Basic Formal Ontology 2.0

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

VENUE for FACE-TO-FACE PARTICIPATION: Room14A, Basement, Baldy Hall, University at Buffalo North Campus, Amherst, NY.

Suggested hotels: [1]

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

• 9:00am The main principles underlying Basic Formal Ontology

What BFO is used for

Starting point for downward population

Annotation of scientific and administrative data

Storehouse of lessons learned

Basis for common training

Works best under the hood

BFO's competitors

DOLCE

SUMO

CYC

What BFO, DOLCE, SUMO, CYC have in common

Arguments in favor of using BFO

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

Realism: Compatibility with common sense and with science

Truthmaker

Non-multiplicative (the statue is the portion of clay during the time when the latter has a certain role)

Perspectivalism

No 'context'

No thoughts, beliefs, meanings, fictions

Relation to logic

Definitions, elucidations

FOL, CLIF, OWL

Relation to Qualitative Spatial Reasoning (rigid bodies occupy spatial regions)

• 10:30am Break

• 11:00pm Overview of BFO Architecture

The Ontological Square

Instances and universals

Dependent entities and independent entities

Continuants and occurrents

First class entities; ontological commitment

Different kinds of relations

Treatment of mass nouns

• 12:30 Lunch

• 13:30 New features of BFO 2.0

New treatment of Relations

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

Representation of boundaries

Regions

Material and immaterial entities

Three subtypes of material entity: objects, object aggregates, and fiat object parts

Object aggregates and the member_of relation, with an application to groups and organizations

Quality instances and how quality instances change over time

Lives and other histories

• 15:00 Break

• 15:30 Process profiles, rates, and process measurement data

• 17:00 Close

Sunday, August 19

• 9:00am BFO applied to disease

An overview of the Ontology for General Medical Science

• 10:30am Break

• 11:00am Creating a domain ontology by extending BFO

• 12:30am Lunch

• 1:00pm Formalization of BFO

Relations between the BFO specification, BFO FOL, BFO CLIF, and 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

• 2:30pm Break

• 3:00pm Concluding discussion

• 5:00pm 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 current draft version of the BFO 2.0 Specification is available here.

For further information please write to Barry Smith.