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From Desktop to Browser ChemAxon Plexus at GlaxoSmithKline Brett Hiemenz GSK

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From Desktop to Browser

ChemAxon Plexus at GlaxoSmithKline

Brett Hiemenz GSK

Abstract

216 Sep 2014ChemAxon UGM Budapest

• GlaxoSmithKline began using ChemAxon tools across its

enterprise systems in late 2009. This presentation will outline

the increasing adoption and the trend from desktop to web

applications will be highlighted. Recent GSK activities in

Plexus components will be highlighted: Compound

Registration, Plexus Library Design, Instant JChem

Web/Plexus Connect.

• Desktop applications are still preferred for some analysis

activities, so a Spotfire visualization tool will be presented.

Agenda

1. Retrospectives on Plexus suite components

• IJC

• Compound Registration

2. Building web applications on core ChemAxon suites

• Enterprise Search enhanced with Chemistry

3. Building chemistry capabilities into remaining desktop tools

4. Alignment with Plexus roadmap – moving from desktop to web

5. Conclusions.

316 Sep 2014ChemAxon UGM Boston

Retrospective 1: Instant JChem Evolution

416 Sep 2014ChemAxon UGM Boston

• Initial replacement for ISISBase began 2009. Rollout 5.6 mid 2011.

– ChemAxon converted H-views to IJC projects like-for-like. 400 H-views approx half converted.

– Bespoke tools to create test-prod environments

– Slow US performance necessitated Citrix.

• Cross Pharma prioritisation of requirements. Uplift to 5.7.2.1 in 2012

• Evaluation of JChem Web Browser 2013

– GSK database architecture made performance slow.

– Joining across multiple data sources

• 2014 Uplift to version 6.2 using ChemAxon Services to replace test/prod

publication mechanism.

– Still using Citrix for US users (databases mostly in UK)

Retrospective 2: Small Molecule Registration

516 Sep 2014ChemAxon UGM Boston

• March 2011 collaboration with ChemAxon to create a new Registration ‘Service’

inside firewall to comply with GSK business rules using standard formats

– Delivered into production at GSK March 2012 (migrated 6 million records)

• Phase 2 collaboration with ChemAxon to deliver as part of ‘product’ mid 2013.

• Now Scientists can use a web app to ‘fix’ compounds that do not auto-register

– Target was 70% non-registrar assisted registrations. Actual is 84%

– 250+ chemists have registered compounds themselves

– Increase from 4% to 7% require some post-registration modification. Mostly handled through training

• Very few issues reported during rollout despite big process change

– Peptide conversions from eLNB CDX format does not maintain orientation and bond lengths correctly

Enterprise Search with Chemistry: Socrates Search

616 Sep 2014ChemAxon UGM Boston

• Using JChem Suite to add Chemistry to the GSK Enterprise Search engine

• Presented to BioIT world in 2013 (and won an innovation award)

• GSK data are crawled and the ‘chemistry’ extracted into an Oracle database with

a ChemAxon powered index

– Substructure search only

– Reaction search is possible but the business did not prioritize it

– Electronic Lab Notebook Reactions are included in the indexing.

– JChem libraries used for format conversions and image rendering

Not All Web: Continued Support for Desktop Analysis Tools

716 Sep 2014ChemAxon UGM Boston

• Chemistry representation in Spotfire. GSK Spotfire Structure Visualizer was not

compatible with Spotfire 6.0. necessitating a replacement

• ChemAxon Services have developed a JChem for Spotfire plug-in replacing all of

the capabilities of the GSK bespoke tool

• Key features:

– Structure renderer can replace SMILES with structures in table cells, plot labels, tooltips, and more

– Grid visualization of structures allows cherry-picking/marking, exporting, display of multiple SMILES

columns (e.g. R-groups)

ChemAxon Structure Visualizer for Spotfire

816 Sep 2014ChemAxon UGM Boston

What’s Next for Chemistry Desktop: Plexus

916 Sep 2014ChemAxon UGM Boston

• Working with ChemAxon to align with the Plexus roadmap and vision.

– Web-based tools allow for more rapid deployment, easier support, fewer desktop conflicts, and easier

migration to touch interfaces

– Web-based tools also address architectural and security problems with desktop data analysis

• Partnership with Schrödinger on LiveDesign

– LiveDesign integrates Marvin for Javascript.

– Plexus Library Design licensed for use in Markush enumeration. Development of reaction-based

enumeration is in progress.

• GSK/ChemAxon beginning collaboration on IJC Web/Plexus Connect

– Beginning October 2014 with an IJC gap analysis and addressing any key gaps

– Planning 2015 project to migrate from IJC desktop to Plexus Connect using ChemAxon Services

In Conclusion

1016 Sep 2014ChemAxon UGM Boston

• ChemAxon began as key vendor for GSK in 2009

• Collaborated on Registration starting in 2011

• Licensed Plexus Library Design in 2013

• Collaborating on Plexus Connect in 2014

• Planned implementation of Plexus Connect in 2015

Thank you for your attention

1116 Sep 2014ChemAxon UGM Boston

Questions?

UGM Presentations. IJC, JChem Cartridge and Web services

1216 Sep 2014ChemAxon UGM Boston

• SOA-at-GSK-Working-in-a-Mixed- Technology-Environment : Brett Hiemenz San Diego 2009

• Implementation of ChemAxon in an SOA environment : Shane Weaver : Budapest 2010

• SAR analysis in Excel using Helium and JChem Karen Worsfold – Budapest 2011

• Deploying Instant JChem on an Enterprise Scale: Brett Hiemenz - San Diego 2011

• Delivering Instant JChem to the Masses - A User Perspective : Stephen Swanson - Budapest

2012

• IJC in the wider enterprise – 18 months on : Karen Worsfold Budapest 2013

UGM Presentations: Compound Registration

1316 Sep 2014ChemAxon UGM Boston

• A-novel-Approach-to- Pharmaceutical-Registration :Charlie Wilkins San Diego 2011

• Going live with registration as a service : Richard Bolton/Akos Papp Budapest 2012

• Registration as a Service: the full story after half a year. Rama Bhamidipati/Akos Papp

Boston2012

Retrospective 2: Small Molecule registration Evolution Phase1

1416 Sep 2014ChemAxon UGM Boston

• CRISP targets registration simplification by conversion to ‘service’. GSK legal

raise concerns about hosting registration outside firewall.

• March 2011 collaboration with ChemAxon to create a new Registration ‘Service’

inside firewall to comply with GSK business rules using standard formats.

• Delivered into production at GSK March 2012 (migrated 6 million records)

• Phase 1 ChemAxon registration approx 48% automated registration. 2013

approx 48k NCE registered of these approx 21k achiral/no stereo

Compound Name

CCE 001

CCE 002

CCE 003

Purchased

Compounds

The purchasing chemist sends the SD File to

Registrars and they are registered as new

entities

optionally, request

assistance from the

registrar

Contract

Chemist

Chemist

PurchasingChemist

eLNB or

WebReg

Fully Specified compounds

Registrar

Tools

Registry

Chemist or contract coordinator

enter compounds to be registered

and is notified of undefined

attributes

Compounds that are fully

describe in regard to

stereochemistry, racemic

content are automatically

registered

Compounds with undefined

attributes are sent to a staging

area for registrar attention

Chemists purchase compound

sets and receive data files with

structure information

Registrars modify compounds

for consistency, confirm with the

chemist then register

Registrar

Business Rules

SD Files

Phase I - Laying the Groundwork

Staging

Business Rules

defined by

Standardizer and

Structure Checker

Configurations

Charlie Wilkins San Diego UGM Sept 2011

Other?

Compound Name

CCE 001

CCE 002

CCE 003

Purchased

Compounds

Compound Collection Enhancement send the SD

File to Registry as received and registered as

new entities

optionally, request

assistance from the

registrar

Phase II – Optimization

Contract

Chemist

Chemist

CCEChemist

eLNB or

WebReg

Fully Specified compounds

Registry

Tools

Compound Collection

Enhancement purchase

compounds and receive data

files with structure information

Registrar

SD FilesSD Files

Fully Specified compounds Business Rules

Staging

Compounds that are fully

describe in regard to

stereochemistry, geometric

isomerism content are

automatically registered

Compounds with undefined

attributes are sent back to

chemists

Registrars or chemists modify

compounds for consistency,

confirm with the chemist then

register

Registry

x

x

x

Charlie Wilkins San Diego UGM Sept 2011

Search Technology Overview

17

Autonomy(Text Entities)

ChemAxon(Chemical Structures)

Socrates Search

Lab Notebook

HazELNut

LeadMine(Text Analytics)

Documentum Lotus

BioIT world 2013

Text Analytics

18

Universally Unique

Tag

Text

Chemical

Fingerprint

Structure

Document

Annotations

Substructure Search

Exact structure search

Aspirin

2-acetoxybenzoic acid (IUPAC)

O=C(Oc1ccccc1C(=O)O)C (SMILES)

CCI133 (GSK ID)

2-acetyloxybenzoic acid

acetylsalicylate

acetylsalicylic acid

O-acetylsalicylic acid

Embedded OLE objects (ChemDraw, ISIS Draw)

Tag

TagGene

Disease

AJSHBSYTW6HSG8KJG9KA

BioIT world 2013