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Vipendra Singh,
Intern chEMBL Group
European Bioinformatics Institute
Final review Meeting Date: 17/06/10
Division of Bioinformatics
SBST
Data Visualization Methods for Exploring the ChEMBL
chemogenomics database
Vipendra Singh
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Contents:
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17.05.20103
1. Introduction
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Introduction
Rapidly increasing data complexity and volume.
Important in datasets containing systems biology and
chemical biology data.
Need to visualize and browse chemical databases has becomelimiting.
We propose a new metaphor for data visualization and organismbrowsing on top of the ChEMBL database.
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Introduction
The ChEMBLdb is a new public domain resource linking chemicaltools and drugs through to bioactivity and molecular targets.
The concepts underlying our approach are based on navigation andvisualization with zooming and portals.
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About chEMBL Group
The ChEMBL team's research focuses on mapping the interactions andfunctional effects of small molecules binding to their macromolecular targets.
The group studies the interactions of pharmacologically active
molecules and their receptors.
In particular the group builds and maintains a series of drug discovery
databases that are components of ChEMBL.
ChEMBL Includes:
ChEMBLdb - medicinal chemistry database Kinase SARfari - www.sarfari.org
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About chEMBLdb
ChEMBL is a database of bioactive drug-like small molecules.
Contains :
2-D structures
Calculated properties (e.g. logP, Molecular Weight, Lipinski Parameters, etc.) and
Abstracted bioactivities (e.g. binding constants, pharmacology and ADMET data)
Where does the data come from?
Data is abstracted and curated from the primary
scientific literature
How is the Data supported?
Funding From Wellcome Trust
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About chEMBLdbDatabase Statistics (from Last release)
Using Database: CHEMBL_02
Created On: 30-NOV-09
Protein targets: 4,364
Cell-line targets: 1,198 Other targets(organisms, etc): 1630
Total targets: 7,192
Total activities: 2,404,622
Total compounds: 622,824 Total publications: 33,956
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About chEMBLdb (current Release)
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About Organism Browser
Organism Browser is a GUI (Graphical User Interface)For Organism Class table in the chEMBL schema
Within chEMBL Schema
N:1 mapping between the Target Dictionary table and
the organism table in the ChEMBL Schema
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About Organism BrowserC
chEMBL schema
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About Organism Browser(GUI)
Web Version:1.0.0
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About Organism Browser(GUI)Web Version:1.0.0
:Features:
Dynamic graphic Display (Pie chart)
Clickable tree
Searching Highlighting nodes in the Tree
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How does it work?
On everclickon the JQuery Tree a request is made to the google charts API
a) Process request on the google server.
Output: Colorful static image (pie chartin our case)
b) Parent Node Level (ex L0,L1LN) and the Entity (ex Eukaryote, Bacteria etc.)
stored in the session variable
- function in the Controller(MVC architecture of codeignitor) is called
- Invoke the childrens of the selected parent
- the tree expands
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About Organism Browser(GUI)Search hits Result Page:
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Scatterplot Module:
Introduction
Interactive data visualization for viewing the hits (against clients Query)
from the chEMBL database.
Scope
2D Scatterplot.
Datapoints are coloured by Lipinskis Rule of Five,
Boundary condition like Molecular weight, LogP, HBA, HDB, PSA etc.
Identify potential Drug Targets.
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Existing system and Procedures (In use)
AlmostAll the graphical libraries generate Static Images for Scatterplot
.None of the other Js Libraries involves Heavy User Interaction.
Highcharts , Best availabe Js library for our Task.
Y not Flash? Additional Plug In Required on client side ( Client says Babyee )
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a) Proposed / Expected Design
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Step Actor Action Step System Response
Select Interaction Analysis Module
1 User Selects the Plot option and Update
the Graph.
2 System displays Scatterplot with
corresponding X-Y axis+Store the event in session.
3 UserChanges the Settings and Updatethe Graph.
4 System displays Scatterplot overwritethe session variables.
5 The user click on the link for theColour Options.
6 The output will be HighSlide Js popup box WithColour Options.
7 UserClick on the input Box and changesthe colour in the Colour Picker.
8 XML:HTTP request sent to server,Session variables overwritten, SeriesRedraw.
9 User Perform Mouse Down and move themouse over the chart, Finally releases it.
10 Zoom in event occurs + Reset zoomAppears on chart.
Primary Scenario
11 User Disable / Enable a series. 12 Series disappear / Appear.
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Model View Controller
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Model View ControllerWhy MVC?
1)Effective separation of logic and view.
2)Speeds up Development
:Components of MVC:
1)Controller : Loads Model and View
2) Model: For operation on the database like select insert update etc.
3) View: For displaying the HTML content.
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26.12.201024
Technologies Used for Organism Browser:
1)PHP
2)Javascript
3)Jquery
4)Google charts
5)SQL6)PLSQL
Database used:
1)Oracle 11g
Materials and Methodology
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26.12.201026 26.12.201026
Softwares Used:
1)CodeIgnitor(Model View Controller Framework)
2)Eclipse
3)SQL Developer
Firebug (For testing)
Framework Used:
CodeIgnitor(PHP framework)
Materials and Methodology
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26.12.201027 26.12.201027
Softwares Used:
To compare with the repository
1)Subversion
2)Trac
Operating System:
1)Mac OS X
Software For installing Windows on Mac OS X
1) Vitual Machine
Materials and Methodology
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Major Issues In development
1).Compatibility issues with the Latest version of PHP and codeignitor.(Y)
(Common problem with Opensource projects)
2) Compatibility issues with Latest version of Mozilla and the Firebug latest version(Y)
(installed lower version of Mozilla and Firebug)
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Scatterplot functional Overview
zoom in / out
Clickable datapoints
Adjustable datapoint size
Adjustable Chart size
(For best performance with Varying desktop resolutions)
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Scatterplot functional Overview
Colour Picker forChanging Series color.
Tooltip bubble with Compound Image & X-Y coordinates information
+ chEMBL ID + Series Detail.
Datastructure Storing X-Y coordinates for each compound.
PopUp showing number of compound representing a given Datapoint
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Scatterplot functional Overview
Link to ChEMBL report card.
Flickr / Facebook Like Top menu Bar.
Display Time to execute SQL Query.
Export options
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HCTEST_SMALL 127 rows of data
HCTEST_MEDIUM 798 rows of data
HCTEST_LARGE 20284 rows of data
Testing:
Initial Testing for performance of Highcharts Js library :
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Inside each table we will find the following columns:
MOLREGNO
CHEBI_ID
MOLWEIGHTSYNONYMS
ALOGP
PSA
HBA
HBD
RO5
SIMILARITY
CHIME
TAG
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Overview of the browsers used to access chembl interface is below,
(firefox is most popular):
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WithTooltip WithoutTool tip
1)Safari 2-3 sec 1-2 sec
2)Chrome 2-3 sec 1-2 sec
3)Firefox 5-6 sec 1-2 sec
4)Opera 3-4 sec 2-3 sec
5)IE not feasible 3-4 sec
6)Sea Monkey 5-6 sec 1-2 sec
Tested with and without tool tip in all the major browsers includes:
For :::::: 2000 ::::::: datapoints
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For ::::: 20000:::::::: datapoint (Disabled zoom)
Firefox: 6 sec
Sarfari: 9-10 sec
Opera: 35-36 sec
chrome: 3-4 sec
IE: not feasible
For5000datapoints (disabled tool tip and zoom)
IE 5-6 sec
For500 data points
All options enabled
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>500
IE zoom disabled
>1500
Firefox Zoom disabled
>5000
For all browsers Zoom Disabled
Best performance with Sarfari & Google chrome (Both uses
same engine i.e. Webkit)
Can show >> 20000 datapoints (optimal performance at 20000
datapoints tested)
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Final Plot Options Dropdown
(Optimised to be User Friendly)Initial Plot option Dropdown (Too long)
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Colour by : Molecular weight boundaries Colour by : R05 violations
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26.12.201042
Snapshot of the application
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Organism Browser Status
Created the organism_class table in the chembl_app_01 schema
ORGANISM_CLASS joined to TARGET_DICTIONARY using the Tax_id (unique identifier)
Created organism browser code using target browser code as template.
Organism browser functions in the same way as the target browser.
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Organism Browser Status
Additional functionality like searching in the tree added.
Searching in the tree case insensitive
Added wild-cards to searches
( ex search for abc in string -----abc-------)
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Snapshot of Organism Browser
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Target result result page
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4. Conclusion and Future Prospects
17.05.201047
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Further enhancements over scatterplot ??
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26.12.201049
IGoogle like Draggable ChEMBL analytics dashboard
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26.12.201050
IGoogle like Draggable ChEMBL analytics dashboard
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Have a good day ahead
Thank you for the patience