Basic Formal Ontology 2.0

DATE: Saturday and Sunday, August 18-19, 2012.

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IMPORTANT NOTE FOR INTENDING PARTICIPANTS

If you intend to participate in this tutorial and have not received an email with instructions please write to phismith@buffalo.edu immediately

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VENUE for FACE-TO-FACE PARTICIPATION: 141 Park Hall, University at Buffalo North Campus, Amherst, NY.

Suggested hotels: [1]

ONLINE PARTICIPATION: Instructions will for Webex participation will be sent by e-mail. The Webex sessions will be recorded and the recordings will be linked from this page.

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 new formalizations of BFO in first-order logic (FOL) and in OWL.

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

The current version of the BFO 2.0 OWL file is available here.

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

DRAFT SCHEDULE

Saturday, August 18

• 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 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

• 12:30 Lunch

• 13:30 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

Dispositions and the treatment of modality

First class entities; ontological commitment

Added in BFO 1.1

Generically and specifically dependent continuants, concretizations, and relations of dependence

• 15:00 Break

• 15:30 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

Add relation of concretization

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

Mutual dependence of qualities: The case of color

How quality instances change over time

Rigid and non-rigid universals

Universals and continuous change

• 17:00 Close of Day 1

Sunday, August 19

• 9:00 Process Profiles, Rates, and Process Measurement Data

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

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

Participants should have some background in ontology (including either philosophical or applied ontology). No specific knowledge of BFO is presupposed. This tutorial allows both face-to-face and on-line participation. Participation may be for credit (with an official university transcript), or the tutorial may be audited (with a certificate of completion if needed). The course will take place on the weekend of August 18-19, 2012, with follow-up meetings as necessary for those taking the course for credit.

Log-on/dial-in instructions for on-line participation will be provided by email to registered participants prior to the meeting.

FOR CREDIT

Participation in this tutorial will yield 1 credit hour; up to 3 further credit hours can be received through completion of a project under the guidance of an assigned faculty member. Projects must be completed before November 30, 2012.

Registration details for students taking this course for credit are available:

here, for face-to-face participation;

here, for on-line participation.

External (non-UB) participants who wish to take this course for credit, either on-line or through face-to-face participation, should use the links above and follow the procedures outlined here under 'Non-matriculated student'. External students will be able to apply credits from participation in this tutorial to the UB Masters and PhD Programs in Ontology, and also to the planned on-line UB Advanced Graduate Certificate Program in Ontology which is currently being established. Further details can be obtained from Barry Smith.

AUDITING

Auditing, both on-line and face-to-face, is free to registered participants. All those wishing to audit this tutorial should fill in the registration form provided here as soon as possible. A certificate of participation will be supplied on request, but auditing the course does not count for credit.

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 is a Principal Scientist at Science Commons and 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.