Slide1 l.jpg
This presentation is the property of its rightful owner.
Sponsored Links
1 / 77

Formal Ontology for the improvement and integration of biomedical terminologies J. Simon* PowerPoint PPT Presentation


  • 112 Views
  • Uploaded on
  • Presentation posted in: General

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.

Download Presentation

Formal Ontology for the improvement and integration of biomedical terminologies J. Simon*

An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -

Presentation Transcript


Slide1 l.jpg

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

  • 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

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

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.).


Slide5 l.jpg

Language A

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

Proprietary Terminologies

L

&

C

LanguageB

Lexicon

Lexicon

Others ...

Grammar

ICPC

Grammar

SNOMED

ICD

Medico-linguistic Ontology

Formal Domain Ontology

Cassandra Linguistic Ontology

MEDDRA

LinKBase


Slide9 l.jpg

BFO/MedO and LinkBase

BFO/MedO

“validates”


Theory of granular partitions b smith l.jpg

Theory of Granular Partitions (B. Smith)

Think of it as Alberti’s grid


Partitions l.jpg

Partitions

  • 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


Slide12 l.jpg

Maryland Congressional Representative Voting Zones


Slide13 l.jpg

Maryland Appellate Judicial Districts


Slide17 l.jpg

A Partition View on Meningitis

meninges

anatomical

partition

disorder of

meninges

disorder

partition

inflammation

of CNS

inflammation

partition

meningitis


Slide18 l.jpg

Partitions and LinkBase®

  • 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

  • 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


Generic dependence l.jpg

Generic Dependence

  • Generic Dependence:

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

  • A person cannot exist without having some temperature


Weak foundation l.jpg

Weak Foundation

  • 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

  • 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

  • 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

  • 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

  • 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.


Endurants and perdurants26 l.jpg

Endurants and Perdurants

  • 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

  • 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

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

  • Perdurants strictly depend on endurants


Participation l.jpg

Participation

  • 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

  • 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

  • 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

  • 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

  • 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

A

A < B

B


Snap bfo l.jpg

SNAP BFO


Span bfo l.jpg

SPAN BFO


Terminology integration in linkbase l.jpg

Terminology Integration in LinKBase

The Endurant/Perdurant Distinction at Work


Slide38 l.jpg

Homonymy!


Terminology integration in linkbase40 l.jpg

Terminology Integration in LinKBase

Mereological Scrutiny at Work


Terminology integration in linkbase42 l.jpg

Terminology Integration in LinKBase

The Function/Realization Distinction at Work


Functions and processes43 l.jpg

Functions and Processes

IS-ACTOR-OF

(HAS-FUNCTION)

LIVER

LIVER ACTIVITY

IS-A

IS-ACTOR-OF

ABERRANT LIVER


Functions and processes44 l.jpg

Functions and Processes

LIVER FUNCTION

IS-REALIZATION-OF

HAS-FUNCTION

HAS-ACTOR

LIVER

LIVER ACTIVITY

IS-A

ABERRANT LIVER


Slide45 l.jpg

LIVER

HAS-FUNCTION

LIVER FUNCTION


The need for a systematic top level l.jpg

The Need for a Systematic Top-Level

  • 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 ?

  • 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

  • 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

  • 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

  • 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

  • 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

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

  • 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

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

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


Slide57 l.jpg

What Does LinKBase Say About the World ?

  • 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.


Slide58 l.jpg

  • everything that is true for a domain-entity is true for all its subsumers


Necessary and sufficient criteria l.jpg

Necessary and Sufficient Criteria

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

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

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

=


Slide65 l.jpg

Implementation of BFO Axioms

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

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

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

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

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


Slide70 l.jpg

Implementation of BFO Axioms

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


Slide71 l.jpg

Axioms at the Domain Ontology Level

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


Slide72 l.jpg

Axioms at the Domain Ontology Level

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

  • 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


Conclusions74 l.jpg

Conclusions

  • 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

  • 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.


Slide76 l.jpg

  • Cervical incompetence - [ Diese Seite übersetzen ]... Studies have found that if surgicaldilatation of the cervix is performed,the risk of CI depends upon the number and degree of dilatation used. ...www.womens-health.co.uk/cxinc.htm - 12k - Im Cache - Ähnliche Seiten

  • Dilatation and Curettage - [ Diese Seite übersetzen ]... of Surgeons, this peer reviewed information brochure is aimed at a lay audienceand provides information on the surgical procedure, dilatation and curettage ...omni.ac.uk/browse/mesh/detail/C0012358L0012358.html - 16k - 8. Nov. 2003 - Im Cache - Ähnliche Seiten

  • DILATATION AND CURETTAGE - Definition by HyperDictionary.com - [ Diese Seite übersetzen ]...DILATATION AND CURETTAGE. WordNet Dictionary. Definition: [n] a surgical procedureusually performed under local anesthesia in which the cervix is dilated and ...www.hyperdictionary.com/dictionary/ dilatation+and+curettage - 7k - Im Cache - Ähnliche Seiten

  • ..misoprostol use in obstetrics and gynecology – a bibliography ...- [ Diese Seite übersetzen ]... Oral misoprostol versus placebo for cervical dilatation before vacuum aspirationin first ... for predilatation of the cervix in first trimester surgical abortion. ...www.misoprostol.org/e-1.html - 10k - Im Cache - Ähnliche Seiten

  • Genetic Issues - [ Diese Seite übersetzen ]... improved surgical techniques for adults wanting vaginoplasties or phalloplasties,increased knowledge and emphasis on non-surgicaldilatation, legal status of ...home.vicnet.net.au/~aissg/genetic_issues.htm - 24k - 8. Nov. 2003 - Im Cache - Ähnliche Seiten


Slide77 l.jpg

  • [PDF]Editorial: Dilation of the Ascending Aorta Due to Medial ...File Format: PDF/Adobe Acrobat - View as HTML... The authors indicated that the “waist- coat aortoplasty” was used exclusivelyin patients with asymmetric dilation of the aorta and they excluded patients ...www.icr-heart.com/journal/pdfs/Mar2003/ TironeDavid_Editorial.pdf - Similar pages

  • Circulation -- Abstracts: Jondeau et al. 99 (20): 2677... Clinical Investigation and Reports. Central Pulse Pressure Is a MajorDeterminant of Ascending AortaDilation in Marfan Syndrome. ...circ.ahajournals.org/cgi/content/abstract/99/20/2677 - Similar pages

  • Circulation -- Abstracts: Yin et al. 79 (4): 854... Laloux, O. Dubourg, JP Bourdarias, and S. Laurent Central Pulse Pressure Is a MajorDeterminant of Ascending AortaDilation in Marfan Syndrome Circulation, May ...circ.ahajournals.org/cgi/content/abstract/79/4/854 - Similar pages[ More results from circ.ahajournals.org ]

  • Aortic Valve Regurgitation -- Overview... Enlarged aorta (dilation of the aortic root), which can be associated with aging,hypertension, inherited diseases such as Marfan's syndrome, and certain ...my.webmd.com/content/healthwise/165/52415 - 44k - Cached - Similar pages


  • Login