Basic Formal Ontology 2.0

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Contents

BACKGROUND INFORMATION

BFO Website

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 (optional) philosophical 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.

The current draft version of the BFO 2.0 Specification is available here.

For further information please write to Barry Smith or see here.

FACULTY: Alan Ruttenberg and Barry Smith (University at Buffalo)

DESCRIPTION

Basic Formal Ontology is currently being used by over 100 ontology-based research projects in biomedical informatics and increasingly in other fields. The course will provide an introduction to the content and use of BFO in ontology development. Attendees will acquire knowledge of the ontology and of its use as top-level ontology in multiple ontology development projects in a variety of fields. They will learn about the most recent developments in the ontology and acquire basic knowledge of the draft version 2.0.

The current version of the draft Specification and User Guide for BFO 2.0 is available here.

The current version of the draft BFO 2.0 OWL file is available here. Please read the release notes

These links, and also further information concerning the draft BFO 2.0 release can be found at the BFO page here: http://code.google.com/p/bfo/

WORKSHOP, Buffalo, August 18-19, 2012

Schedule

Saturday, August 18, 2012

Streaming video

  • 9:00 The main principles underlying Basic Formal Ontology
What BFO is used for
BFO is an upper-level ontology
Ontological realism: an evidence-based strategy for ontology development
Starting point for downward population
Annotation of scientific and administrative data
Part storehouse of lessons learned, part QWERTY keyboard
Basis for common training
Works best under the hood
Brief history of BFO
Pre-History
Aristotle's Ontological Square
Edmund Husserl
Truthmakers
The Naive Physics Manifesto
Mereotopology
The Gene Ontology and the Foundational Model of Anatomy
BFO's competitors
DOLCE
SUMO
CYC
What BFO, DOLCE, SUMO, CYC have in common
Arguments in favor of using BFO
Important users of BFO
OBO Foundry
NIF Standard
OBI
IDO Consortium
Plant Ontology
Universal Core Semantic Layer
How BFO is constructed and maintained
Conservative evolution
Simplicity (two levels; no qualities of qualities)
Strict formality (no overlap with domain ontologies)
Asserted monohierarchy and inferred polyhierarchy
Truthmaker
Non-multiplicative (the statue is the portion of clay during the time when the latter has a certain role)
Perspectivalism
No reductionism, no phenomenalism
No 'context'
No meanings, fictions, non-existents
The Semiotic Triangle
No 'possible worlds'
No abstracta
How to deal with thoughts, beliefs, information artifacts
  • 10:30 Break
  • 11:00 Overview of BFO 1.0
Instances and universals
Continuants and occurrents
Dependent entities and independent entities
PATO qualities
Different kinds of relations
Symmetry, asymmetry and inverses
The all-some rule
What to do with probabilistic and other some-some relations?
Realizables
Roles
Dispositions and the treatment of modality
Functions
Added in BFO 1.1
Generically and specifically dependent continuants, concretizations, and relations of dependence
Information entities
  • 12:30 Lunch
  • 13:30 Introduction to OWL and to the Semantic Web (Alan Ruttenberg)
  • 15:00 Break
  • 15:30 Formalization of Basic Formal Ontology (Alan Ruttenberg)
Relations between the BFO Specification and BFO FOL, BFO CLIF, BFO OWL
BFO in First Order Logic
BFO in OWL
Applications of BFO in OWL
How to migrate from BFO 1.0 to BFO 2.0
The BFO 2.0 OWL temporalization strategy
  • 16:00 New Features of BFO 2.0
The BFO 2.0 Specification and Its Status
Relation to FOL and OWL realizations
Definitions and elucidations
New treatment of Relations
Incorporation of top-level relations into BFO 2.0
Focus primarily on instance-instance relations
Added relation of concretization
A musical work and its performance
Sites and regions
Representation of boundaries
Frames of reference; space, time and spacetime
SpaceR, TimeR and Spacetime
Material and immaterial entities
Three subtypes of material entity: objects, object aggregates, and fiat object parts
Continuant fiat boundaries
Coordinate systems and frames of reference
Object aggregates and the member_of relation, with an application to groups and organizations
Cognitive selection in the realm of continuants
Granularity on the side of continuants
Modeling and simulation
Map-based partitions of reality and the fiat entities they create
Map layers
Cadaster
Environments and ecology
Habitats, niches
Partitions of occurrent reality
Partition sequences
Partitions and plans (two sorts of direction of fit)


Sunday, August 19, 2012

Streaming video

  • 9:00 Process Profiles, Rates, and Process Measurement Data
Mutual dependence of qualities: The case of color
How quality instances change over time
Rigid and non-rigid universals
Universals and continuous change
Complete and partial processses
Lives and other histories
A top is spinning and simultaneously warming up
Process profiles as targets of process measurements
The Wiggers diagram
Cognitive selection
Quality process profiles
What did your temperature do since last night?
Rate process profiles
Relation to object aggregates
Other quantitative process profiles
Process profiles and time-series graphs
  • 10:30 Break
  • 11:00 Qualitative process profiles, granularity and the partitioning of reality
Map-based partitions of occurrent reality and the fiat entities they create
Weather
Granularity on the side of occurrents
Journalism, history
Napoleon's March to Moscow
Many map-based fiat entities existed trillions of years before the technology of maps
Music
Focusing on the cello part when you listen to a string quartet
Dance
Planning
Chess
Football
Experiments and experimental protocols
Language
Speech acts
Zeno Vendler
Accomplishments: processes which have an endpoint and are incremental or gradual (paint a picture, build a house)
Achievements: occur instantaneously (recognize, notice)
Basic Actions
  • 12:00 Lunch
  • 13:00 BFO Applied to Disease Slides
Creating a domain ontology by extending BFO
An overview of the Ontology for General Medical Science
Disease courses are process profiles
Occurrent symptoms are process profiles
  • 14:30 Break
  • 15:00 Concluding Discussion
  • 17:00 Close

Participation details: BFO 2.0 Meeting August 18-19, 2012

See also program of workshop in Buffalo on May 13-14, 2013

FACULTY

Barry Smith is a prominent contributor to both theoretical and applied research in ontology. He is the author of some 500 publications, and his research has been funded by the National Institutes of Health, the US, Swiss and Austrian National Science Foundations, the US Department of Defense, the Volkswagen Foundation, and the European Union. In 2010 he was awarded the first Paolo Bozzi Prize in Ontology by the University of Turin. Smith is one of the principal scientists of the NIH National Center for Biomedical Ontology, a Scientific Advisor to the Gene Ontology Consortium, and a PI on the Protein Ontology and Infectious Disease Ontology projects. He has organized over 100 ontology conferences, workshops and tutorials.

Alan Ruttenberg was a Principal Scientist at Creative Commons for 5 years and is now the Director of the University at Buffalo Clinical and Translational Data Exchange. His project, the Neurocommons, prototypes the use of Semantic Web technology for integrating and querying biomedical knowledge, working on structuring and using biological and clinical knowledge to answer questions and computationally interpret experimental data. He is a Coordinating Editor of the OBO Foundry and a former chair of the OWL Working Group.

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