Problems in Ontology

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Mondays, 4-6pm, Fall 2012, Jacobs 106, UB North Campus

The material below has been incorporated into Ontology Modules, which contains improved versions of some of the video materials).

PHI 531 Graduate Seminar: Problems in Ontology

Crosslisted with PHI 358 Problems in Ontology

Up to 4 Credit Hours

Principal faculty: Barry Smith

All sessions will be accessible both for face-to-face participants and on-line via webex.


This class will consist of a mixture of:

  • presentations by ontologists from UB and elsewhere;
  • ontology development and planning sessions;
  • teaching on specific ontology topics (for examples see here);
  • video presentations (for example from here).

We will cover a variety of topics in theoretical and applied ontology, paying special attention to applications in the areas of biology and medicine on the one hand, and defense and security on the other.


By the end of the class students will be able to:

  • understand the nature, utility and scope of contemporary applied ontology
  • understand methods and rules for ontology development, evaluation, planning and organization
  • contribute to ontological development initiatives
  • engage in discussion of major issues in theoretical and applied ontology


Alternative streaming videos for all sessions are available here

August 27: Introduction to Ontology

We will begin with a basic introduction to ontology by addressing questions such as: What is an ontology? What are the differences and interrelations between ontology (philosophy), ontology (science), and ontology (engineering)? How are ontologies used? We will also provide an introduction to Basic Formal Ontology (BFO), focusing on a discussion of the question: What is a musical score?

September 10: Referent Tracking

Referent Tracking (RT) is a methodology to create digital copies of the parts of the world we are interested in. It is based on Basic Formal Ontology, but focuses on particulars rather than universals. The goal is to create information systems in such a way that (1) the information they contain mimics the structure of the corresponding portions of reality and (2) they can make optimal use of ontologies and terminologies.

September 24: Mental Functioning Ontology

Streaming Video
Janna Hastings (Swiss Center for Affective Sciences and European Bioinformatics Institute): Representing Mental Functioning Slides
Mental functioning includes all the faculties of the mind, e.g., perception, planning, language, memory, emotion, and self-representation. The study of these processes cuts across disciplines such as psychology, psychiatry, neuroscience, and biomedicine. The Mental Functioning Ontology (MFO) is designed to provide a means for the common description of data in all of these disciplines, in order to support data aggregation and comparison. For background material see here (slides) and here (papers).
Barry Smith: Mental Functioning and the Ontology of Language Slides
In this section we will address those kinds of mental functioning which involve overt or covert use of language. We will focus especially on the issue of the directedness of thought and language to extra-mental objects.

September 27: How To Do Things With Diagrams

The talk will explore some of the ways in which the theory of speech acts can throw light on the role of diagrams and of diagrammatic symbologies in areas such as chess, music, chemistry and military planning. The ontology of processes and process representations will play a central role.

October 1: Mental Functioning and the Ontology of Language

  • 1. Ontology and the Austrian Tradition: A discussion of the theory of intentionality (or the directedness of mental processes), and of the roots of this theory in the philosophy of the Brentano school in Austria. Continues the discussions initiated on September 24 of how mental processes are interrelated in different ways with linguistic processes (for example of speaking, reading, and silent siloloquy).
Slides | Streaming Video
  • 2. Mental Functioning Ontology and the ICF: A survey of the WHO's Internal Classification of Functioning
Slides | Streaming Audio - to be used together with slides here
  • 3. Neuroscience and the Ontology of Mind: A discussion of the mainstream neuroscience approach to mental directedness.
Slides| Streaming Video (for first five minutes see slides here)

October 8: Special session on research collaborations in military, healthcare and other fields of information-driven science

Further details are available here.

October 15: Social Ontology

Raw Webex Video | Streaming Video
We will address the foundations of social ontology, considering topics such as the nature of obligations, credentials, authority, and the role of documents in the construction of social reality.
  • The Ontology of Social Reality: Barry Smith
focusing on debts, obligations, prices, the Dow Jones Industrial Average, and the views of John Searle Slides
Background reading
  • Social Ontology and the Biomedical Domain: Mathias Brochhausen and William Hogan (University of Arkansas for Medical Sciences) Slides
includes treatment of the Ontology of Medically Related Social Entities (OMRSE) and related work on demographics, including gender and marital status, organizations, document acts, and guidelines

October 22: Information on this session provided only to students registered for credit

October 29: From the Gene Ontology to the Neurological Disease Ontology with Alexander Diehl (Neurology)

Raw Webex Video | Streaming Video
The first part of the talk will cover the Gene (GO) and Cell Ontologies (CL), covering issues of ontology structure, development, use in annotation, and exploitation for biological research. The second part will cover the Neurological Disease (ND) and Neuropsychological Testing Ontologies (NPT).
Introduction to bio-ontology for absolute beginners Click on: Video/Audio Stream

Background Reading

The Gene Ontology Consortium, "Gene Ontology: tool for the unification of biology", Nat Genet. 2000 May; 25(1): 25–29.
Mungall CJ, el al., "Cross-product extensions of the Gene Ontology", J Biomed Inform. 2011 Feb;44(1):80-6.
Hill DP, et al., "Gene Ontology annotations: what they mean and where they come from", BMC Bioinformatics. 2008 Apr 29;9 Suppl 5:S2.
Meehan TF, et al., "Logical development of the cell ontology", BMC Bioinformatics. 2011 Jan 5;12:6.
Cox AP, et al., "Ontologies for the study of neurological disease", ICBO 2012.
Glossary of biological terms

November 5: The Infectious Disease Ontology (IDO)

  • 1.OGMS: The Ontology for General Medical Science (Barry Smith) Slides
Streaming Video
  • 2. The IDO Core and Its Extensions - Coordination and Interoperability (Lindsay Cowell) Slides
Streaming Video
  • 3. The IDO-Staph Extension (Albert Goldfain) Slides
Streaming Video (for initial 10 minutes use slides from here)
Staph aureus diseases and their differentiation
Antibiotic Resistance (Blocking, Complemenatary and Reciprocal Dispositions) (Albert Goldfain)
A Lattice of Staph aureus Infectious Diseases
  • Background Reading
IDO website
LG Cowell, B Smith, "Infectious Disease Ontology", Chapter 19 in Infectious Disease Informatics, V Sintchenko (ed.), 2010, 373-395.
A Goldfain, B Smith and LG Cowell, “Dispositions and the Infectious Disease Ontology”, in Antony Galton and Riichiro Mizoguchi (eds.), Formal Ontology in Information Systems. Proceedings of the Sixth International Conference (FOIS 2010), Amsterdam: IOS Press, 2010, 400-413.

November 12: Symposium on the Information Artifact Ontology: Part 1 with Alan Ruttenberg (UB) Raw Webex Video

The Information Artifact Ontology (IAO) is an ontology of information entities, originally inspired by needs of the Ontology for Biomedical Investigations (OBI) to represent measurement data and other information entities associated with investigations such as reports and protocols. A number of issues that have emerged and we are developing a second version to address these issues.

Basic ideas

1. information artifacts are about, or are intended to be about, some entity
2. genes are not information artifacts; gene sequences as recorded in computers are information artifacts
3. information artifacts are copyable
4. information artifacts are generically dependent continuants which have concretizations, for example in specifically dependent patterns of ink on a piece of paper or of magnetization on a hard drive
  • Schedule

The session is in two parts. First, an introduction by Alan Ruttenberg; second, a series of 15-second chess discussions of major issues, moderated by Barry Smith, as follows:

  • 4:00pm Introduction outlining the basics of IAO, focusing on cases where it works well, such as measurement data.
  • 4:30pm Discussion: How can we define the 'is about' relation, which forms the core of IAO? What is the current strategy, and what breaks? What can information artifacts be about? Non-problematic is the case of particulars. Can information artifacts be about types and if so, what does that mean?
  • 4:45pm What is a copying process - the process that results in a new concretization of an information content entity (ICE)? How is copying defined? Is there a constraint on how complicated the copying process can be it can be considered not as copying but as new creation? What happens when the copying is partial?
  • 5:00pm How should IAO deal with information artifacts for which the putative topic does not, or might not, exist? Examples are (written) hypotheses, fiction, diagrams of chemical compounds that can't be synthesized, terms such as 'ether' or 'phlogiston' from the history of science, terms such as 'the soup I plan to have for dinner' used in planning.
  • 5:15pm How can we define information artifacts in order to circumscribe the scope of IAO? What primitives do we need to rely on?Candidates include: intention, communication, (cognitive) mental function, output (of realization of cognitive mental function).
  • 5:30 How do we deal with syncategorematica (for example the 'the' and the 'not' in 'the table not beside my bed')?
  • 5:45 How do we deal with different encodings of what is putatively the same information artifact, for example resulting from use of different character sets such as ASCII or Unicode?
Background materials

November 19: Symposium on the Information Artifact Ontology: Part 2 with [1] Werner Ceusters (UB) and Ron Rudnicki (CUBRC)

Raw Webex Video

Werner Ceusters will lead a discussion of the proposed definitions of IAO terms set forth here

Ron Rudnicki will lead a discussion of the two information ontologies represented here, with a view to formulating a plan for the merger of these ontologies within an improved IAO framework. Slides

November 26: Social Ontology


This session continues the discussion of social ontology initiated on October 15, with a view to coordination and integration of social ontologies being developed by different groups, especially in the biological and medical domains.

  • Barry Smith: Introduction
  • Ramona Walls: The Population and Community Ontology (PCO) Slides
The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include ecology, community health care, epidemiology, plant pathology, behavioral studies, and sociology. This presentation will describe the domain of the PCO and how the PCO relates to other OBO Foundry Library ontologies such as PATO, GO, and EnvO. It will conclude with a brief discussion of the utility of the PCO.
  • Shahim Essaid (Oregon Health and Sciences University): Slides
eagle-i and VIVO are two initiatives whose goal is to help scientists and others discover information, especially information on the web. Each uses ontologies to help achieve this goal:
  • the eagle-i ontology is focused on representing research-related resources such as biological specimens, human studies, equipment and software;
  • the VIVO ontology is focused on researchers themselves, for example their activities, expertise, and publications.
The CTSAconnect project is developing an integrated framework that merges the eagle-i and VIVO ontologies into a single integrated ontology to support the work of clinical and translational scientists. Suppose, for example, that you are a scientist in city X working on a certain disease, and you notice that some of your patients show a particular reaction to a certain drug. How would you identify other researchers living in or near X who have studied responses to this specific drug? CTSAconnect is developing a module to represent the expertise of clinicians inferred from data generated during clinical encounters. This presentation will be a brief overview of the project with a focus on discussing some of the social entities that need to be represented within the ontology framework. Examples include:
  • agreement
  • credential
  • authorship
  • position

December 3: Symposium on Ontology Evaluation with Barry Smith, Werner Ceusters, Alan Ruttenberg (UB) and Fabian Neuhaus (National Institute of Standards and Technology)

Background readings

Presentations will include:

  • Fabian Neuhaus (National Institute of Standards and Technologies): Introduction to Ontology Evaluation Slides
  • Barry Smith: Basic Formal Ontology as a Tool for the Evaluation of Ontologies Paper Slides
A Practical Example: Evaluation of the HL7 RIM Ontology
Relation to OntoClean
Alternatives to BFO
Introduction to BFO
  • Werner Ceusters: A Realism-Based Approach to the Evaluation of Ontologies”,
We present a novel methodology for calculating the improvements obtained in successive versions of ontologies, using examples from biomedicine. The theory takes into account changes both in reality itself and in our understanding of this reality. The successful application of the theory rests on the willingness of ontology authors to document changes they make by following a number of simple rules. The theory provides a pathway by which ontology authoring can become a science rather than an art, following principles analogous to those that have fostered the growth of modern evidence-based medicine. Although in this paper we focus on ontologies, the methodology can be generalized to other sorts of terminology-based artifacts, including Electronic Patient Records.

December 10: Social Ontology


We will continue the discussions of social ontology initiated on October 15 and November 26 (see videos and other background material above). Content will include:

  • Shahim Essaid (Oregon Health and Sciences University): Continuation from November 26 Slides
  • William Hogan and Mathias Brochhausen (University of Arkansas for Medical Sciences): "OMRSE: Current status and our strategy for future development" Slides
OMRSE: The Ontology for Medically Related Social Entities

Grading Requirements for this class will depend on the selected number of credit hours, but will include active class participation and completion of some written work or ontology project.

All students taking the class for credit should make an appointment with Dr Smith to discuss further details.


Introductory readings are provided here.

See also the Buffalo Ontology Site.