Introduction to Basic Formal Ontology: Fall 2026

PHI 598 Introduction to Basic Formal Ontology

Fall 2026

Faculty: Dr. Barry Smith

ONLINE, ASYNCHRONOUS, THREE CREDIT COURSE

This course will introduce students to Basic Formal Ontology (BFO), a top-level ISO standard ontology framework that serves as a shared, reusable foundation for domain ontologies in biomedical, scientific, industrial and government domains. It will cover the BFO framework's core distinctions and explore how BFO functions as the upper-level backbone for major ontologies in the Open Biomedical Ontologies (OBO) Foundry, the Industrial Ontologies Foundry (IOF) and the National Security Ontologies Foundry (NSOF). All of these use BFO as a basis for representing real-world domains in a rigorous and interoperable way. It will also address the philosophical underpinnings of BFO's realist approach, its formal axiomatization in OWL and FOL, and practical skills for building and evaluating ontologies aligned with the BFO hierarchy. In this way it will prepare students to contribute to large-scale, cross-domain knowledge integration projects in science, medicine, and beyond.

The courae will be built around a series of videos in week-by-week order as listed below.

Students will find further treatment of many of the issues addressed in the videos in the BFO textbook, which is listed under Background Reading below.

In addition students will be provided with data and documents relating to the uses and the wider reception of BFO. These materials are to be used to prepare an essay, a pointpoint presentation and a youtube vide, addressing issues relating to BFO's use and reception. Guidance will be provided by Dr Smith in the course of the semester, along with feedback on successive drafts of the paper and presentation.

Week 2: Basic Formal Ontology 101

This is an introduction to building ontologies with BFO, with special reference to the rules for deciding whether a given general term designates a universal.

Week 3: BFO Tutorial (2019): A Series of 6 Videos

This is a survey of main features of BFO itself in the form of a series of short tutorials. It deals with BFO 2.0, which differs slightly from BFO 2020, which is the most current version. However the differences relate not to BFO itself, but rather to the new First Order Logic axiomatization of BFO, which was introduced with the ISO standard. Details (for those who are interested in such matters) can be found here: https://ncorwiki.buffalo.edu/index.php/BFO_Release_History.

Week 4: Basic Formal Ontology Tutorial

This is a presentation to an audience of engineers at a meeting of the Industrial Ontologies Foundry. It contains examples of what happens when people argue about BFO. BFO is a realist ontology, which means that all terms of BFO are intended to refer to something that exist. How, then, do we provide a BFO-conformant treatment of the work of an industrial designer, at the point where the object he is designing does not yet exist?

Week 5: The Ontology of Science

Focuses on the Focuses on the ontology of biology, and on the issue of multi-level ontology -- from molecules to cells to organisms, and from functions at the molecular level to downstream biological processes. BFO claims to be a multi-perspectival ontology, and in particular a multi-granularity ontology, which can work on each of these levels.

Wednesday, February 25, 7-8pm: Team meeting

BFO does not contain terms relating to information entities such as words or mathematical equations or poems. Instead it draws on the category of generically dependent continuants (GDCs), which then forms the starting point of the Information Artifact Ontology. Information artifacts are GDCs which are about something.

Week 7: Ontology of Terrorism

Acts of terrorism are often described in terms of "sending a message" (for example to a government) through violence or threats of violence. We present the beginnings of an ontology of terrorism on this basis, drawing on the theory of speech acts but also on a more general theory of language according to which a language is a set of capabilities associated with a set of behaviors.

Week 8: Capabilities (2022);

The first of these two videos proposes a definition of capability as a universal falling between function and disposition as the latter are defined in Basic Formal Ontology (BFO). Capabilities are like functions in that they can be evaluated on the basis of how well they are realized. They differ from functions in that they are not the rationale for the existence of their bearers. Thus, a water pump may have, in addition to its function of pumping water, many capabilities including: to be weatherproof, to run without lubricant, and so forth. We argue, that all functions are capabilities, but not all capabilities are functions, and we develop a series of axioms to distinguish capabilities formally from both dispositions and functions. We provide examples of the use of capability in a variety of domains, focusing on a definition of language as a capability of persons.

==Week 9: BFO and DOLCE

How BFO functions as a support for its users.

Week 10: Relatively isolated systems

Ingarden's work on ontology is one of the principal sources motivating the creation of BFO. We here present Ingarden's work on systems of different types.

Week 11: ISO/IEC 21838

This is the top-level ontology / BFO standard

Week 12: JOWO Part 1, Part 2, Temporalized Relations

Begins with a 2-part video of a tutorial presented at the JOWO (Joint Ontologies Workshops). Part 1 introduces BFO to a technical audience. Part 2 provides a brief exposition of the rationale for including temporalized relations in the OWL specification of BFO 2020 (ISO/IEC 21838:2). Since OWL can accommodate only two-place relations, and since the de facto standard formalization of BFO uses OWL, there is a need for strategies to capture the temporal dimensions of general assertions such as "Milk teeth are lost as children grow" or "Thermally heated machines are inspected every 6 months." The third video provides an attempt at a simplified exposition of the issues involved.

Grading

Students will be graded on the basis of essay and powerpoint presentation

Background reading

ISO standard

Grokipedia on Basic Formal Ontology

Awesome BFO

[1] R. Arp, B. Smith, A. Spear, Building Ontologies with Basic Formal Ontology, Cambridge MA: MIT Press (2015).

[2] Jansen, Ludger, and Barry Smith. "Categories in Top-Level Ontologies: Revisiting the Aristotelian Background," Advances in Knowledge Representation, 5(3) (2025).

[3] Peter M. Simons, "Against Set Theory", in: Experience and Analysis, Vienna: HPT&ÖBV, 143-152 (2005).

[4] Barry Smith, "Beyond concepts: ontology as reality representation," in: Proceedings of the Third International Conference on Formal Ontology in Information Systems (FOIS 2004), 73-84. Amsterdam: IOS Press, 2004.

Supplementary Videos

#	Video Title	Duration	YouTube Link
1	The Ontology of (Supply Chain) Services	11:35	https://www.youtube.com/watch?v=F1Zlunh3eMw
2	Industrial Ontologies Foundry (2022)	7:52	https://www.youtube.com/watch?v=1pfsimHTApU remember to use Closed Captions
3	Ontology of (Social) Services	10:38	https://www.youtube.com/watch?v=9qrwWAISrC8
4	Ontology Foundries	20:51	https://www.youtube.com/watch?v=iFiwmq7f4wQ
5	BFO Tutorial (2019). Part 1: Introduction to BFO ISO	41:11	https://www.youtube.com/watch?v=muafRW0bXgw
6	IOF: Draft BFO Formalization Proposal. 1-25-2019	31:06	https://www.youtube.com/watch?v=ZJgE-O2iREM
7	How BFO Deals with Data from Multiple Contexts	16:31	https://www.youtube.com/watch?v=K9AsCDBRJpM
8	Why Do We Need Upper-Level Ontologies?	20:47	https://www.youtube.com/watch?v=sjf9zeCh_Sw
9	Are there Capabilities on Mars?	1:30:51	https://www.youtube.com/watch?v=Lo7iPP2wKgw
10	Building Ontologies: An Introduction for Engineers (Part 1)	54:17	https://www.youtube.com/watch?v=Gh0f2Us0hr0
11	Building Ontologies: An Introduction for Engineers (Part 2)	53:01	https://www.youtube.com/watch?v=8vdUUhF4JdE