2013 BFO Meeting

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) [1]

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) [2]

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

[https://ub.webex.com/ub/lsr.php?AT=pb&SP=MC&rID=23147017&rKey=9260a30a3fa2a128

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

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)