Ontology Modules

The modules below are designed for use in teaching ontology to multidisciplinary audiences in domains such as government and administration, military and biomedical informatics.

They include:

• presentations by ontologists from UB and elsewhere;
• ontology development and planning sessions;

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General Ontology

Introduction to Ontology

• Slides | Streaming Video

Provides 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?

• Background video providing more detailed information: Introduction to Biomedical Ontology.

Referent Tracking

• Presentation by Werner Ceusters (Bioinformatics/Psychiatry): Particulars in Focus
• Slides | Streaming Video

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.

Basic Formal Ontology

• Teaching material on Basic Formal Ontology is provided here).

Literature on General Ontology

• Introductory readings are provided here.

• See also the Buffalo Ontology Site.

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Ontology of Mind

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

Addresses 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.

Barry Smith: How To Do Things With Diagrams

• Slides | Raw Webex Video | Streaming Video | Short youtube version

Explores 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.

Barry Smith: 'Ontology and the Austrian Tradition

Slides | Streaming Video

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).

Barry Smith: 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

Barry Smith: 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)

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Information Ontology

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

Alan Ruttenberg: The Basics of IAO

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?

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?

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.

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).

How do we deal with syncategorematica (for example the 'the' and the 'not' in 'the table not beside my bed')?

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

• http://code.google.com/p/information-artifact-ontology/
• http://www.bioontology.org/wiki/index.php/From_BFO_to_IAO

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

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

Webex

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.

Slides

Paper

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Social Ontology

• Social Ontology. Part 1

Streaming Video

Barry Smith: The Ontology of Social Reality

Slides

Background reading

Addresses 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, focusing on debts, obligations, prices, the Dow Jones Industrial Average, and the views of John Searle.

Mathias Brochhausen and William Hogan (University of Arkansas for Medical Sciences): Social Ontology and the Biomedical Domain: 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

November 26: Social Ontology Part 2

Video

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

Social Ontology: Part 3

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 Draft 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

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Medical Ontology

Alexander Diehl (Department of Neurology, University at Buffalo): From the Gene Ontology to the Neurological Disease Ontology

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.

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Military Ontology

Video presentations on military ontology are provided here.

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Military Intelligence Ontology

A tutorial on ontology for intelligence analysis is here

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Ontology Software

Teaching material on ontology software is provided here