Problems in Ontology

PHI 531 Graduate Seminar: Problems in Ontology

Crosslisted with PHI 358 Problems in Ontology

Up to 4 Credit Hours

Principal faculty: Barry Smith

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

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

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Content

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.

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Outcomes

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

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Schedule

August 27: Introduction to Ontology

• Slides | Raw Webex Video | Streaming Video

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:

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

September 24: Mental Functioning Ontology

• See link to Video/audio stream here.

4:00pm 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).

4:45pm 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

• Slides | Raw Webex Video | Streaming Video

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.

• 4:00-5:00pm 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

• 5:00-6:00pm 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

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

1) The Gene Ontology Consortium, "Gene Ontology: tool for the unification of biology", Nat Genet. 2000 May; 25(1): 25–29.

2) Mungall CJ, el al., "Cross-product extensions of the Gene Ontology", J Biomed Inform. 2011 Feb;44(1):80-6.

3) Hill DP, et al., "Gene Ontology annotations: what they mean and where they come from", BMC Bioinformatics. 2008 Apr 29;9 Suppl 5:S2.

4) Meehan TF, et al., "Logical development of the cell ontology", BMC Bioinformatics. 2011 Jan 5;12:6.

5) Cox AP, et al., "Ontologies for the study of neurological disease", ICBO 2012.

Glossary of biological terms

November 5: The Infectious Disease Ontology (IDO)

Webex

1. Background in the Ontology for General Medical Science (Barry Smith) Slides

2. The IDO Core and Its Extensions - Coordination and Interoperability (Lindsay Cowell) Slides

IDO as an extension of the OGMS Framework (Lindsay Cowell)

(infectious) disease

(infectious) disorder

(infectious) disease course

Granularity Issues in IDO (Barry Smith / Lindsay Cowell)

Defining 'Infection' (a) as an aggregate/collective and (b) as a unified object

3. The IDO-Staph Extension (Albert Goldfain) Slides

Staph aureus diseases and their differentiation

Antibiotic Resistance (Blocking, Complemenatary and Reciprocal Dispositions) (Albert Goldfain)(

A Lattice of Staph aureus Infectious Diseases

4. Interesting Types of Entities Required by IDO (open discussion with Barry Smith, Lindsay Cowell and Albert Goldfain)

'herd immunity',

'long term non-progressor'

'obligate symbiont'

• 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 with Alan Ruttenberg (UB)

Webex

November 19: Symposium on the Information Artifact Ontology with Ron Rudnicki (CUBRC) and Werner Ceusters (UB) Webex

• November 26: Social Ontology

Webex

Barry Smith: Introduction

Ramona Walls: The Population and Community Ontology (PCO)

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 community health care, plant pathology, behavioral studies, sociology, and ecology.

Shahim Essaid (Oregon Health and Sciences University): TBD

• December 3: TBD

Webex

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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.

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Literature

Introductory readings are provided here.

See also the Buffalo Ontology Site.