Development of domain specific ontologies for health care (Surgery)

DEVELOPMENT OF DOMAIN SPECIFIC

ONTOLOGIES FOR HEALTH CARE (SURGERY)

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Research Proposal

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By
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MD. Sarfraz Ahmed

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Supervisor – Dr. Basir Abidin

Cyberjaya University College Of Medical Sciences
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Development of domain specific ontologies for health care (Surgery)

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 Development of domain specific ontologies for health care (Surgery)

A: Introduction
An ontology can be described as an artifact describing a specific, well delineated domain and
introducing the proper definitions and descriptions for all relevant concepts and relations in
that domain. The concepts are arranged in taxonomy and associated via relations (properties)
by applying formal axiomatic definitions to constrain their interpretation and well-formed
usage. Additionally, textual descriptions explain the meanings and appropriate uses of
concepts and relations in plain language for domain experts and system developers1. It is
well-known that ontologies can be a valuable artifact for data(base) integration. However, for

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ontologies to be useful, one first needs to develop a good ontology that covers the domain
accurately and precisely and has the right balance between utility and ontological correctness

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(the ontological trade-off) 2.

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It is now widely recognized that constructing a domain model, ontology , is an important step

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in the development of knowledge based systems. The advantages of such domain models
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have been widely canvassed , and include enabling the sharing of knowledge , the re-use of
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knowledge, and the better engineering of knowledge based systems with respect to
acquisition , verification and maintenance. If , however , we examine ontologies , we find
significant variety in them, even when they have been constructed for very similar purposes.
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At present the construction of ontologies is very much an art rather than a science8.

As indicated by Keet.C (2005) 2 at the current moment there exist ontologies that have been
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developed extensively in disciplines of biology notably in molecular biology such as GO i ,

OBO ii , FMA iii. However existing ontologies for the healthcare field often covers one
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specific disease or group2,3,4 & matters pertaining to healthcare institutions5. A descriptive

ontology for the domain of surgery has been attempted by the University of Leipzig ,
Germany as indicated in their 2006 research report6 , Their ontology for surgery has been
developed from their own top-level ontology termed as “COCAS”6.

B: Literature Review

i
Gene Ontology: http://www.geneontology.org
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Open Biological Ontologies: http://obo.sourceforge.net
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Foundational Model of Anatomy : http://sig.biostr.washington.edu/projects/fm/index.html

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 Development of domain specific ontologies for health care (Surgery)

Jones et al (1998) and an article published by the SemanticWeb10 have suggested various
methods for ontology development. They have mentioned that at the current moment in time
the nature of ontology development is not standardized and is more dependent on the
objective for building an ontology. However, the models differ in their emphasis
(maintenance is a major focus in the TOVE and Methontology approach for example) and
developmental approach to ontologies (unlike most models, the KBSI IDEF5 model is open-
ended making it an evolving prototype approach based on ongoing refinement). In detailing
the variety of ontology design methods, the authors also cautioned against a ‘cookbook

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approach’ as ontology analyses are open-ended and unique to the ontology in development8.

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According to a research report published by University of Leipzig in 2006 6 , An ontology for

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the domain of surgery was built in order to assist and support software interfaces that would
provide communication with patient data necessary for any kind of surgical intervention.

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These ontologies were developed to function as modular support systems6 that work in
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conjunction with other software systems that assist in surgery , also referred to as ‘SWOnt’6 ,
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The surgical workflow is an abstraction of a surgical intervention , Information which is of
interest to the user (surgeon, medical technician or health expert) that can be ascertained from
reality. In order to enable the use of surgical workflows (e.g. for purposes of analysis), one
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requires technical and formal descriptions of the surgical intervention6. One of the major
advantages of integrating and using a surgical ontology as a support system is that provides a
pre clinical assessment of any surgical procedure. The surgical workflow ontology is highly
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specialized which assists in guiding complex and risky surgical procedures.

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An ontological analysis of surgical deeds was conducted by Mori.R et.al. (1997) , the
objective of the research was to collect a set of words , suffixes and idioms regarding actions
in surgical procedures as defined in a CEN European prestandard. Then this collection was
compared with different authoritative sources for surgical definitions and an ontological
analysis was performed according to the ONIONS methodology9. The result was a formal
model on surgical actions which was an extension of their previous model ON8.5 using
ontolingua with “Frame Ontology”. The study also worked out a criterion to assist domain
experts in organizing hierarchies on surgical actions, according to points of view on
structural, instrumental and functional properties. This ontology however was not designed to
be repository of actual surgical procedures.

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 Development of domain specific ontologies for health care (Surgery)

Another similar study was carried out by Moigno.S et.al (2003) , on the terminology
extraction from standard text to build an ontology in surgical intensive care. Their objective
was to build an ontology of unambiguous surgical terminologies, this was done in part due to
lack of standardization in the way in which ontologies are built , hence acknowledging the
variability in coding which imparts many troubles in identifying specific terms they sought
to build another ontology specifically for the field of surgery. In order to do this they have
taken the use of various natural language processing tools in the construction of ontologies.
Such as NLP , SYNTEX , UPERY , SNOMED-RT , MAOUSSC , GALEN and

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MENELAS11. However these ontologies are mostly towards the various terminologies that
are used in surgery rather than actual surgical procedures.

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Hence a brief literature review reveals that at the current moment in time there have been
some efforts that have been done in order to construct ontologies for the domain of

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healthcare. However they are being created specifically to address the problem of ambiguity
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of medical terms. The objective of this study would be to assess the possibility of
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standardizing a methodology for ontological construction for surgery and at the same time
assess the feasibility of constructing a repository of surgical procedures in the form of an
ontology.
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C: Objectives
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 Development of domain specific ontologies for health care (Surgery)

1. To develop a knowledge base (ontology) for the domain of surgery consisting of 10

common surgical procedures performed in a hospital. The rationale behind choosing
those 10 surgical procedures will be based on the surgical procedures performed by
students in their clinical years. This would be the first phase of development;
subsequent phases would involve the incorporation of more surgical procedures
ranging from simple to the complex that shall be useful to both clinical students and
practitioners alike.

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2. Development of the surgical domain ontology accurately and precisely having a
proper balance between correctness and utility. Since one of the major concerns

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during the development of an ontology, would be to ascertain its correctness in terms

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of relationships between the various concepts within the ontology and their usability
with search engines.

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3. Development of a surgical domain ontology that can be easily integrated with a
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semantic search engine and optimized such that the output of the results would be
accurate enough to be used in a clinical setting.
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D: Methodology & Analysis

An ontology defines a common vocabulary for researchers who need to share information in
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a domain. It includes machine-interpretable definitions of basic concepts in the domain and

relations among them7. During the development of the surgical ontology 3 key areas will be
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focussed on, they are :- 7

1. Accessibility of the information among the software agents.

2. Reusability of the domain knowledge for other similar or coinciding domains.
3. Making the domain assumptions explicit –The information within the domains would
be made such that they can be easily understood to those who are not familiar with
this particular domain.
To address these issues the domains shall be developed in the following manner.

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 Development of domain specific ontologies for health care (Surgery)

Print Sources &

Non print Sources

Specification (Scope Identification) & Knowledge

Acqusition8
Identify the concepts that should be present within the
ontology from both print and non print sources

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Need for appointing Conceptualization
Subject Matter Experts Domain terms are identified as concepts , instances ,
[Clinicians , Specialists] verbs relations or properties and each are represented

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using an applicable informal representation8

nta ida Verification of Scopes

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Of the concepts and relationships for each case by a
Subject Matter Expert [SME’s]
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Formal Evaluation8
Testing the ontology via probable queries and analysis
of the results
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Integration
Integrating the tested and verified ontologies with a
semantic search engine. (MIP – Medical Informatics
Platform)
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FIG 1 - Schematic Representation of Proposed Ontology Development

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1. Collection & Verification of the clinical information shall be conducted by subject

matter experts, who would be clinicians, specialists & domain experts.
2. An ontology prototype for the domain of surgery shall be built which shall be later
analyzed for consistency, data integrity and validity via subject matter experts.

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References
1. Stenzhorn.H et al. (2008), “Developing an Ontology for research and care of Intracranial
Aneurysms” , Institute for Medical Biometry & Medical Informatics , Freiburg University
Medical Center , Freiburg , Germany.

2. Keet.C (2005), "Factors affecting ontology development in ecology" , KRDG Research Center ,
Faculty of Computer Science, Free University of Bozen-Bolzano , Piazza Domenicani, Bozen-
Bolzano , Italy.

3. Overton.J et.al, (2009) , "Open Biomedical Ontologies applied to prostate cancer" , Department
of philosophy, The University of Western Ontario, London , Canada; Department of Medical

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Imaging , London Health Sciences , London , Canada ; Director of Human Health , International
Atomic Agency , Vienna , Austria.

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4. Cantais.J et.al, (2005), “An example of food ontology for diabetes control” , Department of
Computer Science , University of Liverpool, Liverpool , UK ; ITACA , Universidad Politecnica

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de Valencia , Valencia, Spain ; Istituto Scientifico Universitario San Raffaele , Via Olgettina,
Milan , Italy.

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5. Pallavi.M et.al, (2008), “Development of a Comprehensive Error Ontology”, School of Health
Information Sciences, University of Texas Health Science Center at Houston; School of Nursing,
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University of Kansas ; Department of Biomedical Informatics, Arizona State University, USA.

6. “Innovative Center for Computer Assisted Surgery (ICCAS)” (2006) , Forschungs Bericht ,
Research Report 2006 , Universitat Leipzig , Leipzig Germany , Online research report retrieved
on 16/8/09 from http://www.uni-leipzig.de/forschb/06/e89980160.htm , Topic number 13.
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7. Noy.N & McGuinness.D , “Ontology Development 101:A Guide to creating your first Ontology”
, Stanford University , Stanford , California , U.S.A , Online tutorial retrieved on 16/8/09 from
http://protege.stanford.edu/publications/ontology_development/ontology101-noy-
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mcguinness.html.

8. Jones.D et.al., (1998) “Methodologies for ontology development” , Department of Computer

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Science , University of Liverpool , Liverpool , U.K

9. Mori.A et.al., (1997) ,”An ontological Analysis of Surgical Deeds” , Reparto Informatica Medica
, Istituto Tecnologie Biomediche , CNR , Roma , Italy ; IV Clin. Chirurgica and Dottorato
Informatica Medica, Univ. La Sapienza , Roma , Italy.

10. SemanticWeb (n.d) , “Ontology Engineering”, Semantic Webportal retrieved from

http://semanticweb.org/wiki/Ontology_Engineering on 26/8/09.

11. Moigono.S et.al., (2003) , “Terminology extraction from text to build and ontology in surgical
healthcare” , Annual Symposium Proceedings Archive , American Medical Informatics
Association , SPIM , UFR Broussais-Hotel-Dieu , SPIM , Paris , France , Proc AMIA Symp.
2002; 430-434.

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