RegaDB pieter.libin@uz.kuleuven.be Bonn, Arevir Meeting April 23 rd , 2008
Introduction RegaDB Viral Data and Analysis Management environment HIV-1, HIV-2, HCV To be used by Clinicians Researchers Two main usage scenarios: Runs locally On a server in your institute On your local machine On a collaboration server Easy access with Web browser Pieter Libin, 23/04/09
Objective A free and open-source database system Target audiance Clinicians Researchers Pieter Libin, 23/04/09
Objective (Clinicians) Empower clinicians with analysis tools Patient history graph Sequence analyses HIV typing and subtyping Genotypic analyses for resistance interpretation Third party analyses as “web services” Resistance reports Pieter Libin, 23/04/09
Objective (Researchers) Collaboration Facilitate research collaborations Easily interchange data, keeping track of data origin Create collaborative databases keeping track of dataset versions Easily publish data sets to Stanford HIVDB Publishing analyses tools eg.: Tropism prediction tools Querying Visual Query Tool Pieter Libin, 23/04/09
Data entities Event Therapy Attribute Patient Dataset Viral Isolate Test Pieter Libin, 23/04/09
Attributes Annotate Patient with information Adapts to “your (research) interest” Typically clinical and epidemiological information Examples Gender HIV transmission risk group Most of information collected in Collaborative projects WIV related information Attributes can be grouped Pieter Libin, 23/04/09
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Viral Isolates Viral Isolates Nucleotide Sequence A N Amino Acid A Information Sequence L automatically Insertion Y Mutation inferred S E S Protein Pieter Libin, 23/04/09
Analysis services Built-in services Codon correct alignment based on the appropriate reference genome REGA Subtype tool Stanford ASI genotypic resistance algorithms ANRS, HIVDB, REGA HIV-1/HIV-2 Resistance report generation Using your own template documents Integrate with external analysis services Using “web services” Pieter Libin, 23/04/09
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Therapy Consists of drug combination commercial or generic representation dosage information Start & end date Stop motivation Pieter Libin, 23/04/09
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Tests Test (in a general sense) performed at a certain moment in time May be related to a Viral Isolate Drug Combination of a viral isolate and a drug Adapts to “your (research) interest” Pieter Libin, 23/04/09
Tests Tests on a sample: CD4 count Viral Load count Tests on a sample with respect to a drug Therapeutic drug monitoring Tests on a viral isolate: HIV typing and subtyping Tests on a viral isolate with respect to a drug Genotypic/phenotypic resistance test Pieter Libin, 23/04/09
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Pieter Libin, 23/04/09
Events Start and end date Value (comparable to test values) eg.: Aids Defining Events Pieter Libin, 23/04/09
Patient history chart Pieter Libin, 23/04/09
Visual Query Tool Hierarchical query builder export results to csv file query database without the knowledge of SQL Pieter Libin, 23/04/09
Pieter Libin, 23/04/09
Pieter Libin, 23/04/09
Pieter Libin, 23/04/09
Pieter Libin, 23/04/09
Pieter Libin, 23/04/09
Pieter Libin, 23/04/09
Pieter Libin, 23/04/09
Thanks Thanks for the invitation and your attention! Questions? Pieter Libin, 23/04/09
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