen) ND-and-BFO.pptx
14:30 Break
15:00 Issues
- Process profiles
- Rigid vs. non-rigid types
- Can this be applied also to occurrent types?
- Which general terms refer to universals?
- Use case: heavy smoker from Wisconsin
- Qualities with values
- 1 Logical distinction between determinable and determinate quality types
- 2 Representation of qualities with values in OWL.
- Granularity
- Grains
- Aggregates
- Object aggregates vs. sets
- Exists-at-t
- "blood specimen collected at 4:30 pm on May 1st, 2011"
- need for frames of reference for spatial regions and temporal intervals
- BFO and range of IAO:aboutness
- Using 'Domain' and 'Range' to describe ternary temporal relations is confusing or wrong
See also list here
17:00 Addressing the Ontology Needs of the United States Geological Survey (Dalia Varanka) [1]
18:00 Dinner
Tuesday, May 14, 2013
9:00 BFO 2.0 FOL (Dipert) Slides
10:30 Break
11:00 Issues with the BFO 2.0 OWL version
- 1. Temporalized Relations (Ruttenberg)
12:30 Lunch
13:00 Issues with the BFO 2.0 OWL version
- 2. Temporally qualified continuants (Schulz)
- How I Learned to Stop Worrying and Love Temporally Qualified Continuants (Neuhaus) slides
14:30 Break
15:00 Spatial Relations
- Space, Time and Spacetime (Bittner) slides
- Relations between site, material entity, and history (Smith) Slides
- BFO and anatomy
- location
- fiat boundary
- holes
16:30 Plans to create a paper on BFO
18:00 Dinner
Background Reading
The current draft version of the BFO 2.0 Specification is available here.
For further information please write to Barry Smith or see here.
For introductory reading see: Pierre Grenon and Barry Smith: "SNAP and SPAN: Towards Dynamic Spatial Ontology", Spatial Cognition and Computation, 4 (2004), 69-103.
For introductory reading on relations see: Barry Smith, Werner Ceusters, et al., “Relations in Biomedical Ontologies”, Genome Biology (2005), 6 (5), R46.
For discussion of core BFO issues see: Barry Smith and Werner Ceusters, “Ontological Realism as a Methodology for Coordinated Evolution of Scientific Ontologies”, Applied Ontology, 5 (2010), 139–188.
The paper here contains some material pertaining to process profiles: “Classifying Processes: An Essay in Applied Ontology”, Ratio, in press.
And the paper here contains material on the proposed BFO 2.0 classification of objects: “On Classifying Material Entities in Basic Formal Ontology”, in Interdisciplinary Ontology. Proceedings of the Third Interdisciplinary Ontology Meeting, Tokyo: Keio University Press, 2012, 1-13.
Participants
Thomas Bittner (Buffalo)
Judith Blake (Jackson Lab)
Jonathan Bona (Buffalo)
Mathias Brochhausen (Arkansas)
Werner Ceusters (Buffalo)
Alexander Cox (Buffalo)
Alex Diehl (Buffalo)
Randall Dipert (Buffalo)
Bill Duncan (Buffalo)
Louis Goldberg (Buffalo)
Janna Hastings (EBI / Geneva)
Amanda Hicks (Arkansas)
William Hogan (Arkansas)
Leonard Jacuzzo (Buffalo)
Mark Jensen (Buffalo)
Tatiana Malyuta (CUNY)
Darren Natale (Georgetown)
Fabian Neuhaus (NIST)
James Overton (Toronto)
Patrick Ray (Buffalo)
Ron Rudnicki (Buffalo)
Alan Ruttenberg (Buffalo)
Stefan Schulz (Medical University of Graz)
Selja Seppälä (Buffalo)
Barry Smith (Buffalo)
Dalia Varanka (USGS)
Jie Zheng (Penn)
