1. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Ontology Summit 2007 A Realist View on Ontology NIST (Gaithersburg, Maryland, USA) April 23-24, 2007 Werner CEUSTERS, MD Center of Excellence in Bioinformatics and Life Sciences Department of Psychiatry, University at Buffalo, NY, USA http://www.org.buffalo.edu/RTU

2. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U 2 A realist view of the world The world consists of –entities that are Either particulars or universals; Either occurrents or continuants; Either dependent or independent; and, –relationships between these entities are of the form e.g. is-instance-of, e.g. is-part-of e.g. isa (is-subtype-of) Smith B, Kusnierczyk W, Schober D, Ceusters W. Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain. Proceedings of KR-MED 2006, November 8, 2006, Baltimore MD, USA

3. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U 3 Three levels of reality 1.The world exists ‘as it is’ prior to a cognitive agent’s perception thereof; Smith B, Kusnierczyk W, Schober D, Ceusters W. Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain. Proceedings of KR-MED 2006, November 8, 2006, Baltimore MD, USA

4. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U 4 Reality exist before any observation R

5. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U 5 Reality exist before any observation R And also most structures in reality are there in advance.

6. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U 6 Three levels of reality 1.The world exists ‘as it is’ prior to a cognitive agent’s perception thereof; 2.Cognitive agents build up ‘in their minds’ cognitive representations of the world; Smith B, Kusnierczyk W, Schober D, Ceusters W. Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain. Proceedings of KR-MED 2006, November 8, 2006, Baltimore MD, USA

7. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U 7 The ontology author acknowledges the existence of some Portion Of Reality (POR) R B

8. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U 8 R B Some portions of reality escape his attention.

9. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U 9 Three levels of reality 1.The world exists ‘as it is’ prior to a cognitive agent’s perception thereof; 2.Cognitive agents build up ‘in their minds’ cognitive representations of the world; 3.To make these representations publicly accessible in some enduring fashion, they create representational artifacts that are fixed in some medium. Smith B, Kusnierczyk W, Schober D, Ceusters W. Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain. Proceedings of KR-MED 2006, November 8, 2006, Baltimore MD, USA

10. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U 10 R He represents only what he considers relevant O B #1 RU 1 B1 RU 1 O1 Both RU 1 B1 and RU 1 O1 are representational units referring to #1; RU 1 O1 is NOT a representation of RU 1 B1 ; RU 1 O1 is created through concretization of RU 1 B1 in some medium.

11. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U 11 Thus... These concretizations are NOT supposed to be the representations of these cognitive representations; “concept representation” We should not be in the business of

12. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U 12 But beware ! These concretizations are NOT supposed to be the representations of these cognitive representations; They are representations of the corresponding parts of reality –They are like the images taken by means of a high quality camera;

13. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U 13 They are not (or should not be) like the paintings of Salvador Dali Non-canonical (although nice looking) anatomy

14. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U 14 Kinds of representational artifacts ‘TAXONOMY’ –a tree-form graph-theoretic representational artifact with nodes representing universals or classes and edges representing is_a or subset relations. ‘ONTOLOGY’ –a representational artifact, comprising a taxonomy as proper part, whose representational units are intended to designate some combination of universals, defined classes, and certain relations between them. ‘REALISM-BASED ONTOLOGY’ –is built out of terms which are intended to refer exclusively to universals, and corresponds to that part of the content of a scientific theory that is captured by its constituent general terms and their interrelations. ‘TERMINOLOGY’ –is a representational artifact consisting of representational units which are the general terms of some natural language used to refer to entities in some specific domain. ‘INVENTORY’ –is a representa­tional artifact built out of singular referring terms such as proper names or alphanumeric identifiers.

15. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U 15 Some characteristics of representational units 1.each unit is assumed by the creators of the representation to be veridical, i.e. to conform to some relevant POR as conceived on the best current scientific understanding;

16. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U 16 Some characteristics of representational units 1.each unit is assumed by the creators of the representation to be veridical, i.e. to conform to some relevant POR as conceived on the best current scientific understanding; 2.several units may correspond to the same POR by presenting different though still veridical views or perspectives;

17. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U 17 Some characteristics of representational units 1.each unit is assumed by the creators of the representation to be veridical, i.e. to conform to some relevant POR as conceived on the best current scientific understanding; 2.several units may correspond to the same POR by presenting different though still veridical views or perspectives; 3.what is to be represented by the units in a representation depends on the purposes which the representation is designed to serve.

18. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U 18 Some characteristics of an optimal ontology Each representational unit in such an ontology would designate –(1) a single portion of reality (POR), which is –(2) relevant to the purposes of the ontology and such that –(3) the authors of the ontology intended to use this unit to designate this POR, and –(4) there would be no PORs objectively relevant to these purposes that are not referred to in the ontology.