Moving away from ISIS software with ChemAxon's Help · Set up IJC as interface to a large (10 Mi....

Debra Kassabian

Novartis Institutes for Biomedical Research (NIBR) IT

Moving away from ISIS software with ChemAxon's Help

ISIS/Draw

Draw Structures

Chemistry software at NIBR, before ChemAxon

| ChemAxon UGM September 2012 2

ISIS for Excel

Structures in spreadsheets

ISIS/Base

Personal structure databases

Personal reaction databases

CambridgeSoft

ELN

ChemOffice

Direct Cartridge

Chemistry search in Oracle

Duplication of functionality

ISIS software no longer

supported

ELN search very slow

Ceres (ISIS/Base + ISIS/Host)

Historical collection of Novartis reactions

Screening sample database

ACD

Other purchased databases

Chemistry software at NIBR


CambridgeSoft

Chemdraw

CambridgeSoft

Chemdraw/Excel

ChemAxon

JChem Cartridge

Let’s ask ChemAxon

If they can help...

ISIS/Draw

Draw structures

Ceres (ISIS/Base + ISIS/Host)


Screening sample database

ACD

Other purchased databases

ISIS for Excel

Structures in spreadsheets

ISIS/Base

Personal structure databases

Personal reaction databases

Direct Cartridge

Chemistry search in Oracle

ISIS Software Usage at NIBR


Emeryville Cambridge (HQ)

Horsham

Basel

Singapore (NITD)

Shanghai

Over 1600 scientists with ISIS software installed

Instant JChem Evaluation as ISIS/Base replacement


A group of chemists in Basel, Horsham, Cambridge were given an introduction and asked to try it

Collected a list of use cases to test in IJC

Tried local reaction and structure databases

Set up IJC as interface to a large (10 Mi. structures) Oracle database running JChem Cartridge

Chemists liked it! IJC is a valid replacement for ISIS/Base

Fast data import (SDF, RDF)

Fast structure search

Form creation is easier than in ISIS/Base

Connecting to Oracle and searching worked well

A few missing

features were

also identified

IJC Evaluation - continued

Features requested:

Ability to export a subset of data from a central database into a local database

Better support to move projects from Development to Test to Production environments

Improved export to RDF for databases having several structure fields per record

Greater flexibility when adding data to an existing database


Overall experience was very positive. Great support

and responsiveness from ChemAxon. Thanks

IJC Rollout – Deployment


JChem Cartridge

SDF,RDF,CSV...

Local Database

Shared Database Project Team, Lab...

Single User

Java Webstart with UrlWebApp

Oracle instance running JChem Cartridge for shared projects

Customized security module for IJC to integrate with our authentication and authorization infrastructure

IJC Rollout – ISIS/Usage Survey

All ISIS users asked to fill out a survey on ISIS/Base Usage. Around 10% responded.

Some use only ISIS/Draw

Many local ISIS/Base databases

• Personal collections of structures

• Personal reaction databases

• Project databases

• Lab inventories

• Old biological data not available elsewhere

A few ISIS/Host databases we didn’t even know of...

Access ACD and internal reaction collections in Ceres


ISIS/Base -> Instant JChem Migration


What to do:

Export data from ISIS/Base as SDF/RDF

Choose between local and shared database

Set up a project in IJC

Import data

Create forms

How to do it:

Hands-on workshops with chemists bringing their

own databases

Step-by-step how-tos to print out

Short task-oriented videos

LDC Structures

ACD

MDDR, CMC

Metabolite

Chirbase

Current Chemical Reactions


Ceres – ISIS/Base + ISIS/Host


New Web

application

IJC Rollout Summary

ISIS/Base -> IJC Migration is ongoing

Trying to use the possibility to store data in Oracle and create shared projects as much as possible

Scientists will be able to use ISIS Software until it breaks but we hope to persuade as many as possible to move

Greatest hurdle is not technology, but getting people to read their Email and come to the workshops!


IJC beyond ISIS Replacement: accessing the NIBR data warehouse


Data warehouse

Web Services

DART (Data

Analysis and

Reporting Tool)

Query Definition

+ Fields to

display

Data IJC Forms

Define Query

Define Fields to Display

View data in Spreadsheet

1

2

3

4

Query Definition

+ Fields to

display

Data

IJC beyond ISIS Replacement: accessing NIBR Chemical properties calculation Framework


Web Services for

Calculation of

Chemical Properties

Currently not using ChemAxon’s calculators

Web-services framework to allow global deployment of chemistry backend tools

Called by Knime, Spotfire, Focus, Small Molecule Registration and other tools

Services being built and deployed by several groups within NIBR with example

services: Property calculators (e.g. Lipinski properties, pKa, molecular volume, etc.)

R-Group decomposition

Scaffold tree

name2struct

find activity cliffs

IJC integration with NIBR’s framework will provide consistency with values

displayed by other applications

SMILES/Compound Nr.

clogP, PSA....

Why build a new reaction-database application?

Current situation :

• Literature and historic (pre-eLN) reactions: stored in an ISIS/host database; searchable from ISIS/base.

• eLN reactions: stored in the eLN (CambridgeSoft) schema; “searchable” from eLN

Objective:

• allow NIBR scientists to quickly and efficiently search both sets of reactions in one place

Requirements:

• web-based UI for searching and browsing

• web services for searching and retrieving the data


An Aside: services

Serious effort underway to expose every computation possible via web service.

Some examples:

• Querying our new data warehouse

• Calculating descriptors, using predictive models, etc.

• Registering compounds/biologics, querying registration system

Advantages:

• portability

• instantly global

• easy updates/deployments

• write once, use everywhere

• mashups | ChemAxon UGM September 2012 15

Reduction to practice

Collaboration with ChemAxon

Collection of user stories within NIBR

• global team of medicinal chemists driving requirements

• informed by Pistoia Alliance questions together with experience with CERES + various commercial tools

Concrete requirements and design done collaboratively

Implementation by ChemAxon


Query Requirements vs. Data Challenges


Solution: Bring over only the pieces of information that are actually needed for searching/browsing. Present additional data using an alternate “details” page that can be different for each original source

Standardize fields: Reaction, date, chemist, source, project, yield, solvent, reagents

Requires a custom RDF importer for each

historical data source

User wants to…..

Retrieve results based on structure searches (exact and substructure) of reactants and/or products

Retrieve additional information for a particular reaction

Query across multiple data sources

Limit results by yield, reagent, solvent, etc.

But we have data complexities…

Multiple collections of internal data in separate ISIS/Host databases with different structures

Constructing a single schema that can hold everything is unrealistic

Architecture

Oracle/JChem

Data Service

Layer (Tomcat)

Web application

(Tomcat/Wicket)

Web Browser

(javascript)

Oracle/eLN Update

application

Technical requirements:

Interface should be HTML5 and support a range of browsers

Must support our internal authentication/authorization framework

REST-style web services

eLN database updates must be automated


Status

historic reaction data (~400K reactions) loaded

beta version of web interface and services complete

starting to test the application with our chemists

bug fixing

planning eLN -> JChem data migration (~600K additional reactions)

• Starting with lab notebooks for test users

• Obtain metrics for performance for export / import

• Plan incremental update


Interface Overview


Substructure search with results


Search-results filters


Additional search criteria + filters


What’s next?

Get the application out to our test users and collect feedback

Get that eLN data loaded

Start thinking about better ways of organizing the results

Connecting to other web apps

Data analysis – unique reactions


Acknowledgements

NIBR GDC/CPC

Ansgar Schuffenhauer

Graham Bloomfield

Nikolaus Stiefl

Peter Meier

Roger Fujimoto

Wolfgang Miltz


NIBR IT

Anna Pelliccioli

Gregory Landrum

David Wayne Hughes

Manuel Schwarze

Rainer Stock

Sadik Keshwani

Stephanie Weeks

ChemAxon

Alex Drijver

Mihály Medzihradszky

Masoud Kalali

Tim Dudgeon

Thank you


Moving away from ISIS software with ChemAxon's Help · Set up IJC as interface to a large (10 Mi....

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