ECO R European Centre for Ontological Research Introduction

ECO R European Centre for Ontological Research Introduction to Ontology Tutorial for SMBM 2005 Werner Ceusters European Centre for Ontological Research Universität des Saarlandes Saarbrücken, Germany

ECO R European Centre for Ontological Research • • Lecture overview Credentials The many faces of “ontology” Realist ontology Why is the concept-based approach so widespread ? The price you pay if you go for concepts. . . Can Description Logics save the world ? And then there was OWL Take home messages

ECO R European Centre for Ontological Research External members Local members Partners Status April 8, 2005

ECO R European Centre for Ontological Research Directors Management Board Member representatives Advisory Board Status April 8, 2005

ECO R Institute for Formal Ontology European Centre for Ontological Research and Medical Information Science • an interdisciplinary research group – – – Philosophy, Computer and Information Science, Logic, Medicine, Medical Informatics. • a center of theoretically grounded research in both formal and applied ontology. • Main goal: to develop a formal ontology that will be applied and tested in the domain of medical and biomedical information science.

ECO R European Centre for Ontological Research IFOMIS competences • Logics • Formal Ontology / metaphysics • History of philosophy • Philosophy of science Status Dec 2, 2004

ECO R European Centre for Ontological Research Our building

ECO R European Centre for Ontological Research What philosophers are good for. . .

ECO R Short personal history European Centre for Ontological Research 1977 1959 -. . . 2004 1989 2002 1998

ECO R European Centre for Ontological Research “Ontology”

ECO R European Centre for Ontological Research “Ontology” on the web April 7, 2005 Popular Ontology Realist The Inactive John SUO W 3 C Important most Sowa’s ontology Upper ontology Web from since citeda August definition: bioinformatics ontology philosophical editor Ontology in use. 7, from 2004. page Tom Grüber Barry perspective. Manchester Initiative initiative resource Smith 1993 • Increase of 50% in number of hits • Ontology. org disappeared • Wikipedia entry for Ontology appeared Status Nov 29, 2004

ECO R European Centre for Ontological Research • • • • 1 3 4 7 15 20 21 34 53 59 86 188 192 676 Search on Nov 30: What is an Ontology? Gene Ontology Consortium W 3 C Web Ontology (Web. Ont) Working Group (OWL) (Closed) Buffalo Ontology Site MGED NETWORK : : Ontology Working Group (OWG) Laboratory for Applied Ontology (LOA) ONTOLOGY WORKS INC. John Bateman; ontology portal root The Protégé Ontology Editor and Knowledge Acquisition System Institute for Formal Ontology and Medical Information Science. . . Autofellatio and Ontology ? ? ? EUROREC 2004, Implemantation Guidelines, . . . Foundational Ontology (Leeds) Ontology Server research (Star. Lab)

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

ECO R European Centre for Ontological Research 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 often confused 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.

ECO R European Centre for Ontological Research 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.

ECO R The O-word in buzz-speak European Centre for Ontological Research • “An ontology is a classification methodology formalizing a subject's knowledge or belief system in a structured way. Dictionaries and encyclopedias are examples of ontologies. ” (X 1) • “A terminology (or classification) is a kind of ontology by definition and it should preserve (and "understand") the relationships between the 1, 000 s of terms in it or else it would become a mere dictionary (or at best a thesaurus). ” (X 2) • “Ontologies are Web pages that contain a mystical unifying force that gives differing labels common meaning. ” (X 3)

ECO R European Centre for Ontological Research 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.

ECO R European Centre for Ontological Research 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)

ECO R European Centre for Ontological Research Ontology What it means if we use the word A proposal put forward by the SI roadmap pannel • An ontology is a representation of some preexisting domain of reality which – (1) reflects the properties of the objects within its domain in such a way that there obtains a systematic correlation between reality and the representation itself, – (2) is intelligible to a domain expert – (3) is formalized in a way that allows it to support automatic information processing

ECO R European Centre for Ontological Research 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

ECO An example: R Electronic Health Records (1) European Centre for Ontological Research 1. Particular patients, their disorders, their body parts, their worries, . . . , and the relationships amongst them; 2. Statements about 1, made my people (physicians, relatives, patient, . . . ) and machines (lab analysers), as well as statements thereof; 3. Electronic records as collections of 2, and systems that manage these records;

ECO An example: R Electronic Health Records (2) European Centre for Ontological Research 4. 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 5. 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.

ECO R European Centre for Ontological Research Current “state of the art” in biomedical informatics • A pervasive bias towards “concepts” – Content wise: • Work based on ISO/TC 37 that advocates the Ogden -Richards theory of meaning • Corresponds with a linguistic reading of “concept” – Architecture wise: • In Europe: work based on CEN/TC 251 WG 1 & WG 2 that follow ISO/TC 37 • In the US: HL 7, inspired by Speech Act Theory • “Concepts” used as elements of information models, hence mixing a linguistic and engineering reading.

ECO R European Centre for Ontological Research “Ontology” An ontology defines the terms used to describe and represent an area of knowledge, and are used by people, databases, and applications that need to share domain information (a domain is a specific subject area, such as health or medicine). e-Health - making healthcare better for European citizens: An action plan for a European e-Health Area COM (2004) 356 final, 30. 4. 2004, p 17 OWL Web Ontology Language; Use Cases and Requirements W 3 C Recommendation 10 February 2004 http: //www. w 3. org/TR/webont-req/

ECO R European Centre for Ontological Research “Ontology” • Ontologies need to specify descriptions for the following kinds of concepts: – Classes (general things) in the many domains of interest – The relationships that can exist among things – The properties (or attributes) those things may have OWL Web Ontology Language; Use Cases and Requirements W 3 C Recommendation 10 February 2004 http: //www. w 3. org/TR/webont-req/

ECO R Semantic Interoperability European Centre for Ontological Research • Semantic interoperability is the ability for information shared by systems to be understood at the level of formally defined domain concepts so that the information is computer processable by the receiving system – Text used in the CEC documents – Taken over by Artemis

ECO ‘Concepts’ are the bad guys: R European Centre for Ontological Research ‘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

ECO R Concept based terminology European Centre for Ontological Research • “concept” as the core element for organising terms • Concept system: organisation of concepts by means of generic and associative relationships – The concept tool is more generic than the concept hammer – The concept hammer is associated with the concept nail.

ECO R European Centre for Ontological Research A gradual shift in meaning • ISO-1087 (1990) concept: a unit of thought constituted through abstraction on the basis of properties common to a set of objects. • ISO-1087 (2000) concept: a unit 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.

ECO R A refinement of relationships European Centre for Ontological Research but 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.

ECO R European Centre for Ontological Research Realist Ontology

ECO R European Centre for Ontological Research 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.

ECO R European Centre for Ontological Research Realist Ontology Methodology • 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, c – c, p – c, c – p

ECO R European Centre for Ontological Research (multi-) trauma • How many disorders exist in this case ? – What we see was produced one cut of an axe: • • by Skin cut Section of several arteries Fracture. . . • Of what are the existing things instances ?

ECO R Images and their relation to reality European Centre for Ontological Research • “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

ECO R A visit to the operating theatre European Centre for Ontological Research A lot of objects present This surgeon with some relations Part of This mask This amputatio n stump This hand Haydom Lutheran Hospital, Tanzania

ECO R A visit to the operating theatre European Centre for Ontological Research A lot of processes going on This wound being closed by holding. . . with some relations Part of That wound fluid drained This kocher being held in that hand of that surgeon Haydom Lutheran Hospital, Tanzania

ECO R European Centre for Ontological Research “Axiom” 1 epistemology • If the picture is not a fake, we (i. e. , me and this audience) KNOW 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 partrelationship between that hand that surgeon, and the processes going on, are (were) equally real. ontology

ECO R The realist ontological square (Ignacio Angelelli) European Centre for Ontological Research Substance Universals instance differentia exemplify Quality Universals instance inheres Substance Particulars Quality Particulars

ECO R European Centre for Ontological Research How to differentiate qualities from substances ? • Language may fool us: But so does logic: – Being pale – Being human – Being a person – Being sick – Pale(x) – Human(x) – Person(x) – Sick(x) • Can all be properties of particulars, namely me and you !

ECO R European Centre for Ontological Research 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 ?

ECO R European Centre for Ontological Research Identity & instanciation person Living creature child adult caterpillar butterfly animal t

ECO R A practical example: Onto. Clean European Centre for Ontological Research • +I • −I The property carries a common identity criterion for all its instances. The property does not carry a common identity criterion for all its instances. • +U The property carries a common unity criterion for all its instances. • −U The property does not carry a common unity criterion for all its instances. • U No instance of the property satisfies a unity criterion. • +R The property is essential to all its instances: an instance of a rigid property cannot stop satisfying that property. • −R The property is not essential to all its instances: some instances of a non rigid property can stop satisfying that property. • R No instance of the property has it essentially: all instances of the property can stop satisfying it. Guarino & Welty

ECO R European Centre for Ontological Research Ontological theories • = theories between reality and “the ontology” (“ontology” as a representation) – Granular Partition Theory (T Bittner & B. Smith) – Logic of Classes (B. Smith) – Foundational relations

ECO Theory of granular partitions (B. Smith) R European Centre for Ontological Research Think of it as Alberti’s grid

ECO R European Centre for Ontological Research Reality: not just a matter of view Copyright 2001, United Feature Syndicate Inc.

ECO R European Centre for Ontological Research Granular partitions: main principles • a partition is the drawing of a (typically complex) fiat boundary over a certain domain • a partition typically comes with labels and/or an address system • partitions are artefacts of our cognition • a partition is transparent (veridical) • bona fide objects exist independently of our partitions, fiat objects are determined by partitions • different partitions may represent cuts through the same reality which are skew to each other • entities (existing in reality) located in the same cell of a partition share common characteristics

ECO R (Simplified) Logic of classes European Centre for Ontological Research • primitive: – entities: particulars versus universals – relation inst such that: • all classes are universals; all instances are particulars • some particulars are not instances; e. g. some mereological sums • subsumption defined resorting to instances:

ECO R European Centre for Ontological Research Reference Ontology • a theory of a domain of entities in the world • based on realizing the goals of maximal expressiveness and adequacy to reality • sacrificing computational tractability for the sake of representational adequacy

ECO R European Centre for Ontological Research 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: – Snap. BFO, a series of snapshot ontologies (Oti ), indexed by times: continuants – Span. BFO 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.

ECO R European Centre for Ontological Research Occurants and continuants Picture by Vladimir Brajic

ECO R European Centre for Ontological Research

ECO R European Centre for Ontological Research Span. BFO

ECO R European Centre for Ontological Research 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

ECO R European Centre for Ontological Research Parthood as a Relation between Instances • Introduced as primitive: – p part_of p 1 • Illustrated in assertions such as: – My heart part_of Werner Ceusters • Properties: – reflexivity: for all p, p part_of p, – anti-symmetry: for all p, p 1, if p part_of p 1 and p 1 part_of p then p and p 1 are identical, – transitivity: for all p, p 1, p 2, if p part_of p 1 and p 1 part_of p 2, then p part_of p 2.

ECO R European Centre for Ontological Research Parthood as a Relation between Classes • For continuants: (‘heart’, ‘person’) – C part_of C 1 =def. for all c, t, if c instance_of C at t then there is some c 1 such that c 1 instance_of C 1 at t and c part_of c 1 at t. • For processes: (‘menopauze’, ‘aging’) – P part_of P 1 =def. for all p, if p instance_of P, then there is some p 1 such that: p 1 instance_of P 1 and p part_of p 1. These definitions tell you ONLY something about C’s and P’s, but nothing about C 1’s and P 1’s !!!

ECO R European Centre for Ontological Research Possible variants • R 1(A, B) =: x (Inst(x, A) y(Inst(y, B) & Rxy)) – every A stands in relation R to some B • R 2(A, B) =: y (Inst(y, B) x(Inst(x, A) & Rxy)) – for each B there is some A that stands in relation R to it • R 12(A, B) =: R 1(A, B) & R 2(A, B) – every A stands in relation R to some B and for each B there is some A that stands in relation R to it Donnelly and Bittner, 2005

ECOProperties of relations among individuals vs. R properties of relations among classes European Centre for Ontological Research Among Individuals Among Classes R is. . . R 1 must also be. . . ? R 2 must also be. . . ? R 12 must also be. . . ? Reflexive Yes Yes Irreflexive No No No Symmetric No No Yes Asymmetric No No No Antisymmetric No No No Transitive Yes Yes Donnelly and Bittner, 2005

ECO R European Centre for Ontological Research GALEN assertions using is. Division. OF and has. Division GALEN’s is. Division. Of assertion GALEN’s has. Division BIT+Cl relation Female Pelvic Cavity is. Division. Of PP 1 Pelvic Part of Trunk none Prostate Gland is. Division. Of Genito-Urinary System none PP 1 none BIT+Cl relation Pelvic Part of Trunk has. Division Hair (PP-1)1 Left. Heart. Ventricle is. Division. Of Heart PP 12 Heart has. Division Left. Heart. Ventricle (PP-1)12 Prostate Gland is. Division. Of Male Genito-Urinary System PP 12 Male Genito-Urinary System has. Division Prostate Gland (PP-1)12 Urinary Bladder is. Division. Of Genito-Urinary System PP 12 none Pericardium is. Division. Of Heart none Heart has. Division Pericardium none Donnelly and Bittner, 2005

ECO R European Centre for Ontological Research Realist Ontology is alive • The gossip: – We are holding biomedical ontology in a strangle hold • The success stories (some recent examples): – Contributing to OBO ontologies requires adherence to the relations defined in Relations in Biomedical Ontologies, forthcoming in Genome Biology – Foundational Medical Anatomy (FMA) completely reworked, and basis forthcoming CEN standard – Previous IFOMIS collaborator hired by NLM to work on revision of Semantic Network – Barry Smith appointed by De Soto (Institute for Liberty and Democracy), funded by US Agency for International Development, to establish the philosophical underpinnings of property right.

ECO OBO primitive relationships R European Centre for Ontological Research for continuants • c instance_of C at t – a primitive relation between a continuant instance and a class which it instantiates at a specific time • c part_of c 1 at t – a primitive relation between two continuant instances and a time at which the one is part of the other • c located_in r at t – a primitive relation between a continuant instance, a spatial region which it occupies, and a time • c derives_from c 1 – a primitive relation involving a material continuant c in such a way that the spatial region it occupies when it begins to exist overlaps with the spatial region occupied by a previously existing material continuant c 1 in such a way that matter is inherited by the one from the other

ECO OBO primitive relationships R European Centre for Ontological Research for processes • p instance_of P – a primitive relation, between a process instance and a class which it instantiates, holding independently of time • p part_of p 1, r part_of r 1 – a primitive relation of parthood, holding independently of time, either between process instances (one a subprocess of the other), or between spatial regions (one a subregion of the other) • p has_participant c at t – a primitive relation between a process, a continuant, and a time • p has_agent c at t – a primitive relation between a process, a continuant and a time at which the continuant is causally active in the process

ECO R European Centre for Ontological Research Definition of is_a • For continuants: – C is_a C 1 =def. for all c, t, if c instance_of C at t then c instance_of C 1 at t. • For processes: – P is_a P 1 =def. for all p, if p instance_of P then p instance_of P 1.

ECO R Properties of OBO relations European Centre for Ontological Research

ECO R European Centre for Ontological Research Why is the concept-based approach so wide-spread ?

ECO R Back to the operating theatre European Centre for Ontological Research He wants me to remove that blood I must get rid of that blood Suction, please ! Fluid being removed Haydom Lutheran Hospital, Tanzania

ECO R European Centre for Ontological Research This is communication ! =? Give me a kocher, please. kocher

ECO R Triadic models of meaning: European Centre for Ontological Research The Semiotic/Semantic triangle Reference: Concept / Sense / Model / View / Partition Sign: Language/ Term/ Symbol Referent: Reality/ Object

ECO R European Centre for Ontological Research Aristotle’s triadic meaning model pathema semeia gramma/ phoné Words spoken are signs or symbols (symbola) of affections or impressions (pathemata) of the soul (psyche); written words (graphomena) are the signs of words spoken (phoné). As writing (grammatta), so also is speech not the same for all races of men. But the mental affections themselves, of which these words are primarily signs (semeia), are the same for the whole of mankind, as are also the objects (pragmata) of which those affections are representations or likenesses, images, copies (homoiomata). pragma Aristotle, 'On Interpretation', 1. 16. a. 4 -9, Translated by Cooke & Tredennick, Loeb Classical Library, William Heinemann, London, UK, 1938.

ECO R European Centre for Ontological Research An interesting sidestep: “understanding” • “understanding” Latin “substare” – literally: “to stand under” • Websters Dictionary (1961) understanding = the power to render experience intelligible by bringing perceived particulars under appropriate concepts. • “particulars” = what is NOT SAID of a subject (Aristotle) – substances: this patient, that tumor, . . . – qualities: the red of that patient’s skin, his body temperature, blood pressure, . . . – processes: that incision made by that surgeon, the rise of that patient’s temperature, . . . • “concepts”: may be taken in the above definition as Aristotle’s “universals” = what is SAID OF a subject – Substantial concepts: patient, tumor, . . . – Quality concepts: white, temperature –. . .

ECO R Richards’ semantic triangle European Centre for Ontological Research reference my understanding symbol your understanding referent • Reference (“concept”): “indicates the realm of memory where recollections of past experiences and contexts occur”. • Hence: as with Aristotle, the reference is “mindrelated”: thought. • But: not “the same for all”, rather individual mind-related

ECO R European Centre for Ontological Research Don’t confuse with homonymy ! R 1 R 2 R 3 mole (skin lesion) mole (unit) “mole” mole (animal)

ECO R European Centre for Ontological Research Different thoughts Homonymy One concept understanding of x understanding of y R 1 R 2 R 3 mole “skin lesion” mole “unit” symbol referent “mole” mole “animal”

ECO R And by the way, synonymy. . . European Centre for Ontological Research the Aristotelian view “sweat” “perspiration” Richards’ view “sweat” “perspiration”

ECO R European Centre for Ontological Research Frege’s view sense name • “sense” is an objective feature of how words are used and not a thought or concept in somebody’s head • 2 names with the same reference can have different senses (mst/ist) • 2 names with the same sense have the same reference (synonyms) reference • a name with a sense does not need to have a (=referent) reference (“Beethoven’s 10 th symphony”)

ECO R Ontology and the semantic triangle European Centre for Ontological Research • In Information Science: – “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. ” • In Philosophy: – “Ontology is the science of what is, of the kinds and structures of objects, properties, events, processes and relations in every area of reality. ” concept term referent

ECO R European Centre for Ontological Research • • Before the introduction of “concepts”, it was even worse. . . Characteristics of an ideal medical knowledge system a unique code for each term (word, phrase) each code-term being defined each term independent, not defined as the result of other terms in the system synonyms recognisable through the codes to each codes could be attached codes of related terms the system would encompass all of medicine the system would be in the public domain the format of the KB should be functionally described, independent from hard- or software (C. Bishop, 1989)

ECO R With “concepts”, it became: European Centre for Ontological Research • • Characteristics of an ideal medical knowledge system a unique code for each term (word, phrase) and concept each code-term concept being defined each term concept independent, not defined as the result of other terms in the system ? ? ? synonyms recognisable through the codes concepts to each code concept could be attached codes concepts of related terms the system would encompass all of medicine the system would be in the public domain the format of the KB should be functionally described, independent from hard- or software

ECO Requirements for clinical R European Centre for Ontological Research vocabularies (1) • Domain completeness: coverage of all possible terms that lie within a vocabulary’s domain • Non-vagueness: the term should represent the concept behind it as close as possible • Non-ambiguity: the same term cannot refer to more than one concept • Non-redundancy: each concept must be represented by one unique identifier (Cimino, 1989)

ECO R Requirements for clinical European Centre for Ontological Research vocabularies (2) • Synonomy: multiple ways for expressing a word (or concept) must be allowed • Multiple classification: concepts must be allowed to be classified in multiple hierarchies • Consistency of view: concepts must have the same relationships in all views • Explicit relationships: all relationships (e. g. class, synonymy, …) must be explicitly labelled.

ECO R European Centre for Ontological Research The price you pay if you go for concepts. . .

ECO R European Centre for Ontological Research It’s just too funny. . . • UMLS-SN: – Bacterium causes Experimental model of disease – Educational activity associated with pathologic function • HL 7: Individual Allele is_a Act of Observation • GO: Menopause part_of Death • GALEN: – Female Pelvic Cavity Contains Uterus (this is ok, but compare. . . ) – Vomitus Contains Carrot – Speech Contains Verbal Statement

ECO R Border’s classification of medicine European Centre for Ontological Research • Medicine – Mental health – Internal medicine • Endocrinology – Oversized endocrinology • Gastro-enterology • . . . – Pediatrics –. . . – Oversized medicine

ECO R European Centre for Ontological Research Me. SH: Medical Subject Headings • Designed for bibliographic indexing, eg Index Medicus • Basis for Med. LINE • focuses on biomedicine and other basic healthcare sciences • clinically very impoverished • Consistency amongst indexers: – 60% for headings – 30% for sub-headings

ECO R Me. SH Tree Structures - 2004 European Centre for Ontological Research 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. Anatomy [A] Organisms [B] Diseases [C] Chemicals and Drugs [D] Analytical, Diagnostic and Therapeutic Techniques and Equipment [E] Psychiatry and Psychology [F] Biological Sciences [G] Physical Sciences [H] Anthropology, Education, Sociology and Social Phenomena [I] Technology and Food and Beverages [J] Humanities [K] Information Science [L] Persons [M] What about this as a Health Care [N] top ontology ? ? ? Geographic Locations [Z]

ECO R Me. SH Tree Structures - 2004 European Centre for Ontological Research • Cardiovascular Diseases [C 14] – Heart Diseases [C 14. 280] • • Arrhythmia [C 14. 280. 067] + Carcinoid Heart Disease [C 14. 280. 129] Cardiomegaly [C 14. 280. 195] + Endocarditis [C 14. 280. 282] + Heart Aneurysm [C 14. 280. 358] Heart Arrest [C 14. 280. 383] + Heart Defects, Congenital [C 14. 280. 400] – – – Aortic Coarctation [C 14. 280. 400. 090] Arrhythmogenic Right Ventricular Dysplasia [C 14. 280. 400. 145] Cor Triatum [C 14. 280. 400. 200] Coronary Vessel Anomalies [C 14. 280. 400. 210] Crisscross Heart [C 14. 280. 400. 220] Dextrocardia [C 14. 280. 400. 280] +

ECO R Me. SH Tree Structures - 2004 European Centre for Ontological Research • Body Regions [A 01] – Extremities [A 01. 378] • Lower Extremity [A 01. 378. 610] – Buttocks [A 01. 378. 610. 100] – Foot [A 01. 378. 610. 250] » Ankle [A 01. 378. 610. 250. 149] » Forefoot, Human [A 01. 378. 610. 250. 300] + » Heel [A 01. 378. 610. 250. 510] – Hip [A 01. 378. 610. 400] – Knee [A 01. 378. 610. 450] The most abundant – Leg [A 01. 378. 610. 500] sort of mistakes ! – Thigh [A 01. 378. 610. 750]

ECO R Me. SH Tree Structures - 2004 European Centre for Ontological Research • Body Regions [A 01] – – Abdomen [A 01. 047] + Back [A 01. 176] + Breast [A 01. 236] + Extremities [A 01. 378] • Amputation Stumps [A 01. 378. 100] • Lower Extremity [A 01. 378. 610] + • Upper Extremity [A 01. 378. 800] + – – – Head [A 01. 456] + Neck [A 01. 598] Pelvis [A 01. 673] + Perineum [A 01. 719] Thorax [A 01. 911] + Viscera [A 01. 960] And here ?

ECO R SNOMED International (1995) European Centre for Ontological Research • Multi-axial coding system: – morphology, disease, function, procedure, . . . • Each axis has an hierarchical structure • Translations in other languages than English only for older versions • Informal internal structuring • Being translated in CG formalism, but with only internal consistency • Possibility to generate meaningless concepts • Mixing of hierarchies: – Bone • Long Bone • Periosteum • Shaft

ECO R Snomed International (1995) European Centre for Ontological Research Number of records (V 3. 1) • • • T M F L C A D P S J G Topography 12, 385 Morphology 4, 991 Function 16, 352 Living Organisms 24, 265 Drugs &Biological Products 14, 075 Physical Agents, Forces and Activities 1, 355 Disease/ Diagnosis 28, 623 Procedures 27, 033 Social Context 433 Occupations 1, 886 General Modifiers 1, 176 TOTAL RECORDS 132, 641

ECO R Snomed International (1995): European Centre for Ontological Research knowledge in the codes. T - 3 5 3 2 2 posterior leaflet anatomic mitral cardiac valve cardiovascular Why was this not a good idea ?

ECO R Snomed International : multiple ways to express the same thing European Centre for Ontological Research D 5 -46210 Acute appendicitis, NOS D 5 -46100 G-A 231 Appendicitis, NOS Acute M-41000 G-C 006 T-59200 Acute inflammation, NOS In Appendix, NOS G-A 231 M-40000 G-C 006 T-59200 Acute Inflammation, NOS In Appendix, NOS

ECO R The International Classification European Centre for Ontological Research • • • • of diseases (WHO). . Chapter II: Neoplasms (C 00 -D 48) Chapter III: Diseases of the Blood and Blood-forming organs and certain disorders involving the immune mechanism (D 50 -D 89) Excludes : auto-immune disease (systemic) NOS (M 35. 9). . Nutritional Anemias (D 50 -D 53) D 50 Iron deficiency anaemia Includes: . . . D 50. 0 Iron deficiency anaemia secondary to blood loss (chronic) Excludes : . . . D 50. 1. . . D 51 Vit B 12 deficiency anaemia Haemolytic Anemias (D 55 -D 59) . . . Chapter IV: . . .

ECO R European Centre for Ontological Research UMLS: Unified Medical Language System (NLM) • Tool for information retrieval of 4 components: – Metathesaurus contains information about biomedical concepts and how they are represented in diverse terminological systems. – Semantic Network contains information about concept categories and the permissible relationships among them – Information Sources Map contains both humanreadable and machine-processable information about all kinds of biomedical terminological systems – Specialist lexicon: english words with POS • “The” tool from and for the U. S. : -)

ECO UMLS Semantic Network R European Centre for Ontological Research

ECO R European Centre for Ontological Research • • • Semantic Network Relationships Is_a physically related to spatially related to temporally related to functionally related to conceptually related to

ECO Semantic Network “Biologic R Function” Hierarchy European Centre for Ontological Research

ECO R European Centre for Ontological Research Semantic Network "affects" Hierarchy UMLS Semantic Network – What does A relation B means ? – Normally: for all a’s that are A’s, there is some b that is a B, such that the relation holds from a to b – Very relaxed: for some a’s there might be a b such that a relation b – But even that doesn’t work for the relationship prevents

ECO R European Centre for Ontological Research “Axiom” 2 • Concept-based terminology (and standardisation thereof) is there as a mechanism to improve understanding of messages by humans. • It is NOT the right device – to explain why reality is what it is, how it is organised, etc. , (although it is needed to allow communication), – to reason about reality, – to make machines understand what is real, – to integrate across different views, languages, conceptualisations, . . .

ECO R European Centre for Ontological Research Why not ? • Does not take care of universals and particulars appropriately • Concepts not necessarily correspond to something that (will) exist(ed) – Sorcerer, unicorn, leprechaun, . . . • Definitions set the conditions under which terms may be used, and may not be abused as conditions an entity must satisfy to be what it is • Language can make strings of words look as if it were terms – “Middle lobe of left lung” • . . .

ECO R European Centre for Ontological Research Ok, then Description Logics will save us. . . ?

ECO R European Centre for Ontological Research Description Logics • A decidable fragment of FOL • A propositional modal logic • A classes and properties (concepts and roles) oriented KR language • Subsumption and satisfiability (consistency) are the key inferences • Most DLs are supersets of ALC – Boolean operators on concepts – Existential and Universal quantifiers • OWL-DL is a large superset (SHOIN): – – Property hierarchies & Transitive roles (SH) Inverse (I) Nominals (O) (has. Value and one of) Number restrictions (counting quantifiers)

ECO R European Centre for Ontological Research ‘Well, that’s because they don’t use description logics or OWL’ You really think so ? SNOMED-RT (2000) SNOMED-CT (2003) DL don’t guarantee you to get parthood right !

ECO R European Centre for Ontological Research F-DL (Frankenstein’s DL)

ECO R Use of description logics does not European Centre for Ontological Research guarantee correct representations !

ECO R Sloppiness in definitions European Centre for Ontological Research new-1 new-2

ECO R European Centre for Ontological Research NCI Thesaurus • a biomedical thesaurus created specifically to meet the needs of the National Cancer Institute. • semantically modeled cancer-related terminology built using description logics

ECO R NCI Thesaurus Root concepts European Centre for Ontological Research Substance ? know If yes, towhy is gene Anatomic Or ? Does Structure, the NCI not Anatomic System, which category or product subsumed it ? If no, ? why are Anatomic Any itemnot classified Substance there ? by belongs drugs and chemicals not subsumed by it ?

ECO R European Centre for Ontological Research Conceptual entity • Definition: none • Semantic type: – Conceptual entity – Classification • Subconcepts: – Action: • definition: action; a thing done – And: • Definition: an article which expresses the relation of connection or addition, used to conjoin a word with a word, . . . – Classification • Definition: the grouping of things into classes or categories

ECO R Definition of “cancer gene” European Centre for Ontological Research

ECO R NCI Thesaurus architecture European Centre for Ontological Research Findings-And. Disorders-Kind Anatomy-Kind What diseases have a diameter of over 3 cm ? Disease ISA “Kinds” “Associative” “Formal restrict the relationships subsumption” domain andproviding range or of associative “inheritance” “differentiae” relationships Breast neoplasm Breast Disease-has-associated-anatomy

ECO R European Centre for Ontological Research Ontology versus Description Logics • In the Description Logic world – terms and definitions come first, – the job is to validate them and reason with them by means of a model – but whether the model correspond to reality is not its problem (Workshop on DL, Saarbrücken, 22 -23/11/2004) • In the realist ontology world – robust ontology (with all its reasoning power) comes first – terms, term-hierarchies and record architectures must be subjected to the constraints of ontological coherence

ECO R European Centre for Ontological Research Thanks x there is OWL ? Where x { , , , } ,

ECO R Understanding content (1) European Centre for Ontological Research “John Doe has a pyogenic granuloma of the left thumb” John Doe has a pyogenic granuloma of the left thumb

ECO R Understanding content (2) European Centre for Ontological Research <record> <patient>John Doe</patient> <diagnosis>pyogenic granuloma of the left thumb</diagnosis> </record> <subject> John Doe </subject> <diagnosis> pyogenic granuloma of the left thumb </diagnosis> </record>

ECO R Understanding content (3) European Centre for Ontological Research <129465004> <116154003>John Doe</116154003> < 8319008 > 17372009 <finding site> 76505004 <laterality>7771000</laterality> </finding site> </ 8319008 > </129465004>

ECO R European Centre for Ontological Research XML OWL • XML – Pure syntax – Simulated semantics • OWL: – Very precise semantics – But is the semantics of the right sort to faithfully describe simple medical facts ?

ECO R NCIT’s “Lung” in OWL European Centre for Ontological Research <owl: Class rdf: ID="Lung"> <rdfs: label>Lung</rdfs: label> “All instances of lung must be located in at least one instance <code>C 12468</code> of thoracic cavity” <has. Type>primitive</has. Type> Hence: total lung excision is <rdfs: sub. Class. Of rdf: resource="#Organ"/> impossible. <rdfs: sub. Class. Of> <owl: Restriction> <owl: on. Property rdf: resource="#r. Anatomic_Structure_Has_Location"/> <owl: some. Values. From rdf: resource="#Thoracic_Cavity"/> </owl: Restriction> </rdfs: sub. Class. Of>. . . </owl>

ECO R NCIT’s “Lung” in OWL European Centre for Ontological Research <owl: Class rdf: ID="Lung"> “every assigned location of <rdfs: label>Lung</rdfs: label> pleura must be an instance of <code>C 12468</code> the class Thoracic Cavity” <has. Type>primitive</has. Type> Allows lungs not to be located <rdfs: sub. Class. Of rdf: resource="#Organ"/> at all. <rdfs: sub. Class. Of> <owl: Restriction> <owl: on. Property rdf: resource="#r. Anatomic_Structure_Has_Location"/> <owl: all. Values. From rdf: resource="#Thoracic_Cavity"/> </owl: Restriction> </rdfs: sub. Class. Of>. . . </owl>

ECO R European Centre for Ontological Research Take home messages • Very few “ontologies” are ontologies. • Realist ontology offers a good methodology for building consistent representations. • DLs are helpful, but only if you know how to use them properly. • OWL is inadequate to represent even the most obvious facts. • Please. . . be critical when buzz words are used.