Realism-based Ontologies in Biomedicine: Resolving Terminology and Ontology Confusion

1. Discovery Seminar 118330/UE 141 CC – Fall 2007Difficult Problems, Easy Solutions: Referent Tracking in BiomedicineSession 3: 09/17/2007Realism-based ontologies Werner CEUSTERS Center of Excellence in Bioinformatics and Life Sciences Ontology Research Group University at Buffalo, NY, USA

2. If you use the word “ontology”, ALWAYS be specific about what you mean by it. If, later, you can remember just one thing of this presentation, then make sure it is this one:

3. Why ??? Tom Gruber’s view • The word "ontology" seems to generate a lot of controversy in discussions about AI. It has a long history in philosophy, in which it refers to the subject of existence. It is also oftenconfused with epistemology, which is about knowledge and knowing. • In the context of knowledge sharing, I use the term ontology to mean a specification of a conceptualization. That is, an ontology is a description (like a formal specification of a program) of the concepts and relationships that can exist for an agent or a community of agents. This definition is consistent with the usage of ontology as set-of-concept-definitions, but more general. And it is certainly a different sense of the word than its use in philosophy.

4. The O-word in science N. Guarino, P. Giaretta, "Ontologies and Knowledge Bases: Towards a Terminological Clarification". In Towards Very Large Knowledge Bases: Knowledge Building and Knowledge Sharing, N. Mars (ed.), pp 25-32. IOS Press, Amsterdam, 1995.

5. The O-word in buzz-speak • “An ontology is a classification methodology for formalizing a subject's knowledge or belief system in a structured way. Dictionaries and encyclopedias are examples of ontologies.” (X1) • “A terminology (or classification) is a kind of ontology by definition and it should preserve (and "understand") the relationships between the 1,000s of terms in it or else it would become a mere dictionary (or at best a thesaurus).” (X2) • “Ontologies are Web pages that contain a mystical unifying force that gives differing labels common meaning.” (X3)

6. Today’s biggest problem:a confusion between “terminology” and “ontology” • The conditions to be agreed upon when to use a certain term to denote an entity, are often different from the conditions which make an entity what it is. • Trees would still be different from rabbits even if there were no humans to agree on what names we should use to refer to them • “ontos” means “being”. The link with reality tends to be forgotten: one concentrates on the models instead of on the reality.

7. Terminology • A theory concerned with those aspects of the nature and the functions of language which permit the efficient representation and transmission of items of knowledge (J. Sager) • Precise and appropriate terminologies provide important facilities for human communication(J. Gamper)

8. Ontology • An ontology is a representation of some pre-existing domain of realitywhich • (1) reflects the properties of the objects within its domain in such a waythat there obtains a systematic correlation between realityand the representation itself, • (2) is intelligible to a domain expert • (3) is formalized in a way that allows it to support automatic information processing

9. A division of labour • Terminology: • Communication amongst humans • Communication between human and machine • Ontology: • Representation inside a machine of reality as it exists outside the machine • a representation is not a model or a simplification; ‘cats’ is not a simplification of cats • Communication amongst machines • Interpretation by machines

10. An example:Electronic Health Records (1) • Particular patients, their disorders, their body parts, their worries, ..., and the relationships amongst them; • Statements about 1, made my people (physicians, relatives, patient,...) and machines (lab analysers), as well as statements thereof; • Electronic records as collections of 2, and systems that manage these records;

11. An example:Electronic Health Records (2) • Terminologies, classification systems, biomedical KBs, and “ontologies”, • forced upon the producers of statements, restricting the semantics • designed on the basis of various theories on how reality can be looked at • Architectures of record systems • Forced upon the producers of statements restricting the syntax • Designed on the basis of various theories on how reality can be looked at, AND how healtcare workers operate therein.

12. Current “state of the art” inbiomedical informatics • A pervasive bias towards “concepts” • Content wise: • Work based on ISO/TC37 that advocates the Ogden-Richards theory of meaning • Corresponds with a linguistic reading of “concept” • Architecture wise: • In Europe: work based on CEN/TC251 WG1 & WG2 that follow ISO/TC37 • In the US: HL7, inspired by Speech Act Theory • “Concepts” used as elements of information models, hence mixing a linguistic and engineering reading.

13. ‘Concepts’ are the bad guys:‘Concept’ used in ‘ontology’is used for different things • meaning shared in common by synonymous terms • idea shared in common in the minds of those who use these terms • unit of knowledge describing meanings • universal, feature or property shared in common by entities in the world

14. A gradual shift in meaning • ISO-1087 (1990)concept: aunit of thought constituted through abstraction on the basis of properties common to a set of objects. • ISO-1087 (2000)concept: aunit of knowledge created by a unique combination of characteristics. Characteristic itself is defined as: an abstraction of a property of an object or of a set of objects.

15. A refinement of relationshipsbut at the wrong level • Only associative relationships can hold between concepts à la ISO-1987 in 1990. • Both associative and generic relationships can hold between concepts à la ISO-1987 in 2000. • A partonomy relationship can hold for the 2000-definition, but here the meaning is different than partonomy at the level of the real world entities.

16. Realist Ontology

17. Realist ontology • describes what is fundamental in the totality of what exists, • defines the most general categories to which we need to refer in constructing a description of reality, • tells us how these categories are related. • is able to be used to describe reality at any point in time.

18. Realist OntologyMethodology • Central are the “particulars” (p) • Me, you, my heart, that patient’s fracture, that car accident (which caused his fracture),… • ‘Referent tracking’ • Particulars instanciate classes (c) distinguished on the basis of ontological properties: • Essence, dependency, identity, relationship with time, … • Some classes are “universals” (u) • Define relationships axiomatically at four levels: • p – p, c – c, p – c, c – p

19. (multi-) trauma • How many disorders exist in this case ? • What we see was produced by one cut of an axe: • Skin cut • Section of several arteries • Fracture • ... • Of what are the existing things instances ? • How do they relate to each other ?

20. Images and their relation to reality • “This is not a brain” • This is a “Wrap around artefact”: • This artefact occurs in the phase encoding direction of an MRI image when the field of view selected is not wide enough. Structures outside the field of view are therefore assumed by the computer to be on the other side of the image. • Statements about what is seen on an image

21. This surgeon with some relations Part of This mask This amputation stump This hand Haydom Lutheran Hospital, Tanzania A visit to the operating theatre A lot of objects present

22. This wound being closed by holding ... with some relations That woundfluid drained Part of This kocher being held in that hand of that surgeon A visit to the operating theatre A lot of processes going on Haydom Lutheran Hospital, Tanzania

23. epistemology ontology “Axiom” 1 • If the picture is not a fake, we (i.e., me and this audience) KNOW that that hand, that surgeon, ... EXIST(ed), i.e. ARE (were) REAL. • But importantly: that hand, surgeon, kocher, mask, ... EXIST(ed) independent of our knowledge about them and also the part-relationship between that hand and that surgeon, and the processes going on, are (were) equally real.

24. The realist ontological square (Ignacio Angelelli) Quality Universals Substance Universals differentia exemplify instance instance inheres SubstanceParticulars QualityParticulars

25. How to differentiatequalities from substances ? • Language may fool us: • Being pale • Being human • Being a person • Being sick • Can all be properties of particulars, namely me and you ! • But so does logic: • Pale(x) • Human(x) • Person(x) • Sick(x)

26. Basic Ontological Notions • Identity • How are particulars distinguished from each other ? • Unity • How are all the parts of a particular isolated ? • Essence • Can a property change over time ? • Dependence • Can an entity exist without some others ?

27. person t child adult Living creature animal caterpillar butterfly Identity & instanciation

28. Basic Formal Ontology Basic Formal Ontology consists in a series of sub-ontologies (most properly conceived as a series of perspectives on reality), the most important of which are: • SnapBFO, a series of snapshot ontologies (Oti ), indexed by times: continuants • SpanBFO a single videoscopic ontology (Ov): occurants. Each Oti is an inventory of all entities existing at a time. Ov is an inventory (processory) of all processes unfolding through time.

30. SpanBFO

31. Kinds of relations • <instance, instance>: • my heart part_of me • <instance, class>: • me instance_of human being • <class, instance>: • president of the US empowered_by US constitution (?) • <class, class>: • gene expression has_agent RNA polymerase