Development of DNA Profile Information Retrieval System 유전자 프로필 검색 시스템 구축 December 1, 2000 Hwan-Seung Yong, Hun-Joo Lee * Dept. of Computer Science and Engineering, Ewha Womans University ** Chem.I.Net Inc.

Introduction DNA Profile Database can be heavily used – For Scientific Investigation – For Research – For Medicine Trends – DNA Profile Database System in England, USA – DNA Profile Venture business starts in Korea IDGENE

Purpose of Development Build DNA profile Database for Identification in NISI (National Instibute of Scientific Investigation) – Data insert/retrieval – Web based approach – Can be used from NISI branches – Additional Personal Profile Data should also managed Asset for further research – Use Data Mining Technique for high level analysis

System Characteristics Current Web Database Technology High Retrieval Performance Use International Standard – For Image Data format – For interoperability with other system

SystemDiagram

Server OSMS Windows2000 Server DBMSMS-SQL Server 7.0 Web Server MS Internet Information Server Client OSMS Windows95 above Internet Explorer 5.0 above Software tools Rational Rose '98 MS Visual C++6.0 MS Visual Interdev Operating Environment

CE (Capillary Electrophoresis ) Visualizer and Input Interface Manage GENO-TYPER output for DNA Locus Analysis USE-CASE Model of CE Visualizer – Object-oriented Visual Tool Rational Rose’s USE CASE VIEW Active X Component for CE data input – ASTM AIA Andi(Analytical Data Exchange Format) Category 3.0 – International Standard CE Visualizer 의 사양 -1

Experiment Select Andi.cdf file Visualize chromatogram Identify Chromatogram Register chromatogram Visualize Event Analyst Specify ISTD peak ChromView Entry System > Extract prelimilary features

Object Model for CE Visualizer Class and Class Relationshop Model Use UML(Unified Modeling Language) Class Component – RawDataManager class – ResultDataManager class – ChromInforCenterManager class – ReportManager class – ChromGraphManager class – SampleList class – FeatureExtractor class – ErrorManager class CE Visualizer 의 사양 -3

Developed System: Window Interface Starting Page and Login Input of DNA Profile Data Retrieval of DNA Profile Detail Information Retrieval Report Writing System Management

Starting Page and Login 시스템 개발내용 -1

DNA Profile Data Registration Suspect Personal Information and DNA Profile Registration CE (Capillary Electrophoresis) Raw chromatogram Registration DNA Locus Registration based on Category – Locus Name and Data – Probability Data for Korean 시스템 개발내용 -2

Suspect Information and DNA Profile registration

CE(Capillary Electrophoresis) Raw chromatogram Registration

DNA Locus Registration Interface

DNA Profile database retrieval DNA Profile Retrieval from Personal Data Suspect Information Retrieval from Unsolved Case DNA Profile Data Chromatogram Retrieval using CE-Visualizer 시스템 개발내용 -3

DNA Profile data retrieval using Personal Profile data

Suspect Retrieval from Unsolved Case DNA Profile Data

Registration for Center and Branches of NISI

User Management, Compatible with LIMS in NISI

Performance Evaluaton At present, only 1,000 DNA Profile Data – This data will increase rapidly Example DNA profile data generation – Based on Probability of DNA Locus Distribution – Number of Generated DNA Profile: 500,000 – Table size : 500,000 tuples, 61MB – For Index: 9MB for each Locus – Number of Locus: 20 Hardware: – PC Server (Dual Pentium CPU) – H/W Cost: 5,000,000 Won

Retrieval time for 20 Exact Match (All under 1.4 sec) 검색 성능 평가

Retrieval time for 19 Exact Match (All under 1.4 sec) 검색 성능 평가

Database Size with Number of Index (Under 250MB)

Conclusions Develop DNA Profile Retrieval System Based on State of Art Web Database Technology All H/W and S/W Environment are Cheap – PC Server, Microsoft SQL Server, Windows NT Extendibility for Later Upgrade Achieve High Performance – For 500,000 DNA Profile Data, Without index: under 1.4 sec With index: 0.2 sec.

Further Research and Development OLAP(Online Analytical Processsing) – Multi-dimensional Analysis DNA Data Mining – Knowledge Discovery – New Fact Finding Technology Some Critical Mass DNA Profile Data is required