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Formal Ontology for the improvement and integration of biomedical terminologies J. Simon* Ontology-based algorithms for error checking and semantic relationships expansion M. Casella dos Santos**. AMIA 2003.

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Formal Ontology for the improvement and integration of biomedical terminologies

J. Simon*

Ontology-based algorithms for error checking and semantic relationships expansion

M. Casella dos Santos**

AMIA

2003

*Institute for Formal Ontology and Medical Information Science (IFOMIS), Leipzig, Germany

** Language & Computing nv, Zonnegem, Belgium


Presentation overview l.jpg
PRESENTATION OVERVIEW biomedical terminologies

  • Introducing LinKBase

  • Introducing BFO; The Philosophical Ground

  • Ontology integration problems and solutions

  • Applying correct subsumption

  • Axiomatizing LinKBase with BFO

  • Conclusion


An integrated approach l.jpg
An Integrated Approach biomedical terminologies

L

L

L

&

&

&

C

C

C

NLU enabling tools for

knowledge supported

data-entry and -retrieval

Linguistic

application components

Medical and linguistic

knowledge required for

language understanding

LinKBase

Data structure and

function library for

language understanding

LinKFactory


Linkbase l.jpg
LinKBase biomedical terminologies

A Medical Domain Ontology designed to support

NLP applications and to integrate different medical

terminologies and ontologies.

  • Enables cross-mappings between external medical terminologies

  • (i.e. ICD-9-CM, ICD-10, SNOMED, Mesh, MedDRA, etc.).

  • The world’s largest medical ontology totalling more than 2,000,000

  • concepts and 5,300,000 links.

  • The ontological elements (concepts, linktypes, criteria) are language

  • independent and are linked to about 3,500,000 terms in various

  • languages (English, Spanish, French, etc.).


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Language A biomedical terminologies

Proprietary Terminologies

L

&

C

LanguageB

Lexicon

Lexicon

Others ...

Grammar

ICPC

Grammar

SNOMED

ICD

Medico-linguistic Ontology

Formal Domain Ontology

Cassandra Linguistic Ontology

MEDDRA

LinKBase


Slide7 l.jpg

Language A biomedical terminologies

Proprietary Terminologies

L

&

C

LanguageB

Lexicon

Lexicon

Others ...

Grammar

ICPC

Grammar

SNOMED

ICD

Medico-linguistic Ontology

Formal Domain Ontology

Cassandra Linguistic Ontology

MEDDRA

LinKBase


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BFO/MedO and LinkBase biomedical terminologies

BFO/MedO

“validates”


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Theory of Granular Partitions (B. Smith) biomedical terminologies

Think of it as Alberti’s grid


Partitions l.jpg
Partitions biomedical terminologies

  • An ontology is a partition of reality

  • A partition cuts the world in a certain way

  • There can be many different partitions of the same reality



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Maryland Appellate Judicial Districts biomedical terminologies


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A Partition View on Meningitis biomedical terminologies

meninges

anatomical

partition

disorder of

meninges

disorder

partition

inflammation

of CNS

inflammation

partition

meningitis


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Partitions and LinkBase biomedical terminologies®

  • domain-entity: represents cells of different partitions of reality

    • MENINGITIS (captured e.g. by the inflammation partition)

    • MENINGES (captured by an anatomical map)

  • meta-entity: represents cells of a partition prepared by third parties

    • ICD-10 : G03.9 : MENINGITIS, UNSPECIFIED

  • domain-entity-link: aspect of domain-entities determining a partition/perspective

    • HAS-SYSTEMIC-MEDIUM

    • HAS-CONSEQUENCE

  • criterion: perspective on a domain-entity yielded by a given partition

    • HAS-SYSTEMIC-MEDIUM MENINGES

    • HAS-CONSEQUENCE HEADACHE


Substances states powers and functions l.jpg
Substances, States, Powers and Functions biomedical terminologies

  • Strict Dependence: ODP(A,B)

  • A strictly depends on B whenever A cannot exist unless B does

  • John’s headache depends on John

  • Mary’s smile depends on Mary

  • Peter’s power of performing weddings depends on Peter

  • The beating function of Sarah’s heart depends on Sarah’s heart


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Generic Dependence biomedical terminologies

  • Generic Dependence:

  • A generically depends on Bs whenever A cannot exist without there being some B

  • A person cannot exist without having some temperature


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Weak Foundation biomedical terminologies

  • Weak Foundation: WF(A,B)

  • A is weakly founded on B whenever A strictly depends on B and all parts of B


Substances l.jpg
Substances biomedical terminologies

  • A Substance is an entity which is not strictly dependent on anything

  • SB(x)

  • SB(x) iff

  • y (x strictly depends on y)


States powers and functions l.jpg
States, Powers and Functions biomedical terminologies

  • States (the state of being happy, having a headache, having a temperature of 98.6°)

  • Powers (The power to wed people)

  • Functions (the function of pumping blood)

  • These are not substances; they have bearers on whom they strictly depend


Inherence l.jpg
Inherence biomedical terminologies

  • States, Powers and Functions inhere on the substances that bear them

  • IH(x,y)

  • Thus,

  • Inhere(x,y)  StrictlyDepends(x,y)


Endurants and perdurants l.jpg
Endurants and Perdurants biomedical terminologies

  • Some things persist differently through time than others

  • There are on the one hand objects: tables, chairs, countries, and people. These entities are said to endure through time, which means that they do not have temporal parts, but rather are wholly present at every moment in which they exist.


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Endurants and Perdurants biomedical terminologies

  • On the other hand are processes like brain surgeries, heart attacks, lives. These are said to perdure through time, which means that they do have temporal parts, such as the first half of the surgery, the last phase of the heart attack, one’s childhood


Endurants and perdurants27 l.jpg
Endurants and Perdurants biomedical terminologies

  • We call enduring, objectual entities “Endurants”: End(x)

  • We call perduring, processual entities “perdurants”: Perd(x)

  • No endurant is a perdurant, and no perdurant is an endurant


Endurants and perdurants28 l.jpg
Endurants and Perdurants biomedical terminologies

  • Endurants and perdurants relate in the relationships of participation and realization

  • Perdurants strictly depend on endurants


Participation l.jpg
Participation biomedical terminologies

  • The surgeon operates, the heart beats, lungs inhale

  • PP(x,y)

  • PP(surgeon, surgery)

  • PP(heart,beating processes)

  • PP(lungs, respiratory processes)


Realization l.jpg
Realization biomedical terminologies

  • Powers and Functions may go unrealized

  • A stopped heart is not realizing its function of pumping blood

  • The heart of a tachycardic is not fulfilling the function of beating at a proper rate

  • Peter may not currently be realizing his power of wedding couples


Participation and realization l.jpg
Participation and Realization biomedical terminologies

  • Participation is generally a relation between a substance and a process which depends on it (it would not have been the same particular surgery if Dr. Jones had not been there)

  • Realization is a relation between a power or function and a process


Functions and processes l.jpg
Functions and Processes biomedical terminologies

  • No function is the same as a process realizing it

  • No process is the same as any endurant participating in it


Parts and wholes l.jpg
Parts and Wholes biomedical terminologies

  • Proper Parthood: 

  • x  x

  • x  y   y  x

  • x  y & y  z  x  z

  • Parthood: 

  • x  y iff x  y or x = y


Parthood l.jpg
Parthood biomedical terminologies

A

A < B

B


Snap bfo l.jpg
SNAP BFO biomedical terminologies


Span bfo l.jpg
SPAN BFO biomedical terminologies


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Terminology Integration in LinKBase biomedical terminologies

The Endurant/Perdurant Distinction at Work


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Homonymy! biomedical terminologies


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Terminology Integration in LinKBase biomedical terminologies

Mereological Scrutiny at Work


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Terminology Integration in LinKBase biomedical terminologies

The Function/Realization Distinction at Work


Functions and processes43 l.jpg
Functions and Processes biomedical terminologies

IS-ACTOR-OF

(HAS-FUNCTION)

LIVER

LIVER ACTIVITY

IS-A

IS-ACTOR-OF

ABERRANT LIVER


Functions and processes44 l.jpg
Functions and Processes biomedical terminologies

LIVER FUNCTION

IS-REALIZATION-OF

HAS-FUNCTION

HAS-ACTOR

LIVER

LIVER ACTIVITY

IS-A

ABERRANT LIVER


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LIVER biomedical terminologies

HAS-FUNCTION

LIVER FUNCTION


The need for a systematic top level l.jpg
The Need for a Systematic Top-Level biomedical terminologies

  • While LinkBase currently features certain reasoning capabilities, it lacks the sort of coherent underlying structure necessary for advanced reasoning applications

  • A more systematic top-level is needed


Slide47 l.jpg

What Does LinKBase Say About the World ? biomedical terminologies

  • if a real-world entity is an instance of a domain-entity, all that is said about the domain-entity applies to the instance;

  • the statement “A-Link-B” says something about all instances of A, but nothing about instances of B unless the Link is declared to have an inverse;


The bfo top level standard l.jpg
The BFO Top-Level Standard biomedical terminologies

  • To each concept and link there is already a space for definitions and characterization, but this is specified informally, – it is not relevant to current applications, and there are no standards governing definitions of links or concepts

  • This means there is no systematic uniformity to how we understand them, and consequently their information content is much lower than it could be


The bfo top level standard49 l.jpg
The BFO Top-Level Standard biomedical terminologies

  • Define a standard protocol for definitions of concepts and links (ideally in some formal language with as concise a set of predicates as possible).

  • This is a repair-the-ship-at-sea kind of project: It may be necessary to revise the links, as well as to try and be creative enough to find a logical form common to all of them


The bfo top level standard50 l.jpg
The BFO Top-Level Standard biomedical terminologies

  • An extra level of structure and coherent information will allow for the automation of processes currently run by hand

  • Preliminary work already enables L&C to infer flaws in their taxonomy: links that unite categories and are missing, existing links that are misclassified


The bfo top level standard51 l.jpg
The BFO Top-Level Standard biomedical terminologies

  • The Proposed reading (in explicit logical form) of : CONCEPT A- LINK -CONCEPT B is:

  • For all a in the class associated with CONCEPT A, there is a b in the class associated with CONCEPT B, such that aRb

  • R is some relation expressed in the logical language of BFO or MEDo (ideally)


The bfo top level standard52 l.jpg
The BFO Top-Level Standard biomedical terminologies

In technical terms:

For every LinKBase link: X–LINK–Y, the definition is a mapping to a п2 – complexity formula:

x (xX  y (yY & xRy))

(where X and Y are variables ranging over LinKBase concepts, and R is a relation on instances in the formal language of BFO):


The bfo top level standard53 l.jpg
The BFO Top-Level Standard biomedical terminologies

  • Example:

  • Liver Activity – Has-Actor – Liver

  • For every (actual particular process of) liver activity, A, there is some liver, B, and B is the principal participant of A.


Slide54 l.jpg

Multiple Inheritance Problem biomedical terminologies

IS-A INCISION

HAS-PARTICIPANT LARYNX

IS-A EXCISION

HAS-PARTICIPANT TUMOR

FULLY DEFINED BY

FULLY DEFINED BY

INCISION OF LARYNX

TUMOR EXCISION

IS-A

IS-A

LARYNGOTOMY WITH REMOVAL OF TUMOR

FULLY DEFINED BY

IS-A INCISION

IS-A EXCISION

HAS-PARTICIPANT TUMOR

HAS-PARTICIPANT LARYNX

IS-A INCISION OF LARYNX

IS-A TUMOR EXCISION

=


Multiple inheritance problem l.jpg
Multiple Inheritance Problem biomedical terminologies

WRONG SUBSUMPTION!

LARYNGECTOMY

IS-A

FULLY DEFINED BY

LARYNGOTOMY WITH REMOVAL OF TUMOR

IS-A EXCISION

HAS-PARTICIPANT LARYNX

FULLY DEFINED BY

IS-A INCISION

IS-A EXCISION

HAS-PARTICIPANT TUMOR

HAS-PARTICIPANT LARYNX


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What Does LinKBase Say About the World ? biomedical terminologies

  • if you know that a real-world entity satisfies the Full Definition of a domain-entity-type, then you may infer that that object is an instance of that type.



Necessary and sufficient criteria l.jpg
Necessary and Sufficient Criteria its subsumers

WRONG SUBSUMPTION!

IS-A

LARYNGECTOMY

FULLY DEFINED BY

REMOVAL OF LARINGEAL TUMOR

IS-A EXCISION

HAS-PARTICIPANT LARYNX

FULLY DEFINED BY

IS-A EXCISION

HAS-PARTICIPANT TUMOR

HAS-PARTICIPANT LARYNX


Necessary and sufficient criteria60 l.jpg
Necessary and Sufficient Criteria its subsumers

LARYNGECTOMY

FULLY DEFINED BY

REMOVAL OF LARINGEAL TUMOR

IS-A EXCISION

HAS-THEME LARYNX

FULLY DEFINED BY

IS-A EXCISION

HAS-THEME TUMOR

HAS SOURCE LARYNX


Necessary and sufficient criteria61 l.jpg
Necessary and Sufficient Criteria its subsumers

CORRECT SUBSUMPTION

NOT FOUND!

IS-A

ABDOMINAL ORGAN INFLAMMATION

IS-A

GASTRITIS

ULCERATIVE GASTRITIS

FULLY DEFINED BY

HAS-SYSTEMIC-MEDIUM

STOMACH

IS-A INFLAMMATORY PROCESS

HAS-SYSTEMIC-MEDIUM STOMACH

“AFFECTS” GASTRIC ACTIVITY


Slide64 l.jpg

= its subsumers


Slide65 l.jpg

Implementation of BFO Axioms its subsumers

Axiom is then applied, what allows

properties and states (temperature, shape,

colour...) to inhere in the HUMAN BODY.

IS-A

HUMAN BODY

BFO entities axioms: apply when LinkBase concepts are subsumed by a BFO entity.

BFO SUBSTANCE

Specified by axiom: SBx <=> y(yIHx)

SUBSUMED BY

BODY OF ORGANISM


Slide66 l.jpg

Implementation of BFO Axioms its subsumers

INFECTED CYST

INFECTION

IS-ACTEE-OF

Axiom is then applied, what allows the deduction that INFECTION is a

Perdurant and consequentely has temporal parts.

BFO formal relations axioms: apply on instances of particular Linktype mapped to BFO formal relations.

Linktype

IS-ACTEE-OF

BFO formal relation PARTICIPATION

Specified by axiom: xPPy => End(x) & Perd(y)

MAPS TO


Other examples of mapped relations l.jpg
Other examples of mapped relations its subsumers

MAPS TO

Linktype

IS-STATE-OF-WE-OF

BFO formal relation INHERENCE

Linktype

IS-CONSEQUENCE-OF

MAPS TO

BFO formal relation FOUNDATION

Linktype

HAS-THEME

BFO formal relation PARTICIPATION

MAPS TO


Slide68 l.jpg

Implementation of BFO Axioms its subsumers

ABDOMINAL

PAIN

PERDURANT

ENDURANT

PARTICIPATION

SUBSUMED BY

SUBSUMED BY

HAS-CONSEQUENCE

CRAMP

ABDOMEN

HAS-SYSTEMIC

MEDIUM

::

::

ABDOMINAL

CRAMP

“The patient complained of cramps in his abdomen.”

::

Identified relation: HAS-SYSTEMIC-MEDIUM

(mapped to PARTICIPATION)

Instance level (NLP applications) X Domain ontology level (LinkBase)

Applied at instance level axioms help to transform natural language text into formal

semantic representation by:

- Inferring semantic relations between instances of concepts in the ontology.

- Identifying new instances of concepts not explicitily mentioned or mapped.


Slide69 l.jpg

Implementation of BFO Axioms its subsumers

IS-STATE-OF-WE-OF

CAPILLARY HYPERPERMEABILITY

ONE-SIDEDDEPENDENCY?

NECESSITY FOR REVERSE

AXIOM.

CAPILLARY

IS-O-S-DEPENDENT-ON

HAS-WE-STATE

CAPILLARY

PERMEABILITY

Domain ontology level (LinkBase)

*BFO is an “upper level” ontology formalized according to a first order language

of logical entailments that work on the instance level. LinkBase, however, is a

system of generalizations, or categorical relations.

*In LinkBase most linktypes, for example HAS-MATERIAL-PART, have a reverse link, IS-MATERIAL-PART-OF. We determined that the reverse links require reverse axioms in order to be maintain the generalizability governed by the 2 formula.

BFO INHERENCE

Specified by axiom: xIHy => xODPy

MAPS TO

Linktype

IS-STATE-OF-WE-OF

Linktype

HAS-WE-STATE

CONTRA-LINK


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Implementation of BFO Axioms its subsumers

HAS-WE-STATE

Link violates the Π2 formula:

Not all instances of CAPILARRY

have a hyperpermeability.

Domain ontology level (LinkBase)

*The requirement of generalizability in LinkBase entails that we cannot simply reverse

the terms from x <IS-STATE-OF-WE-OF> y (xIHy) to y <HAS-WE-STATE>x (yRIHx),

an operation perfectly valid at the instance level. Consequently axioms cannot be reverted by

reverting the variables!

IS-STATE-OF-WE-OF

CAPILLARY HYPERPERMEABILITY

CAPILLARY

Reverse axiom xRIHy => yODPxis then incorrect!

*Our solution then, has been to introduce a set of reverse axioms through the entire chain of

formal relations, till the most primitive BFO formal relation (Weak Foundation). For the example

above the correct reverse axiom is: xRIHy => xRODPy


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Axioms at the Domain Ontology Level its subsumers

HAS-ACTEE

Applied at domain ontology level axioms help us improve and expand the ontology by:

- Inferring new relations between concepts in the ontology.

- Supporting automated check for ontological errors.

- Constraining the modelling space.

HAS-ACTEE

SKIN

INFECTION OF SKIN ULCER

HAS-ACTEE

ULCER

IS-PROPER-

MATERIAL-

PART-OF

The link HAS-ACTEE is mapped to the BFO relation PARTICIPATION which leads to Weak Foundation and its axiom:

xWFy & zy => xWFz

IS-A

SKIN ULCER


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Axioms at the Domain Ontology Level its subsumers

The link HAS-THEME is mapped to the reverse BFO relation PARTICIPATION,

defined by the axiom:

xRPPy => Perd(x) & End(y)

Link is not allowed because

according to the axiom the target

congept must be an Endurant!

HAS-THEME

HAS-THEME

REMOVAL OF BYPASS OF OESOPHAGUS

Supporting automated check for ontological errors & Constraining the modelling space

ENDURANT

PERDURANT

IS-A

IS-A

SURGICALLY ALTERED

STRUCTURE

BYPASS SURGERY

IS-A

IS-A

OESOPHAGUS BYPASS

BYPASS OF OESOPHAGUS


Conclusions l.jpg
Conclusions its subsumers

  • Our collaboration still in its infancy

  • Already, philosophically inspired changes have led to greater internal consistency of LinKBase, and aided its capacity to integrate diverse ontology and terminology systems


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Conclusions its subsumers

  • Integration and efficiency problems arise from ad hoc solutions to constraints on database and algorithm design.

  • Ad hoc solutions solve local problems, but generate further ones later on


Conclusions75 l.jpg
Conclusions its subsumers

  • The project of philosophical ontology is to achieve natural, elegant and accurate organizational partitions of reality

  • By heeding its lessons, we may design comprehensive applications ontologies without feet of clay, that are able to tackle global integration and efficiency problems.


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