eco r european centre for ontological research introduction to ontology tutorial for smbm 2005...

ECOREuropean Centre forOntological Research

Introduction to Ontology

Tutorial for SMBM 2005

Werner CeustersEuropean Centre for Ontological Research

Universität des Saarlandes

Saarbrücken, Germany


Lecture overview

• Credentials• The many faces of “ontology”• Realist ontology• Why is the concept-based approach so wide-

spread ?• The price you pay if you go for concepts ...• Can Description Logics save the world ?• And then there was OWL• Take home messages


European Centre forOntological Research

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Status April 8, 2005


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Institute for Formal Ontologyand 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.


IFOMIS competences•Logics X X X

•Informatics X X

•Spatio-temporal reasoning X

•Medicine X X X

•Knowledge engineering X

•Formal Ontology / metaphysics X X X X X

•Mathematics X X

•Qualitative spatial reasoning X X

•Ontological engineering X X

•History of philosophy X

•Philosophy of science X

•Linguistics X

Status Dec 2, 2004

•Formal Ontology / metaphysics

•Logics

•History of philosophy•Philosophy of science


Our building


What philosophers are good for...


Short personal history

1959 - ...1977

1989

1992

1998

2002

2004


“Ontology”


“Ontology” on the web

Status Nov 29, 2004

The most cited definition: Tom

Grüber 1993

Inactive since August 7, 2004.

W3C Web Ontology initiative

Ontology from a philosophical perspective.

Important bioinformatics

resource

Realist ontology in use.

Barry Smith

Popular ontology editor from Manchester

SUO Upper Ontology Initiative

John Sowa’s ontology pageApril 7, 2005

• Increase of 50% in number of hits• Ontology.org disappeared• Wikipedia entry for Ontology appeared


Search on Nov 30:

• 1 What is an Ontology?• 3 Gene Ontology Consortium• 4 W3C Web Ontology (WebOnt) Working Group (OWL) (Closed)• 7 Buffalo Ontology Site• 15 MGED NETWORK :: Ontology Working Group (OWG)• 20 Laboratory for Applied Ontology (LOA)• 21 ONTOLOGY WORKS INC.• 34 John Bateman; ontology portal root• 53 The Protégé Ontology Editor and Knowledge Acquisition System• 59 Institute for Formal Ontology and Medical Information Science ...• 86 Autofellatio and Ontology• 188 EUROREC 2004, Implemantation Guidelines, ...• 192 Foundational Ontology (Leeds)• 676 Ontology Server research (StarLab)

?????


If, later, you can remember just one 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.


Tom Gruber’s view

• 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.

• 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.

ECOREuropean Centre forOntological 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.

ECOREuropean Centre forOntological Research 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)


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.


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)

ECOREuropean Centre forOntological Research Ontology

What it means if we use the wordA proposal put forward by the SI roadmap

pannel

• An ontology is a representation of some pre-existing 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


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


An example:Electronic Health Records (1)

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;


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.

An example:Electronic Health Records (2)


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.


“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).

OWL Web Ontology Language; Use Cases and RequirementsW3C Recommendation 10 February 2004

http://www.w3.org/TR/webont-req/

e-Health - making healthcare better for European citizens: An action plan for a European e-Health Area

COM (2004) 356 final, 30.4.2004, p17


• 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 RequirementsW3C Recommendation 10 February 2004

http://www.w3.org/TR/webont-req/

“Ontology”


Semantic Interoperability

• 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

ECOREuropean Centre forOntological Research ‘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


Concept based terminology

• “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.


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.


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.


Realist Ontology


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.

ECOREuropean Centre forOntological 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 – p, c – c, p – c, c – p

ECOREuropean Centre forOntological Research (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 ?

ECOREuropean Centre forOntological ResearchImages 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


A visit to the operating theatre

Haydom Lutheran Hospital, Tanzania

This surgeon

This amputation stump

A lot ofobjects present

This mask

This hand

with some relations

Part of



This wound being closed by holding ...

That wound fluid

drained

A lot ofprocesses going on

This kocher being held in that hand of that surgeon

with some relations

Part of

A visit to the operating theatre

ECOREuropean Centre forOntological Research “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.

epistemology

ontology


The realist ontological square (Ignacio Angelelli)

Substance Particulars Quality Particulars

SubstanceUniversals

QualityUniversals

instance instance

differentia

exemplify

inheres


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)


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 ?

ECOREuropean Centre forOntological Research Identity & instanciation

child adult

caterpillar butterfly

t

person

animal

Livingcreature


• +I The property carries a common identity criterion for all its instances.

• −I 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.

A practical example: OntoClean

Guarino & Welty


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


Theory of granular partitions (B. Smith)

Think of it as Alberti’s grid


Copyright 2001, United Feature Syndicate Inc.

Reality: not just a matter of view


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

ECOREuropean Centre forOntological Research (Simplified) Logic of classes

• 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:


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

ECOREuropean Centre forOntological Research 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.


Occurants and continuants

Picture by Vladimir Brajic


SpanBFO


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


Parthood as a Relation between Instances

• Introduced as primitive:– p part_of p1

• 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, p1, if p part_of p1

and p1 part_of p then p and p1 are identical,– transitivity: for all p, p1, p2, if p part_of p1 and

p1 part_of p2, then p part_of p2.


Parthood as a Relation between Classes

• For continuants: (‘heart’, ‘person’)– C part_of C1 =def. for all c, t, if c instance_of

C at t then there is some c1 such that c1 instance_of C1 at t and c part_of c1 at t.

• For processes: (‘menopauze’, ‘aging’)– P part_of P1 =def. for all p, if p instance_of P,

then there is some p1 such that: p1 instance_of P1 and p part_of p1.

These definitions tell you ONLY something about C’s and P’s, but nothing about C1’s and P1’s !!!


Possible variants

• R1(A, B) =: x (Inst(x, A) y(Inst(y, B) & Rxy)) – every A stands in relation R to some B

• R2(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

• R12(A, B) =: R1(A, B) & R2(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 itDonnelly and Bittner, 2005


Properties of relations among individuals vs. properties of relations among classes

Among Individuals

Among Classes

R is... R1 must also

be...?

R2 must also

be...?

R12 must also

be...?

Reflexive Yes Yes Yes

Irreflexive No No No

Symmetric No No Yes

Asymmetric No No No

Antisymmetric No No No

Transitive Yes Yes Yes

Donnelly and Bittner, 2005


GALEN assertions using isDivisionOF and hasDivision

GALEN’s isDivisionOf assertion BIT+Clrelation

GALEN’s hasDivision BIT+Clrelation

Female Pelvic Cavity isDivisionOf Pelvic Part of Trunk

PP1 none

Prostate Gland isDivisionOf Genito-Urinary System

PP1 none

none Pelvic Part of Trunk hasDivision Hair

(PP-1)1

LeftHeartVentricle isDivisionOf Heart

PP12 Heart hasDivision LeftHeartVentricle

(PP-1)12

Prostate Gland isDivisionOf Male Genito-Urinary System

PP12 Male Genito-Urinary System hasDivision Prostate Gland

(PP-1)12

Urinary Bladder isDivisionOf Genito-Urinary System

PP12 none

Pericardium isDivisionOf Heart none Heart hasDivision Pericardium none

Donnelly and Bittner, 2005

ECOREuropean Centre forOntological 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 for 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.

ECOREuropean Centre forOntological Research OBO primitive relationships

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 c1 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 c1 – 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 c1 in such a way that matter is inherited by the one from the other

ECOREuropean Centre forOntological Research OBO primitive relationships

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 p1, r part_of r1 – 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


Definition of is_a

• For continuants:– C is_a C1 =def. for all c, t, if c instance_of C at t

then c instance_of C1 at t.

• For processes:– P is_a P1 =def. for all p, if p instance_of P then

p instance_of P1.


Properties of OBO relations

Relation type transitive symmetric reflexive antisymmetric

is_a + – + +

part_of + – + +

located_in + – + –

contained_in – – – –

adjacent_to – + – –

transformation_of + – – –

derives_ from – – + –

preceded_by + – – –

has_participant – – – –

has_agent – – – –


Why is the concept-basedapproach so wide-spread ?

ECOREuropean Centre forOntological Research Back to the operating theatre


I must get rid of that

blood

Suction, please !

He wants me to

remove that blood

Fluid being removed


= ?

This is communication !

kocher Give me a kocher, please.


Triadic models of meaning: The Semiotic/Semantic triangle

Sign:Language/

Term/Symbol

Referent:Reality/Object

Reference: Concept / Sense / Model / View / Partition

ECOREuropean Centre forOntological Research Aristotle’s triadic meaning

model

semeia

gramma/ phoné pragma

pathemaWords 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).

Aristotle, 'On Interpretation', 1.16.a.4-9, Translated by Cooke & Tredennick,

Loeb Classical Library, William Heinemann, London, UK, 1938.

ECOREuropean Centre forOntological 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– ...

ECOREuropean Centre forOntological Research Richards’ semantic triangle

• Reference (“concept”): “indicates the realm of memory where recollections of past experiences and contexts occur”.

• Hence: as with Aristotle, the reference is “mind-related”: thought.

• But: not “the same for all”, rather individual mind-related

symbol referent

referenceunderstandingmy your understanding


Don’t confuse with homonymy !

“mole” mole (animal)

R1

mole (unit)

R2

mole (skin lesion)

R3


Different thoughts Homonymy

“mole” mole “animal”

R1

mole “unit”

R2

mole“skin lesion”

R3

symbol referent

understanding

One conceptof x understanding of y


And by the way, synonymy...

the Aristotelian view Richards’ view

“perspiration”

“sweat”“sweat”

“perspiration”

ECOREuropean Centre forOntological Research Frege’s view

• “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)

• a name with a sense does not need to have a reference (“Beethoven’s 10th symphony”)

reference(=referent)

sense

name


Ontology and the semantic triangle• 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

ECOREuropean Centre forOntological 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)


With “concepts”, it became:

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

ECOREuropean Centre forOntological Research Requirements for clinical

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)

ECOREuropean Centre forOntological Research Requirements for clinical

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.


The price you pay if you gofor concepts ...

ECOREuropean Centre forOntological Research It’s just too funny...

• UMLS-SN: – Bacterium causes Experimental model of disease– Educational activity associated with pathologic function

• HL7: 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


Border’s classification of medicine

• Medicine– Mental health– Internal medicine

• Endocrinology–Oversized endocrinology

• Gastro-enterology• ...

– Pediatrics– ...– Oversized medicine

ECOREuropean Centre forOntological Research MeSH:

Medical Subject Headings

• Designed for bibliographic indexing, eg Index Medicus

• Basis for MedLINE• focuses on biomedicine and other basic

healthcare sciences• clinically very impoverished• Consistency amongst indexers:

– 60% for headings– 30% for sub-headings


MeSH Tree Structures - 20041. Anatomy [A] 2. Organisms [B] 3. Diseases [C] 4. Chemicals and Drugs [D] 5. Analytical, Diagnostic and Therapeutic Techniques and Equipment [E] 6. Psychiatry and Psychology [F] 7. Biological Sciences [G] 8. Physical Sciences [H] 9. Anthropology, Education, Sociology and Social Phenomena [I] 10. Technology and Food and Beverages [J] 11. Humanities [K] 12. Information Science [L] 13. Persons [M] 14. Health Care [N] 15. Geographic Locations [Z]

What about this as a top ontology ???


• Cardiovascular Diseases [C14] – Heart Diseases [C14.280]

• Arrhythmia [C14.280.067] + • Carcinoid Heart Disease [C14.280.129] • Cardiomegaly [C14.280.195] + • Endocarditis [C14.280.282] + • Heart Aneurysm [C14.280.358] • Heart Arrest [C14.280.383] + • Heart Defects, Congenital [C14.280.400]

– Aortic Coarctation [C14.280.400.090] – Arrhythmogenic Right Ventricular Dysplasia [C14.280.400.145] – Cor Triatriatum [C14.280.400.200] – Coronary Vessel Anomalies [C14.280.400.210] – Crisscross Heart [C14.280.400.220] – Dextrocardia [C14.280.400.280] +

MeSH Tree Structures - 2004


• Body Regions [A01] – Extremities [A01.378]

• Lower Extremity [A01.378.610] – Buttocks [A01.378.610.100] – Foot [A01.378.610.250]

» Ankle [A01.378.610.250.149] » Forefoot, Human [A01.378.610.250.300] + » Heel [A01.378.610.250.510]

– Hip [A01.378.610.400] – Knee [A01.378.610.450] – Leg [A01.378.610.500] – Thigh [A01.378.610.750]


The most abundantsort of mistakes !


• Body Regions [A01] – Abdomen [A01.047] + – Back [A01.176] + – Breast [A01.236] + – Extremities [A01.378]

• Amputation Stumps [A01.378.100] • Lower Extremity [A01.378.610] + • Upper Extremity [A01.378.800] +

– Head [A01.456] + – Neck [A01.598] – Pelvis [A01.673] + – Perineum [A01.719] – Thorax [A01.911] + – Viscera [A01.960]


And here ?

ECOREuropean Centre forOntological Research SNOMED International (1995)

• 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

ECOREuropean Centre forOntological Research Snomed International (1995)

Number of records (V3.1)• T Topography 12,385• M Morphology 4,991• F Function 16,352• L Living Organisms 24,265• C Drugs &Biological Products 14,075• A Physical Agents, Forces and Activities 1,355• D Disease/ Diagnosis 28,623• P Procedures 27,033• S Social Context 433• J Occupations 1,886• G General Modifiers 1,176• TOTAL RECORDS 132,641

ECOREuropean Centre forOntological Research Snomed International (1995):

knowledge in the codes.

posterior anatomic leaflet

mitral cardiac valve

cardiovascular

T - 23 5 3 2

Why was this not a good idea ?

ECOREuropean Centre forOntological Research Snomed International :

multiple ways to express the same thing

D5-46210 Acute appendicitis, NOS

D5-46100 Appendicitis, NOS

G-A231 Acute

M-41000 Acute inflammation, NOS

G-C006 In

T-59200 Appendix, NOS

G-A231 Acute

M-40000 Inflammation, NOS

G-C006 In

T-59200 Appendix, NOS

ECOREuropean Centre forOntological Research The International

Classification of diseases (WHO).• ...

• Chapter II: Neoplasms (C00-D48)• Chapter III: Diseases of the Blood and Blood-forming organs and

certain disorders involving the immune mechanism (D50-D89)• Excludes : auto-immune disease (systemic) NOS (M35.9)• ....• Nutritional Anemias (D50-D53)• D50 Iron deficiency anaemia• Includes: ...• D50.0 Iron deficiency anaemia secondary to blood loss (chronic)• Excludes : ...• D50.1 ...• D51 Vit B12 deficiency anaemia• Haemolytic Anemias (D55-D59) • ...• Chapter IV: ...

ECOREuropean Centre forOntological 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 human-readable 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. :-)


UMLS Semantic Network

ECOREuropean Centre forOntological Research Semantic Network

Relationships• Is_a

• physically related to

• spatially related to

• temporally related to

• functionally related to

• conceptually related to

ECOREuropean Centre forOntological Research Semantic Network “Biologic

Function” Hierarchy


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


“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, ...


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”

• ...


Ok, then Description Logicswill save us ... ?


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) (hasValue and one of)– Number restrictions (counting quantifiers)


‘Well, that’s because they don’t

use description logics or OWL’

SNOMED-RT (2000)

SNOMED-CT (2003)

DL don’t guarantee you to get parthood right !

You really think so ?


F-DL

(Frankenstein’s DL)

ECOREuropean Centre forOntological Research Use of description logics does not

guarantee correct representations !

ECOREuropean Centre forOntological Research Sloppiness in definitions

new-1

new-2


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


NCI Thesaurus Root concepts

Anatomic Structure, Anatomic System, or Anatomic Substance ?Or ? Does the NCI not know to which categoryAny item classified there belongs ?Anatomic Substance ? If yes, why is geneproduct not subsumed by it ? If no, why aredrugs and chemicals not subsumed by it ?


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


Definition of “cancer gene”


NCI Thesaurus architecture

Disease

BreastBreast neoplasmDisease-has-associated-anatomy

ISA

Findings-And-Disorders-Kind Anatomy-Kind

“Formal subsumption” or

“inheritance”

“Associative” relationships providing

“differentiae”

“Kinds” restrict the domain and range of

associative relationships

What diseases have a diameter of over 3 cm ?


Ontology versusDescription 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


Thanks x there is OWL ?

Where x {

}

, , ,

,


Understanding content (1)

“John Doe has a pyogenic granuloma of the left thumb”



<record><patient>John Doe</patient>

<diagnosis>pyogenic granuloma of the left thumb</diagnosis>

</record>

< >

< > </ >

< > </ >

</ >



<129465004><116154003>John Doe</116154003>

< 8319008 > 17372009

<finding site> 76505004

<laterality>7771000</laterality>

</finding site>

</ 8319008 >

</129465004>


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 ?

ECOREuropean Centre forOntological Research NCIT’s “Lung” in OWL

<owl:Class rdf:ID="Lung"><rdfs:label>Lung</rdfs:label><code>C12468</code><hasType>primitive</hasType><rdfs:subClassOf rdf:resource="#Organ"/><rdfs:subClassOf>

<owl:Restriction><owl:onProperty

rdf:resource="#rAnatomic_Structure_Has_Location"/><owl:someValuesFrom rdf:resource="#Thoracic_Cavity"/>

</owl:Restriction></rdfs:subClassOf>...</owl>

“All instances of lung must be located in at least one

instance of thoracic cavity”Hence: total lung excision is

impossible.

ECOREuropean Centre forOntological Research NCIT’s “Lung” in OWL

<owl:Class rdf:ID="Lung"><rdfs:label>Lung</rdfs:label><code>C12468</code><hasType>primitive</hasType><rdfs:subClassOf rdf:resource="#Organ"/><rdfs:subClassOf>

<owl:Restriction><owl:onProperty

rdf:resource="#rAnatomic_Structure_Has_Location"/><owl:allValuesFrom rdf:resource="#Thoracic_Cavity"/>

</owl:Restriction></rdfs:subClassOf>...</owl>

“every assigned location of pleura must be an instance of

the class Thoracic Cavity”Allows lungs not to be

located at all.


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.

eco r european centre for ontological research introduction to ontology tutorial for smbm 2005...

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