Introduction Motivation & Objectives Tools Used Architecture Conclusion Bibliography

ONTOLOGICAL FRAMEWORK FOR MEDICAL

INFORMATION RETRIEVAL AND
INFERENCING MECHANISM

Absheer K.K
Ashwin Thomas
Shafeeque M.K.M
Siju Pavithran
Varghese K Renny
Project Guide : Dr.K.Najeeb

Government Engineering College

Sreekrishnapuram Palakkad

September 6, 2010
Introduction Motivation & Objectives Tools Used Architecture Conclusion Bibliography

CONTENTS

1 Introduction

2 Motivation & Objectives

3 Tools Used

4 Architecture

5 Conclusion

6 Bibliography
Introduction Motivation & Objectives Tools Used Architecture Conclusion Bibliography

INTRODUCTION

The basic motivation behind the project is to design a

knowledge based expert system for rural areas.
In the villages, where people may be lacking basic medical
amenities, this system can be used effectively.
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INTRODUCTION Contd.

The ontological framework can be used to efficiently give a

basic diagnosis about the disease
The system is capable of deducing possible diseases from the
symptoms
Also, an idea can be obtained about the treatment related
issues such as medicines and concerned doctors
expert systems for doctors and practitioners.
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BASIC TERMINOLOGY

Ontology
explicit specification of a conceptualization

example given by Genesereth and Nilsson(a, b, c, d, e, on,

above, clear, table)
In Computer Science and Information Science,ontology defines
set of representational premitives with which to model a
domain of knowledge or discourse.
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Ontology Contd.

independent of data modelling strategy or implementation.

It is a rigorous and exhaustive organisation of some knowledge
domain that is usually hierarchical and contains all the
relevant entities and their relations
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OWL
The Web Ontology Language(OWL) is a family of knowledge
representation languages for authoring ontologies, and is
endorsed by the World Wide Web Consortium.
The OWL is intended to provide a language that can be used
to describe the classes and relationship between entities that
are inherent in Web documents and applications.
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OWL contd.

An OWL Ontology contains:

Classes +Class Hierarchy
Relations between the classes(inheritance , disjoints etc)
Restrictions on the properties(types, cardinality etc)
Individuals
types of OWL.
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MOTIVATION FOR THE PROJECT

Ontologies are more general and reusable than traditional data

models
They are easily shareable
They are intended for multiple purposes, goals and users
Take stand on the semantics of the concepts (as opposed to
mere structure and integrity)
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OBJECTIVES OF THE PROJECT

Design and develop an ontology for a Medical domain.

Propose a system architecture for retrieving information and
enrichment of the ontology.
Retrieve the results in a way that can be used for further
processes
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LITERATURE REVIEW

Recognizing and filtering web documents using an Ontology

Authors:Abadi, R.M.B, Yektaie, M.H., Abbasi, M.
Azad University Of Oloum va Tahghighat, Ahwaz, Iran
This paper puts to evaluation the extent of relationship
between a semi structured HTML and ontology using some
statistical techniques.
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Automatic ontology-based knowledge extraction from Web

documents
Authors:Alani, H., Sanghee Kim, Millard D.E., Hall W, Lewis,
P.H., Shadbolt N.R
Southampton University UK
Specialized knowledge services require tools that can search
and extract specific knowledge directly from unstructured text
on the Web.This paper links a knowledge extraction tool with
an ontology to achieve continuous knowledge support and
guide information extraction
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Active User-Based and Ontology-Based Web Log Data

Preprocessing for Web Usage Mining
Authors:Natheer Khansawneh, Jordan University of Science
and Technology, Jordan
Chien-Chung Chan, University of Akron, US
User and session identification are two major steps in web log
data for web usage mining. This paper introduces a fast active
user-based user identification algorithm with time complexity
O(n)
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Building Semantic Rich Model for Web Documents Using

Domain Ontology
Authors: ShahrulAzmanNoah, LailatulqadriZakaria,
ArifahCheAlhadi,SaidahSaad,
National University of Malaysia
The paper proposes an approach meant to assist in
constructing semantic document models using natural
language analysis technique and a domain specific
ontology,which simplifies the working of search engines and
other such applications
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TOOLS USED

Protege
Jena API
Pellet API
SPARQL
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Protege

Protege is a free , open source platform that provides a

growing user community with a suite of tools to construct
domain models and knowledge based applications with
ontologies
Protege has an open architecture that allows programmers to
integrate plugins
The plugins can appear as separate tabs, specific user
interface components(widgets), or perform any other specified
operation on the user model
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Protege Contd.

The Protege platform supports two main ways of modelling

ontologies:
The Protege-Frames editor enables users to build and populate
ontologies that are frame-based, in accordance with the Open
Knowledge Base Connectivity protocol (OKBC). In this model,
an ontology consists of a set of classes organized in a
subsumption hierarchy to represent a domain’s salient
concepts.
The Protege-OWL editor enables users to build ontologies for
the Semantic Web, in particular in the W3C’s Web Ontology
Language.
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Protege Features

Extension to handle OWL ontologies

Loading and saving OWL files and databases
Graphical editors for class expressions
Integrated reasoner to ensure consistency
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Introduction Motivation & Objectives Tools Used Architecture Conclusion Bibliography

JENA

It is an open source semantic web framework written in Java

Jena is composed of:
RDF processing API
OWL processing API
A rule- based inference engine
SPARQL query engine
In-memory and persistent storage.
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JENA Contd.

Can parse,create and search RDF models

ModelFactory for creating models. So that application code
remains independent of the implementation, it is best if it
uses interfaces wherever possible, not specific class
implementations.
JENA has a special model class called OntModel
This can be used to derive meaningful relationship that the
model does not express directly
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Pellet API

Pellet is an open source Java based OWL DL reasoner

It can be used in conjunction with both Jena and OWL API
libraries and also provides a DIG interface
provides functionalities to see the species validation, check
consistency of ontologies, classify the taxonomy
Special features
Ontology analysis and repair
Data type reasoning
Rule integration
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SPARQL

Simple Protocol And RDF Query Language

SPARQL query consist of triple
patterns,disjunctions,conjunctions and optional patterns
SPARQL queries are created and executed with Jena via
classes in the com.hp.hpl.jena.query package
SPARQL is data oriented in that it only queries information
held in the models,there is no inference in the query language
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PLATFORM USED

Linux
Java runtime environment
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ARCHITECTURE
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The architecture consists of 4 main modules. They

are:-
Hierarchy viewing module
Consistency checking module
Query processing module
Enrichment module
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Introduction Motivation & Objectives Tools Used Architecture Conclusion Bibliography

HIERARCHY VIEWING MODULE

This module shows the user the hierarchical structure of the

ontology
Different axioms like the classes, objects and data properties
are also displayed
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Introduction Motivation & Objectives Tools Used Architecture Conclusion Bibliography

CONSISTENCY CHECKING MODULE

This module makes use of a reasoner like pellet,racer etc to

check the consistency status of the domain ontology
Consistency checking module has to be activated while the
user enriches the ontology, to ensure validity of the ontology
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Introduction Motivation & Objectives Tools Used Architecture Conclusion Bibliography

Query processing module

Query processing can be handled in two ways

User can enter the SPARQL query directly
SPARQL query generation
Information retrieval can also be done by node searching
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Introduction Motivation & Objectives Tools Used Architecture Conclusion Bibliography
Introduction Motivation & Objectives Tools Used Architecture Conclusion Bibliography

ENRICHMENT MODULE

This module allows user to add new information to the

domain ontology
We have provided two options to enrich the ontology:
User may delete an existing class
User may add a valid class
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CONCLUSION

The project puts emphasis on some valuable points in the field

of patient oriented medical information system
Since the application is aimed at the general public, the
interface has a simple and easy-to-understand design
It is also possible to add newer ontologies to the
application(from websites such as swoogle.com) directly to
our application
System runs through java run time environment that is
platform independent.
System implements disambiguation feature.
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FUTURE ENHANCEMENTS

Developing a Semantic search engine utilizing several

heterogeneous open source technologies
Designing an Auto enriching Ontology, which is capable of
making transitive deductions, based on user input
Designing an online ontology knowledge based system,
capable of sharing and enriching information by using suitable
networking among them.
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FUTURE ENHANCEMENTS Contd.

User can enter queries in XML format and also add

information as XML file.
It is possible to generate XML file so that it can be used as
input for further processing.
Caching of query is yet another feature that can be
implemented
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BIBLIOGRAPHY

Natalya F. Noy, Deborah L McGuinness, Ontology

Development 101: A Guide to Creating your own Ontology
Matthew Horridge, Holger Knublauch, Alan Rector, Robert
Stevens and Chris Roe: A Practical guide to building OWL
Ontologies Using the Protg OWL Plugin
Herbert Schildt : Java 2- The Complete Reference, Tata
McGraw Hill
Amandeep Sidhu, Tharam S. Dillon, Elizabeth Chang,
Baldeep Sidhu:Medical Ontology Development using OWL,
OWLED, Volume 188 of CEUR Workshop proceedings,
CEUR-WS.org, 2005
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http://protege.stanford.edu/
http://jena.sourceforge.net/ARQ/Tutorial
http://www.w3.org/TR/rdf-sparql-query/
http://www.swoogle.com/