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From Desktop to BrowserChemAxon Plexus at GlaxoSmithKlineBrett Hiemenz GSK
Abstract GlaxoSmithKline began using ChemAxon tools across itsenterprise systems in late 2009. This presentation will outlinethe increasing adoption and the trend from desktop to webapplications will be highlighted. Recent GSK activities inPlexus components will be highlighted: CompoundRegistration, Plexus Library Design, Instant JChemWeb/Plexus Connect. Desktop applications are still preferred for some analysisactivities, so a Spotfire visualization tool will be presented.ChemAxon UGM Budapest16 Sep 20142
Agenda1. Retrospectives on Plexus suite components IJC Compound Registration2. Building web applications on core ChemAxon suites Enterprise Search enhanced with Chemistry3. Building chemistry capabilities into remaining desktop tools4. Alignment with Plexus roadmap – moving from desktop to web5. Conclusions.ChemAxon UGM Boston16 Sep 20143
Retrospective 1: Instant JChem Evolution 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/prodpublication mechanism.– Still using Citrix for US users (databases mostly in UK)ChemAxon UGM Boston16 Sep 20144
Retrospective 2: Small Molecule Registration 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 correctlyChemAxon UGM Boston16 Sep 20145
Enterprise Search with Chemistry: Socrates Search 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 witha 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 renderingChemAxon UGM Boston16 Sep 20146
Not All Web: Continued Support for Desktop Analysis Tools Chemistry representation in Spotfire. GSK Spotfire Structure Visualizer was notcompatible with Spotfire 6.0. necessitating a replacement ChemAxon Services have developed a JChem for Spotfire plug-in replacing all ofthe 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 SMILEScolumns (e.g. R-groups)ChemAxon UGM Boston16 Sep 20147
ChemAxon Structure Visualizer for SpotfireChemAxon UGM Boston16 Sep 20148
What’s Next for Chemistry Desktop: Plexus 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 easiermigration 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-basedenumeration 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 ServicesChemAxon UGM Boston16 Sep 20149
In Conclusion 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 2015ChemAxon UGM Boston16 Sep 201410
Thank you for your attentionQuestions?ChemAxon UGM Boston16 Sep 201411
UGM Presentations. IJC, JChem Cartridge and Web services 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 - Budapest2012 IJC in the wider enterprise – 18 months on : Karen Worsfold Budapest 2013ChemAxon UGM Boston16 Sep 201412
UGM Presentations: Compound Registration 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 PappBoston2012ChemAxon UGM Boston16 Sep 201413
Retrospective 2: Small Molecule registration Evolution Phase1 CRISP targets registration simplification by conversion to ‘service’. GSK legalraise 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. 2013approx 48k NCE registered of these approx 21k achiral/no stereoChemAxon UGM Boston16 Sep 201414
Phase I - Laying the GroundworkRegistryChemist or contract coordinatorenter compounds to be registeredand is notified of undefinedattributesContractChemistCompounds that are fullydescribe in regard tostereochemistry, racemiccontent are automaticallyregisteredBusiness RulesFully Specified compoundseLNB orWebRegCompounds with undefinedattributes are sent to a stagingarea for registrar attentionChemistRegistrars modify compoundsfor consistency, confirm with thechemist then registerChemists purchase compoundsets and receive data files withstructure informationStagingBusiness Rulesdefined byStandardizer andStructure sedCompoundsPurchasingChemistCompoundoptionally, requestassistance from theregistrarNameCCE 001CCE 002SD FilesCCE 003The purchasing chemist sends the SD File toRegistrars and they are registered as newentitiesCharlie Wilkins San Diego UGM Sept 2011
Phase II – OptimizationRegistryxxCompounds that are fullydescribe in regard tostereochemistry, geometricisomerism content areautomatically registeredxOther?ContractChemistBusiness RulesFully Specified compoundseLNB orWebRegChemistRegistryToolsCompound CollectionEnhancement purchasecompounds and receive datafiles with structure informationStagingRegistrars or chemists modifycompounds for consistency,confirm with the chemist pounds with undefinedattributes are sent back tochemistsoptionally, requestassistance from theregistrarNameCCECCE 001ChemistCCE 002SD FilesCCE 003Compound Collection Enhancement send the SDFile to Registry as received and registered asnew entitiesCharlie Wilkins San Diego UGM Sept 2011
Search Technology OverviewSocrates SearchAutonomyChemAxon(Text Entities)(Chemical Structures)LeadMine(Text Analytics)HazELNutLab NotebookDocumentumLotusBioIT world 201317
Text AnalyticsExact structure searchDiseaseGeneDocumentAnnotationsUniversally etoxybenzoic acid (IUPAC)O C(Oc1ccccc1C( O)O)C (SMILES)CCI133 (GSK ID)2-acetyloxybenzoic acidacetylsalicylateacetylsalicylic acidO-acetylsalicylic acidEmbedded OLE objects (ChemDraw, ISIS Draw)StructureChemicalFingerprintSubstructure SearchBioIT world 201318
Not All Web: Continued Support for Desktop Analysis Tools ChemAxon UGM Boston 16 Sep 2014 7 Chemistry representation in Spotfire. GSK Spotfire Structure Visualizer was not compatible with Spotfire 6.0. necessitating a replacement ChemAxon Services have developed a JCh
