Moving away from ISIS software with ChemAxon's Help. Debra Kassabian Novartis Institutes for Biomedical Research (NIBR) IT

Transcription

1 Moving away from ISIS software with ChemAxon's Help Debra Kassabian Novartis Institutes for Biomedical Research (NIBR) IT

2 Chemistry software at NIBR, before ChemAxon Direct Cartridge Chemistry search in Oracle ISIS/Draw Draw Structures CambridgeSoft ELN ChemOffice ISIS/Base Personal structure databases Personal reaction databases Ceres (ISIS/Base + ISIS/Host) Historical collection of Novartis reactions Screening sample database ACD Other purchased databases Duplication of functionality ISIS software no longer supported ELN search very slow ISIS for Excel Structures in spreadsheets 2 ChemAxon UGM September 2012

3 Chemistry software at NIBR Direct Cartridge Chemistry search in Oracle ChemAxon JChem Cartridge ISIS/Draw Draw structures CambridgeSoft Chemdraw ISIS/Base Personal structure databases Personal reaction databases Ceres (ISIS/Base + ISIS/Host) Historical collection of Novartis reactions Screening sample database ACD Other purchased databases Let s ask ChemAxon If they can help... ISIS for Excel Structures in spreadsheets CambridgeSoft Chemdraw/Excel 3 ChemAxon UGM September 2012

4 ISIS Software Usage at NIBR Emeryville Cambridge (HQ) Horsham Basel Singapore (NITD) Shanghai Over 1600 scientists with ISIS software installed 4 ChemAxon UGM September 2012

5 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 A few missing features were also identified Connecting to Oracle and searching worked well 5 ChemAxon UGM September 2012

6 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 6 ChemAxon UGM September 2012

7 IJC Rollout Deployment 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 Local Database Single User SDF,RDF,CSV... JChem Cartridge Shared Database Project Team, Lab... 7 ChemAxon UGM September 2012

8 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 8 ChemAxon UGM September 2012

9 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 9 ChemAxon UGM September 2012

10 Ceres ISIS/Base + ISIS/Host LDC Structures ACD MDDR, CMC Metabolite Chirbase Current Chemical Reactions Historical collection of Novartis reactions New Web application 10 ChemAxon UGM September 2012

11 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 and come to the workshops! 11 ChemAxon UGM September 2012

12 IJC beyond ISIS Replacement: accessing the NIBR data warehouse DART (Data Analysis and Reporting Tool) Define Query Define Fields to Display View data in Spreadsheet Data Query Definition + Fields to display Query Definition + Fields to display 1 Web Services 2 3 Data 4 IJC Forms Data warehouse 12 ChemAxon UGM September 2012

13 IJC beyond ISIS Replacement: accessing NIBR Chemical properties calculation Framework SMILES/Compound Nr. clogp, PSA... 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 13 ChemAxon UGM September 2012

14 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 14 ChemAxon UGM September 2012

15 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 15 ChemAxon UGM September 2012

16 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 16 ChemAxon UGM September 2012

17 Query Requirements vs. Data Challenges 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 17 ChemAxon UGM September 2012 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

18 Architecture Web Browser (javascript) Web application (Tomcat/Wicket) Data Service Layer (Tomcat) 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 Oracle/JChem Update application Oracle/eLN 18 ChemAxon UGM September 2012

19 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 19 ChemAxon UGM September 2012

20 Interface Overview 20 ChemAxon UGM September 2012

21 Substructure search with results 21 ChemAxon UGM September 2012

22 Search-results filters 22 ChemAxon UGM September 2012

23 Additional search criteria + filters 23 ChemAxon UGM September 2012

24 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 24 ChemAxon UGM September 2012

25 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 25 ChemAxon UGM September 2012

26 26 ChemAxon UGM September 2012 Thank you