Basic Formal Ontology 2.0

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/

SCHEDULE

• Smith slides

• Ruttenberg slides

Saturday, August 18

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

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

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.

FURTHER INFORMATION

Background information concerning BFO is available 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 (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.