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
- How BFO is constructed and maintained
- Conservative evolution
- Simplicity (two levels)
- Strict formality (no overlap with domain ontologies)
- Asserted monohierarchy and inferred polyhierarchy
- Realism: Compatibility with common sense and with science
- 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
- Instances and universals
- Dependent entities and independent entities
- Continuants and occurrents
- 12:30 Lunch
- 13:30 New features of BFO 2.0
- 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.
- 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.
The current draft version of the BFO 2.0 Specification is available here.
For further information please write to Barry Smith.
