Realist Ontology for the Semantic Web: Applications in Biomedical Informatics

1
Realist Ontology for the Semantic Web
Applications in Biomedical Informatics

• Werner Ceusters
• European Centre for Ontological Research
• Universität des Saarlandes
• Saarbrücken, Germany

2
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

3
European Centre forOntological Research
External members
Local members
Partners
Status Dec 2, 2004
4
European Centre forOntological Research
Directors
Member representatives
Management Board
Advisory Board
Status Dec 2, 2004
5
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.

6
IFOMIS competences
Status Dec 2, 2004
7
Our building
8
What philosophers are good for...
9
Short personal history
10
Ontology

11
WordNet 2.0 - 2003
Is this going to realise the Semantic
Web ?????????????
12
Ontology on the web
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 Sowas ontology page
Status Nov 29, 2004
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New search on Nov 3010.000 results more

• 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)

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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.

15
Tom Grubers view

• An ontology is a specification of a
  conceptualization.
• 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.

16
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.
17
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)

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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, p17
OWL Web Ontology Language Use Cases and
Requirements W3C Recommendation 10 February 2004

http//www.w3.org/TR/webont-req/
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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 W3C Recommendation 10 February 2004

http//www.w3.org/TR/webont-req/
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Realist Ontology
21
A visit to the operating theatre
A lot of objects present
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A visit to the operating theatre
A lot of processes going on
Haydom Lutheran Hospital, Tanzania
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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.

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The realist ontological square (Ignacio Angelelli)
Quality Universals
Substance Universals
differentia
exemplify
instance
instance
inheres
Substance Particulars
Quality Particulars
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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)

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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.

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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 ?

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Identity instanciation
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A practical example OntoClean

• 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.

Guarino Welty
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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

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Theory of granular partitions (B. Smith)
Think of it as Albertis grid
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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

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(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

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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

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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.

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Occurants and continuants
Picture by Vladimir Brajic
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(No Transcript)
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SpanBFO
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A Realist Ontology

• a for a computer understable representation of
  some pre-existing domain of REALITY, reflecting
  the properties of the objects within its domain
  in such a way that there obtain substantial and
  systematic correlations between reality and the
  ontology itself.

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Why is the concept-basedapproach so wide-spread ?
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Back to the operating theatre
He wants me to remove that blood
I must get rid of that blood
Suction, please !
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This is communication !
Give me a kocher, please.
kocher
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Triadic models of meaning The Semiotic/Semantic
triangle
Reference Concept / Sense / Model / View /
Partition
Sign Language/ Term/ Symbol
Referent Reality/ Object
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Aristotles triadic meaning model
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).
Aristotle, 'On Interpretation', 1.16.a.4-9,
Translated by Cooke Tredennick, Loeb Classical
Library, William Heinemann, London, UK, 1938.
pathema
semeia ? gramma/ phoné
pragma
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An interesting sidestepunderstanding

• 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 patients skin, his
  body temperature, blood pressure, ...
• processes that incision made by that surgeon,
  the rise of that patients temperature,...
• concepts may be taken in the above definition
  as Aristotles universals what is SAID OF a
  subject
• Substantial concepts patient, tumor, ...
• Quality concepts white, temperature
• ...

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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

reference
symbol
referent
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Dont confuse with homonymy !
mole
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Different thoughts Homonymy
R2
R3
R1
mole skin lesion
mole unit
mole
mole animal
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And by the way, synonymy...
the Aristotelian view
Richards view
sweat
sweat
perspiration
perspiration
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Freges view

• sense is an objective feature of how words are
  used and not a thought or concept in somebodys
  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 (Beethovens 10th symphony)

sense
name
reference (referent)
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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.

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Current state of the art onmeaning in
biomedical 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.

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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)
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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

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Requirements for clinical vocabularies (1)

• Domain completeness coverage of all possible
  terms that lie within a vocabularys 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)
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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.

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The price you pay if you gofor concepts ...
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Borders classification of medicine

• Medicine
• Mental health
• Internal medicine
• Endocrinology
• Oversized endocrinology
• Gastro-enterology
• ...
• Pediatrics
• ...
• Oversized medicine

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MeSHMedical 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

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MeSH Tree Structures - 2004

•  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
•  Health Care N
• Geographic Locations Z

What about this as a top ontology ???
61
MeSH Tree Structures - 2004

• 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

62
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 abundant sort of mistakes !
63
MeSH Tree Structures - 2004

• 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 ?
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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

65
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

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Snomed International (1995)knowledge in the
codes.

• posterior
• anatomic leaflet
• mitral
• cardiac valve
• cardiovascular

Why was this not a good idea ?
67
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

68
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 ...

69
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. -)

70
UMLS Semantic Network
71
Semantic Network Relationships

• Is_a
• physically related to
• spatially related to
• temporally related to
• functionally related to
• conceptually related to

72
Semantic Network Biologic Function Hierarchy
73
Semantic Network "affects" Hierarchy 
74
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, ...

75
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
• ...

76
Ok, then Description Logicswill save us ... ?
77
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)

78
Snomed and DL
SNOMED-RT (2000)
DL dont guarantee you to get parthood right !
79
Use of description logics does not guarantee
correct representations !
80
Sloppiness in definitions
81
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

82
NCI Thesaurus Root concepts
83
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

84
Definition of cancer gene
85
NCI Thesaurus architecture
Findings-And- Disorders-Kind
Anatomy-Kind
Disease
Formal subsumption or inheritance
Associative relationships providing
differentiae
Kinds restrict the domain and range of
associative relationships
ISA
Breast
Breast neoplasm
Disease-has-associated-anatomy
86
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

87
Thanks x there is OWL ?Where x ?


,
,
,
,
88
Understanding content (1)
John Doe has a pyogenic granuloma of the left
thumb
John Doe has a pyogenic granuloma of the left
thumb
89
Understanding content (2)
ltrecordgt ltpatientgtJohn Doelt/patientgt ltdiagnosisgtpy
ogenic granuloma of the left thumblt/diagnosisgt lt/r
ecordgt
ltrecordgt ltsubjectgt John Doe lt/subjectgt ltdiagnosisgt
pyogenic granuloma of the left thumb
lt/diagnosisgt lt/recordgt
90
Understanding content (3)
lt129465004gt lt116154003gtJohn Doelt/116154003gt lt
8319008 gt 17372009 ltfinding sitegt 76505004
ltlateralitygt7771000lt/lateralitygt lt/finding
sitegt lt/ 8319008 gt lt/129465004gt
91
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 ?

92
NCITs Lung in OWL

• ltowlClass rdfID"Lung"gt
• ltrdfslabelgtLunglt/rdfslabelgt
• ltcodegtC12468lt/codegt
• lthasTypegtprimitivelt/hasTypegt
• ltrdfssubClassOf rdfresource"Organ"/gt
• ltrdfssubClassOfgt
• ltowlRestrictiongt
• ltowlonProperty
• rdfresource"rAnatomic_Structure_Has_Location
  "/gt
• ltowlsomeValuesFrom rdfresource"Thoracic_Cavi
  ty"/gt
• lt/owlRestrictiongt
• lt/rdfssubClassOfgt
• ...
• lt/owlgt

All instances of lung must be located in at
least one instance of thoracic cavity Hence
total lung excision is impossible.
93
NCITs Lung in OWL

• ltowlClass rdfID"Lung"gt
• ltrdfslabelgtLunglt/rdfslabelgt
• ltcodegtC12468lt/codegt
• lthasTypegtprimitivelt/hasTypegt
• ltrdfssubClassOf rdfresource"Organ"/gt
• ltrdfssubClassOfgt
• ltowlRestrictiongt
• ltowlonProperty
• rdfresource"rAnatomic_Structure_Has_Location
  "/gt
• ltowlallValuesFrom rdfresource"Thoracic_Cavit
  y"/gt
• lt/owlRestrictiongt
• lt/rdfssubClassOfgt
• ...
• lt/owlgt

every assigned location of pleura must be an
instance of the class Thoracic Cavity Allows
lungs not to be located at all.
94
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.