RegaDB pieter.libin@uz.kuleuven.be Bonn, Arevir Meeting April 23 rd - - PowerPoint PPT Presentation

▶

Nov 18, 2022 774 likes •1.16k views

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

SLIDE 1

RegaDB

pieter.libin@uz.kuleuven.be

Bonn, Arevir Meeting April 23rd, 2008

SLIDE 2

Pieter Libin, 23/04/09

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

SLIDE 3

Pieter Libin, 23/04/09

Objective

A free and open-source database system Target audiance

Clinicians Researchers

SLIDE 4

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

SLIDE 5

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

SLIDE 6

Pieter Libin, 23/04/09

Data entities

Patient Therapy Dataset Test Viral Isolate Attribute Event

SLIDE 7

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

SLIDE 8

Pieter Libin, 23/04/09

SLIDE 9

Pieter Libin, 23/04/09

SLIDE 10

Pieter Libin, 23/04/09

SLIDE 11

Pieter Libin, 23/04/09

SLIDE 12

Pieter Libin, 23/04/09

Viral Isolates

Viral Isolates Insertion Nucleotide Sequence Amino Acid Sequence Mutation Protein Information automatically inferred A N A L Y S E S

SLIDE 13

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”

SLIDE 14

Pieter Libin, 23/04/09

SLIDE 15

Pieter Libin, 23/04/09

SLIDE 16

Pieter Libin, 23/04/09

SLIDE 17

Pieter Libin, 23/04/09

SLIDE 18

Pieter Libin, 23/04/09

SLIDE 19

Pieter Libin, 23/04/09

SLIDE 20

Pieter Libin, 23/04/09

Therapy

Consists of drug combination

commercial or generic representation dosage information

Start & end date Stop motivation

SLIDE 21

Pieter Libin, 23/04/09

SLIDE 22

Pieter Libin, 23/04/09

SLIDE 23

Pieter Libin, 23/04/09

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”

SLIDE 24

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

SLIDE 25

Pieter Libin, 23/04/09

SLIDE 26

Pieter Libin, 23/04/09

SLIDE 27

Pieter Libin, 23/04/09

Events

Start and end date Value (comparable to test values) eg.: Aids Defining Events

SLIDE 28

Pieter Libin, 23/04/09

Patient history chart

SLIDE 29

Pieter Libin, 23/04/09

Visual Query Tool

Hierarchical query builder

export results to csv file query database without the knowledge of SQL

SLIDE 30

Pieter Libin, 23/04/09

SLIDE 31

Pieter Libin, 23/04/09

SLIDE 32

Pieter Libin, 23/04/09

SLIDE 33

Pieter Libin, 23/04/09

SLIDE 34

Pieter Libin, 23/04/09

SLIDE 35

Pieter Libin, 23/04/09

SLIDE 36

Pieter Libin, 23/04/09

SLIDE 37

Pieter Libin, 23/04/09

RegaDB

pieter.libin@uz.kuleuven.be

Bonn, Arevir Meeting April 23rd, 2008

Introduction

RegaDB

Viral Data and Analysis Management environment

To be used by

Two main usage scenarios:

Runs locally

On a collaboration server Easy access with Web browser

Objective

A free and open-source database system Target audiance

Clinicians Researchers

Objective (Clinicians)

Empower clinicians with analysis tools

Patient history graph Sequence analyses

Third party analyses as “web services” Resistance reports

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

Data entities

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

Viral Isolates

Analysis services

Built-in services

Codon correct alignment based on the appropriate reference genome REGA Subtype tool Stanford ASI genotypic resistance algorithms

Resistance report generation

Integrate with external analysis services

Using “web services”

Therapy

Consists of drug combination

commercial or generic representation dosage information

Start & end date Stop motivation

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

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

Events

Start and end date Value (comparable to test values) eg.: Aids Defining Events

Patient history chart

Visual Query Tool

Hierarchical query builder

export results to csv file query database without the knowledge of SQL

Thanks

Thanks for the invitation and your attention! Questions?