Transcription
5 years with ChemAxonA Developing PartnershipRichard Bolton GSK
Abstract GlaxoSmithKline began using ChemAxon tools across itsenterprise systems in late 2009. A selection of presentationsfrom previous UGM which reflect the increasing usage andshow the developing relationship between the two companieswill be highlighted and key status updated. A new use forChemAxon tools in Enterprise Search will be presented.ChemAxon UGM Budapest21 May 20142
Agenda1. Where did we start?2. Two retrospectives illustrating changes in working model1. IJC2. Compound registration3. Enterprise Search with added ChemAxon capabilities4. What next?5. Conclusions.ChemAxon UGM Budapest21 May 20143
Where did we start? GSK began a major chemistry tools simplification effort in 2008.– Chemistry Research IT simplification programme (CRISP).– In 2013 this began again as ‘IT Fitness.’ across Discovery The ChemAxon Chemistry engine was chosen to replace Daylight, Accord andMDL(RCG) backend systems and IJC to replace ISIS. In 2009 GSK began to work with ChemAxon tools in the CRISP programme tomove from a complex collection of legacy tools; planned to take approximately24 months.– ISIS to IJC– Web services that powered chemistry methods had ChemAxon methods added.– Computational Scientists began to use ChemAxon toolset in replacement of Daylight toolkit. Success led to a collaboration on Small Molecule Registration in March 2011ChemAxon UGM Budapest21 May 20144
Major themes of CRISP as presented at ChemAxon UGM. Migration of Oracle Cartridges and remediation of 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 Structure Activity Relationship (SAR) Tools replaced by Helium and JChem 4 Excel– SAR analysis in Excel using Helium and JChem Karen Worsfold – Budapest 2011 ISIS to IJC– 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 Simplification of small molecule 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 Papp Boston2012ChemAxon UGM Budapest21 May 20145
SAR Tools ObjectivesTibco SpotfireExcel 2007Jchem for ExcelStephen Swanson Budapest UGM 2012
Retrospective 1: IJC 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) 2015 Proposed uplift to Browser resourced by ChemAxon ServicesChemAxon UGM Budapest21 May 20147
Timeline for deployment of IJCIJC 5.6.0 Roll-OutCitrix available for US &AsiaWeb Admin page availableIJC 5.7.2.1 UpgradeACD Finder & GSKChem releasedto usersGSKChem and ACD Finder removedfrom ISIS NETFirst programme Hview topass UATScript for adding KATE tablesreleased to LUGDecision to use Citrix for US& AsiaAll programme Hviews removed fromISIS NETACD Finder & GSKChem released to LUGStart ofdecommissioningof ISISPrototype ACD finder demo’d to LUGContract Signed2009201020112012Karen Worsfold Budapest UGM 2013
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) Current ChemAxon registration approx 50% automated registration. 2013approx 48k NCE registered of these approx 21k achiral/no stereoChemAxon UGM Budapest21 May 20149
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, racemiccontent are automaticallyregisteredChemist or contract coordinatorenter compounds to be registeredandregisterabilitybefore submittingxOther?ContractChemistBusiness RulesFully Specified compoundseLNB orWebRegCompounds with undefinedattributes are sent to theregistrarsChemistRegistrars modify compoundsfor consistency, confirm with thechemist then registerCompound CollectionEnhancement purchasecompounds and receive datafiles with structure CompoundsCompoundoptionally, 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
Small Molecule registration Evolution Phase 2 RaaS2 Collaboration with ChemAxon to deliver feedback capability as part of‘product’ mid 2013. Target of 70% auto-registration with 80% potential. For compounds that do not auto-register scientist will be able to edit and ‘fix’using new compound checker tools. If a structure is too complex it can be sent to registrar to complete. Rollout is imminentChemAxon UGM Budapest21 May 201412
Enterprise Search with Chemistry: Socrates Search Chemistry has been added to the GSK Enterprise Search engine usingChemAxon technology Presented to BioIT world in 2013 (and won an innovation award)– Not yet presented at a ChemAxon UGM GSK data is crawled and the ‘chemistry’ extracted into an Oracle database with aChemAxon 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 Budapest00 Month 000013
Insight Search Objectives- Search: Enabling findable and interpretable data1.2.3.4.Internal content: eLNB, CLS, Team Sites, Lotus Notes, IMMS, PIERChemistry entities by structure or nameIntegration with external sources: Reaxys, Pharmapendium, NCBI, Clintrial.govExposing eLNB attachmentsBioIT world 201314
Search Technology OverviewSocrates SearchAutonomyChemAxon(Text Entities)(Chemical Structures)LeadMine(Text Analytics)HazELNutLab NotebookDocumentumLotusBioIT world 201315
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 201316
Search ComponentsInsight SearchFederated SearchWeb ServicesGSKSearch(Text)ChemAxon(Chemistry)Content IndexesExternal SourcesCrawlerseLNBTeamSitePier Unstructured ContentBioIT world 201317
Chemistry Crawling Chemistry representationsNamesStructure/ReactionOtherGSK NumbersTrade/common namesIUPAC namesSMILESCDXMLMol FilesMicrosoft OLE controlsImagesChemDrawISIS Chemistry Sources eLNB GSK/CRO, eE, Core Lab Systems LNB, Team Sites, Pier (Documentum), Lotus NotesBioIT world 2013
What Next? Support for Chemistry representation in Spotfire. ChemAxon servicesdeveloping a Spotfire plugin using a GSK tool as the model. Precompetitive IP. Computational Scientists evaluating in-memory databases. Move to the Web: Plexus. Working with ChemAxon to ensure that our roadmapaligns with delivery plans. Partnership with Schrödinger, integrated with Plexus Library Design tools. Support services for ChemAxon tools. How can my Support services work withChemAxon Support to maintain component currency without a project.ChemAxon UGM Budapest21 May 201419
In Conclusion ChemAxon began as key vendor for GSK in 2009– Deployment of IJC and key CRISP programme technology. Became a co collaborator in 2011– Registration ‘as a service’ Service provider in 2014.– Continued collaboration on Registration roadmap.– Assistance with Socrates Search– Services development (Spotfire, reaction databases, academic DPU proof of concept work)– Services uplift of IJC 5 years on and the JChem Platform is now the default ‘Chemistry engine’ .ChemAxon UGM Budapest21 May 201420
Thank you for your attentionQuestions?ChemAxon UGM Budapest21 May 201421
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 Budapest21 May 201422
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 Budapest21 May 201423
Tibco Spotfire Excel 2007 Jchem for Excel Stephen Swanson Budapest UGM 2012 . Retrospective 1: IJC evolution ChemAxon UGM Budapest 21 May 2014 7 Initial replacement for ISISBase began 2009. Rollout 5.6 mid 2011. . -GSK database architecture made performance slow.
