1. DecisionSite and DiscoveryLink Doug Del Prete IBM Life Sciences dougdp@us.ibm.com Visualizing data in novel ways Spotfire User Conference Boston, MA October 28, 2003

2. DecisionSite and DiscoveryLink 1 What is DiscoveryLink?  DiscoveryLink (DL) is a powerful technology available from IBM that will allow you to view many data sources – even non-relational ones like BLAST and HMMER – as one heterogeneous “virtual relational database”  Basically, a wide variety of data sources are all made to look like SQL-based tables/views, which makes it easy to access them and integrate all of this data together in an optimized way

3. DecisionSite and DiscoveryLink 2 What is DiscoveryLink?  DiscoveryLink is based on the latest Information Integrator middleware technology, now a major IBM software initiative for data federation/integration  All data sources essentially become “SQL aware”, and do so under a cost-based optimizer that works against both relational and non-relational data sources and their associated queries

4. DecisionSite and DiscoveryLink 3 Information Integration: Issues For Scientists For IT

5. DecisionSite and DiscoveryLink 4 Information Integration: Solution For Scientists For IT

6. DecisionSite and DiscoveryLink 5 Information Integration: Question Q: Show me all the compounds similar to ketanserin that have been tested against members of the serotonin family and have characteristics of a good drug.

7. DecisionSite and DiscoveryLink 6 Term Operator Value Compound SimilarTo Ketanserin ReceptorHomologousSerotonin IC50<=1E-8 Molwt>375 Molwt<425 logP>4 <6 BLAST WrapperXML Wrapper Oracle Wrapper ODBC Wrapper BLAST Data Source Oracle Compound DB in Germany Assay Results in MySQL Discovery Link Result Set (Visualization ) Parameters IIM Query Solution XML Document Q: Show me all the compounds similar to ketanserin that have been tested against members of the serotonin family and have characteristics of a good drug. Architecture Information Integration: IT Translation

8. DecisionSite and DiscoveryLink 7 Solution Architecture SELECT a.compound_id, b.ic50, b.screen_name FROM CMPNDDBS a, ACTIVITY_DATA b, BLASTP c WHERE a.compound_id = b.compound_id AND SimilarTo(a.compound_struct,:KETANSERIN_MOL) > 0.88 AND c.input_seq = :SEROTONIN AND c.protein_id = b.screen_name AND b.ic50 <= 0.000000001 AND a.mol_wt BETWEEN 375 AND 425 AND a.logP BETWEEN 4 AND 5 DL Query BLAST WrapperXML WrapperOracle WrapperODBC Wrapper BLAST Data Source Oracle Coumpound DB in Germany Assay Results in MySQL Discovery Link Result Set (Visulaizati on) IIM Query XML Document Q: Show me all the compounds similar to ketanserin that have been tested against members of the serotonin family and have characteristics of a good drug. Information Integration: IT Translation

9. DecisionSite and DiscoveryLink 8 Q: Show me all the compounds similar to ketanserin that have been tested against members of the serotonin family and have characteristics of a good drug. Results Information Integration: Final Result Compnd ID HTR1A US1111 HTR1B US1234 HTR1D US2534 HTR1E US 1111 HTR1F US2534 HTR2A US 1111 HTR2B US4791 HTR2C US 1111 HTR4 US1234 HTR5A US1111 HTR6 US1111 US-3451230.001 0.520@1.2 2.1 3.8 1.10.001 53.5@5 0.010.0253@1.2 UK-567345<0.003>5.017@2.5 <6.0 8.85.5 5.916@5 5.64.326@1.2 US-2340120.0025>5.723@10<6.08.95.47.015@54.819.085@1.2 US-3215430.052.083@9.08.90.06.710.048@53.332.613@1.2

10. DecisionSite and DiscoveryLink 9 Wrapper instance definition RDB, Spreadsheet, Flat Files, Algorithms, etc. In diverse locations text Rq rs Rq rs Spotfire DecisionSite, Synapsia, Customer Application, SQL command line, etc. (JDBC/ODBC) Information Integrator Views Administration through Information Integrator Control center Catalog DB2 Data loader SwissProt KEGG dbEST Locus Link UNIGENE and more … Wrappers DB2 Oracle Oracle Cartridge MS SQL Server Sybase Informix Teradata ODBC (MySQL, Postgres…) Excel Flat Files in CSV format Documentum Blast XML ENTREZ (NCBI portal) HMMer Extended Search BioRS Wrapper Development Toolkit Server Definition User Mapping Nicknames Definition Optimizer Log Wrappers plan DiscoveryLink – Overall Architecture

11. DecisionSite and DiscoveryLink 10 DiscoveryLink: A Robust Solution Access to multiple, heterogeneous sources Complex queries across distributed data sources Leverage existing IT infrastructure and use specialized functions of existing databases Integrating analysis tools and business intelligence Can put a SQL front-end and user security on data sources such as BLAST, Pubmed, Genbank, HMMER, XML Can use for fast and easy ad-hoc extensions to a data warehouse/mart Benefits

12. DecisionSite and DiscoveryLink 11 DiscoveryLink Value Proposition A proven scalable data integration solution that enables efficient and effective queries across disparate data sources, thereby improving R&D efficiencies and productivity. This translates into greater flexibility and competitive advantage in the marketplace.

13. DecisionSite and DiscoveryLink 12 DecisionSite and DiscoveryLink

14. 13 DecisionSite and DiscoveryLink  DecisionSite, in its own right, can access many data sources to drive its powerful set of visualizations – i.e. any data source that is JDBC compliant can be configured as a data source  But DiscoveryLink as the data access engine can extend the reach of DecisionSite in both the types of data sources and performance/scalability  These two products together provide a robust, flexible “best of breed” approach to analyzing your data:  DecisionSite as the user interface/front-end to DL  DiscoveryLink as a federated data source access engine for DS

15. DecisionSite and DiscoveryLink 14 DecisionSite Server Information Interaction Services Relational DBMiddleware DB2/ DiscoveryLink JDBC WebServices Txt/csv/etc… DecisionSite and DiscoveryLink BLAST/ HMMER XML Relational (Optimized Joins) Pubmed/ Genbank …

16. DecisionSite and DiscoveryLink 15 Benefits Overview  Access more data sources – BLAST, HMMER, Genbank, Documentum, BioRS, etc.  Access existing DecisionSite data sources faster/easier – XML, Postgres, MS Access, etc.  Extend/augment an existing visualization with information from any of the above data sources  Optimized queries cross-joined across all data sources – relational and non-relational – all under one JDBC connection

17. DecisionSite and DiscoveryLink 16 Visualize a BLAST result under DS/DL!

18. DecisionSite and DiscoveryLink 17 DecisionSite and DiscoveryLink  Based on the natural fit of DiscoveryLink into DecisionSite’s IIM (Information Interaction Model)  Under the Information Interaction Designer (IID), you reference “Nicknames”, which are “virtual tables”, pointing to other tables/views and non- relational objects pre-configured under DiscoveryLink  These data sources naturally available to Information Builder and Information Library/Links, and beyond

19. DecisionSite and DiscoveryLink 18 DecisionSite and BLAST See how easy it is to configure a data source like BLAST to be used under DecisionSite

20. DecisionSite and DiscoveryLink 19 Indicate BLAST Server/Algorithm

21. DecisionSite and DiscoveryLink 20 Configure Defline

22. DecisionSite and DiscoveryLink 21 View complete BLAST Nickname

23. DecisionSite and DiscoveryLink 22 Configure under Information Designer

24. DecisionSite and DiscoveryLink 23 Configure under Information Builder

25. DecisionSite and DiscoveryLink 24 This is all done quickly and easily, even though there is no JDBC driver for BLAST readily available! DecisionSite and BLAST

26. DecisionSite and DiscoveryLink 25 DecisionSite and XML Similarly, see how easy it is to configure XML to be used under DecisionSite

27. DecisionSite and DiscoveryLink 26 Provide XML Schema/File Location

28. DecisionSite and DiscoveryLink 27 Create all the relational Nicknames

29. DecisionSite and DiscoveryLink 28 Configure Parent/Child Join

30. DecisionSite and DiscoveryLink 29 Again, this can all be done quickly and easily, without having to find and manually configure a JDBC driver via a text editor, and then restarting DecisionSite, etc. DecisionSite and XML

31. DecisionSite and DiscoveryLink 30 Merged Queries - Example  In IID, set up the BLAST and Entrez Data Models  Also the Nucleotide/BLAST join via Accession #  Configure a BLAST Information Link  Configure a Nucleotide Information Link  Run BLAST visualization  From the visualization, run the Entrez Information Link to get all the applicable metadata information about each displayed Accession (in Details-on- Demand, Table, etc.)

32. DecisionSite and DiscoveryLink 31 Query Optimization  Under IID, configure key Joins under DB2/ DiscoveryLink  This includes established DecisionSite data like Oracle and MySQL (very quickly configured in DiscoveryLink Control Center)  The Information Link makes only one JDBC connection to access all the data sources!  The underlying SQL query invokes the DB2 Optimizer to improve performance even more

33. DecisionSite and DiscoveryLink 32 Query Optimization  Great for large relational data sets such as joining assay results with a chemical compound database, etc.

34. DecisionSite and DiscoveryLink 33 DecisionSite and DiscoveryLink - Summary You can extend all the powerful features of DecisionSite, like guided analytics and posters, to visualize information from more data sources, in an easier manner, and do so in an optimized environment

35. DecisionSite and DiscoveryLink 34 DEMO Visualize a BLAST protein similarity search against SwissProt

36. Thank you. Doug Del Prete IBM Life Sciences USA dougdp@us.ibm.com Questions?