2013 BFO Meeting: Difference between revisions

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'''Date''': May 13-14, 2013.  
'''Date''': May 13-14, 2013.  


'''Starting and Ending Times''': The meeting will start with lunch at noon on May 13, and conclude with dinner on May 14.  
This meeting is co-located with the [http://wiki.plantontology.org/index.php/PRO-PO-GO_Meeting PRO-PO-GO] meeting, to be held on May 15-16, 2013.  


'''Day 1:''' The BFO 2.0 Specification;
== '''Goal''' ==


'''Day 2:''' BFO 2.0 OWL; specifically
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 treatment of time and relations in BFO 2.0 OWL.
::spatial relations.  


This meeting is co-located with the [http://wiki.plantontology.org/index.php/PRO-PO-GO_Meeting PRO-PO-GO] meeting, to be held on May 15-16, 2013.
== Schedule ==
 
<u>Monday, May 13, 2013</u>


'''Goals'''
11:30 Registration and Lunch 


The goal of the meeting is to finalize the BFO 2.0 specification and to resolve issues with BFO 2.0 OWL.
[https://ub.webex.com/ub/lsr.php?AT=pb&SP=MC&rID=23137982&rKey=31170c5a9077ab9e  Webex recording]


'''Draft Schedule'''
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


<u>Monday, May 13, 2013</u>
13:10 [http://ontology.buffalo.edu/bfo/2013/ Seppälä Making BFO categories explicit for increased user-friendliness] (Seppälä)


12:00 Lunch 
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]


12:30 The BFO 2.0 Specification
13:50 CHEBI's experience with BFO 2.0 (Hastings) [http://ontology.buffalo.edu/bfo/2013/chebi-and-bfo.pptx Slides]


:1. Brief introduction (Barry Smith)
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]
:2. Relation to BFO 2.0 Specification to BFO 2.0 FOL, CLIF and OWL
:3. Survey of current users of BFO 2.0


14:30 Break
14:30 Break


:4. Issues with the Specification, especially as concerns
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?
:*Use case: heavy smoker from Wisconsin
:[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


:*Process profiles
See also list [http://code.google.com/p/bfo/issues/list here]
:*BFO and IAO
 
:*Rigid vs. non-rigid types
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


:Issues with the BFO 2.0 OWL version
13:00 Issues with the BFO 2.0 OWL version


12:30 Lunch
[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]


13:00 Issues with the BFO 2.0 OWL version (continued)
[[Mungall paper]]


14:30 Break
14:30 Break


15:00 Issues with the BFO 2.0 OWL version (continued)
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
::fiat boundary
::holes
 
16:30 Plans to create a paper on BFO


16:30 Release strategy and plans to create a definitive paper on BFO 2.0
18:00 Dinner
 
== Background Reading ==


The current draft version of the BFO 2.0 Specification is available [http://bfo.googlecode.com/svn/trunk/docs/bfo2-reference/BFO2-Reference.docx here].  
The current draft version of the BFO 2.0 Specification is available [http://bfo.googlecode.com/svn/trunk/docs/bfo2-reference/BFO2-Reference.docx here].  
Line 63: Line 110:
For further information please write to [mailto:phismith@buffalo.edu Barry Smith] or see [http://www.ifomis.uni-saarland.de/bfo/ here].  
For further information please write to [mailto:phismith@buffalo.edu Barry Smith] or see [http://www.ifomis.uni-saarland.de/bfo/ here].  


----
For introductory reading see: Pierre Grenon and Barry Smith: "[http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf 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., “[http://genomebiology.com/2005/6/5/R46 Relations in Biomedical Ontologies]”, ''Genome Biology'' (2005), 6 (5), R46.
 
For discussion of core BFO issues see: Barry Smith and Werner Ceusters, “[http://iospress.metapress.com/content/1551884412214u67/fulltext.pdf Ontological Realism as a Methodology for Coordinated Evolution of Scientific Ontologies]”, ''Applied Ontology'', 5 (2010), 139–188.
 
The paper [http://ontology.buffalo.edu/smith/articles/Classifying_Processes.pdf here] contains some material pertaining to process profiles: “Classifying Processes: An Essay in Applied Ontology”, ''Ratio'', in press.
 
And the paper [http://ontology.buffalo.edu/smith/articles/Material_Entities.pdf 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)


== Participants will include ==
Jonathan Bona (Buffalo)


Matthias Brochhausen (Arkansas)
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 88: Line 157:


Fabian Neuhaus (NIST)
Fabian Neuhaus (NIST)
James Overton (Toronto)
Patrick Ray (Buffalo)
Ron Rudnicki (Buffalo)


Alan Ruttenberg (Buffalo)
Alan Ruttenberg (Buffalo)
Line 97: Line 172:
Barry Smith (Buffalo)
Barry Smith (Buffalo)


==Background Reading==
Dalia Varanka (USGS)
 
For introductory reading see: Pierre Grenon and Barry Smith: "[http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf 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., “[http://genomebiology.com/2005/6/5/R46 Relations in Biomedical Ontologies]”, ''Genome Biology'' (2005), 6 (5), R46.
Jie Zheng (Penn)
 
For discussion of core BFO issues see: Barry Smith and Werner Ceusters, “[http://iospress.metapress.com/content/1551884412214u67/fulltext.pdf Ontological Realism as a Methodology for Coordinated Evolution of Scientific Ontologies]”, ''Applied Ontology'', 5 (2010), 139–188.
 
The paper [http://ontology.buffalo.edu/smith/articles/Classifying_Processes.pdf here] contains some material pertaining to process profiles: “Classifying Processes: An Essay in Applied Ontology”, ''Ratio'', in press.
 
And the paper [http://ontology.buffalo.edu/smith/articles/Material_Entities.pdf 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.

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

Webex recording

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

Webex recording

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

Webex recording

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

Webex recording

  • 2. Temporally qualified continuants (Schulz)
slides
ontology
How I Learned to Stop Worrying and Love Temporally Qualified Continuants (Neuhaus) slides

Mungall paper

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)

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