RegaDB AREVIR Meeting, Bonn 10-11 April 2008 Pieter Libin
Agenda � RegaDB software � ViroLab data integration � ViroLab – EUResist collaboration
Introduction � RegaDB − HIV Data and Analysis Management environment − To be used by � Clinicians � Researchers � Two main usage scenarios: − Runs locally � On a server in your institute � On your laptop − On a collaboration web site − Easy access with Web browser
Objective � A free and open-source database system � 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 � 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
Data Entities Therapy Attribute Patient Viral Dataset Isolate Test
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 SPREAD � Attributes may be grouped (like “SPREAD”)
Viral Isolates Viral Isolates Nucleotide Sequence Amino Acid Sequence Information automatically Insertion Mutation inferred Protein
Treatment � Consists of a drug combination − commercial or generic representation − dosage information � Start & end date − support for therapy ending motivation � Commercial drug representation can be automatically mapped to the generic representation, facilitating use of this data during research
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”
Tests vs Test Types Test Concrete Test Type Concept Test Concrete Test Test Concrete Concrete
Tests vs Test Types Viral Load Generic Viral Load Viral Load Abbot Viral Load Viral Load “In house” Roche
Test examples � 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
Research datasets � Patient can be tagged by 1/more datasets � User can have access to 1/more datasets � Fine grained access to a Patient can be established � User access towards a dataset can be − anonymous-read-only (researchers) − read-only − full read/write (clinicians)
Analysis Services � Built-in services − REGA Subtype tool − Stanford ASI genotypic resistance algorithms � ANRS, HIVDB, REGA − Resistance report generation � Using your own template documents − Patient history visualisation � Integrate with external analysis services − Using “web services”
Collaborative Edition RegaDB Collaborative Edition Local RegaDB Local RegaDB Local RegaDB Local RegaDB
Collaborative Version � Easy and secure collaboration � The sharing partner stays in control of his data − Access can be assigned in a very fine-grained way − Privileges can be removed when necessary � Same user environment as the local version of RegaDB
Research oriented features � Reproducibility − A single version of a dataset is “immutable” � You can always rerun your analyses by going back to the original patient group � Research tools − Query tool to create queries � e.g. “Get one sequence per patient of patients failing a specific treatment” � possibility to parametrize queries and store them in RegaDB � dataset security on query level − Export data to statistical / data mining packages
Synchronize auxiliary data � Auto-update services for − Drug definitions − New (versions of) resistance algorithms − Test types / Tests − Attribute types / Attribute groups
RegaDB technologies � RegaDB is built on the foundations of − Witty; a AJAX enabled Web Toolkit − Hibernate; a versatile DB layer � Currently we're extending RegaDB towards other viruses − HCV, HBV, influenza, ...
RegaDB usage scenarios � Data management at a local institute � Collaboration based on the “Collaborative Edition” � Data integration − providing a local institute with clinical/research tools − providing data as a unified schema
ViroLab data integration � RegaDB is used to integrate ViroLab datasources − locally installed at the institute − data conversion, extraction, and anonymization is done within each hospital
ViroLab data integration
EUResist – ViroLab � HL7 − standard developed by IBM to communicate clinical data − a connector is under developement to convert from RegaDB <-> HL7 � Solution will ensure data origin of the different partners
Thanks � Thanks for the invitation and your attention! � Questions?
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