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DecisionSite and DiscoveryLink Visualizing data in novel ways Spotfire User Conference Boston, MA October 28, 2003 Doug Del Prete IBM Life Sciences [email protected] 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 DecisionSite and DiscoveryLink 1 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 DecisionSite and DiscoveryLink 2 Information Integration: Issues For Scientists Without a Data Integration Layer Application Application Application Application Application Web Servers For IT Application Layer Data Layer ASCII data file Excel Spreadsheet Oracle DB2 Multiple, varied sources Data freshness DecisionSite and DiscoveryLink SQL Server Multiple queries Legacy Databases 3 Information Integration: Solution Textual Data Compound Data For Scientists Proteomic Data Other Other Data Data Sources Sources Genomic Data DiscoveryLink Gene Expression Data Legacy Data Toxicology Data Application Application Application Application Application Web Servers For IT DiscoveryLink ™ ASCII data file Excel Spreadsheet Oracle DB2 Multiple, varied sources Data freshness DecisionSite and DiscoveryLink SQL Server Multiple queries Legacy Databases 4 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. Compound Data Other Other Data Data Sources Sources Proteomic Data Genomic Data DiscoveryLink Gene Expression Data DecisionSite and DiscoveryLink Textual Data Toxicology Data Legacy Data 5 Information Integration: IT Translation Solution 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. Textual Data Compound Data Proteomic Data Other Other Data Data Sources Sources Genomic Data DiscoveryLink Gene Expression Data Toxicology Data Legacy Data Architecture Parameters IIM Query Term Operator Value Compound SimilarTo Ketanserin Receptor Homologous Serotonin Result Set (Visualization) Discovery Link IC50 <= 1E-8 Molwt > 375 Molwt < 425 logP > 4 logP < 6 DecisionSite and DiscoveryLink BLAST Wrapper XML Wrapper BLAST Data Source XML Document Oracle Wrapper Oracle Compound DB in Germany ODBC Wrapper Assay Results in MySQL 6 Information Integration: IT Translation 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. Solution Compound Data Other Other Data Data Sources Sources 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 DecisionSite and DiscoveryLink Proteomic Data Genomic Data DiscoveryLink Gene Expression Data DL Query Textual Data Legacy Data Toxicology Data Architecture Result Set IIM Query (Visulaizati on) Discovery Link BLAST Wrapper BLAST Data Source XML Wrapper Oracle Wrapper XML Document Oracle Coumpound DB in Germany ODBC Wrapper Assay Results in MySQL 7 Information Integration: Final Result 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 Compnd ID HTR1A US1111 HTR1B US1234 HTR1D US2534 HTR1E US HTR1F 1111 US2534 HTR2A US HTR2B 1111 US4791 HTR2C US 1111 HTR4 US1234 HTR5A US1111 HTR6 US1111 US-345123 0.001 0.5 [email protected] 2.1 3.8 1.1 0.001 53.5@5 0.01 0.02 [email protected] UK-567345 <0.003 >5.0 [email protected] <6.0 8.8 5.5 5.9 16@5 5.6 4.3 [email protected] US-234012 0.0025 >5.7 23@10 <6.0 8.9 5.4 7.0 15@5 4.8 19.0 [email protected] US-321543 0.05 2.0 [email protected] 8.9 0.0 6.7 10.0 48@5 3.33 2.6 [email protected] DecisionSite and DiscoveryLink 8 DiscoveryLink – Overall Architecture Wrapper instance definition SwissProt KEGG dbEST Locus Link UNIGENE and more … Server Definition User Mapping Nicknames Definition Spotfire DecisionSite, Synapsia, Customer Application, SQL command line, etc. (JDBC/ODBC) Rq Data loader DB2 rs Information Integrator Optimizer Wrappers plan Catalog Log •Oracle Cartridge Wrappers Administration through Information Integrator Control center Rq Rq Rq rs •DB2 •Oracle rs rs <XML> text </XML> •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 RDB, Spreadsheet, Flat Files, Algorithms, etc. In diverse locations DecisionSite and DiscoveryLink 9 DiscoveryLink: A Robust Solution Benefits • 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 DecisionSite and DiscoveryLink 10 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. DecisionSite and DiscoveryLink 11 DecisionSite and DiscoveryLink DecisionSite and DiscoveryLink 12 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 DecisionSite and DiscoveryLink 13 DecisionSite and DiscoveryLink WebServices DecisionSite Server Information Interaction Services JDBC Txt/csv/etc… Relational DB Relational (Optimized Joins) DecisionSite and DiscoveryLink DB2/ DiscoveryLink Middleware BLAST/ HMMER XML Pubmed/ Genbank … 14 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 DecisionSite and DiscoveryLink 15 Visualize a BLAST result under DS/DL! DecisionSite and DiscoveryLink 16 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 nonrelational objects pre-configured under DiscoveryLink These data sources naturally available to Information Builder and Information Library/Links, and beyond DecisionSite and DiscoveryLink 17 DecisionSite and BLAST See how easy it is to configure a data source like BLAST to be used under DecisionSite DecisionSite and DiscoveryLink 18 Indicate BLAST Server/Algorithm DecisionSite and DiscoveryLink 19 Configure Defline DecisionSite and DiscoveryLink 20 View complete BLAST Nickname DecisionSite and DiscoveryLink 21 Configure under Information Designer DecisionSite and DiscoveryLink 22 Configure under Information Builder DecisionSite and DiscoveryLink 23 DecisionSite and BLAST This is all done quickly and easily, even though there is no JDBC driver for BLAST readily available! DecisionSite and DiscoveryLink 24 DecisionSite and XML Similarly, see how easy it is to configure XML to be used under DecisionSite DecisionSite and DiscoveryLink 25 Provide XML Schema/File Location DecisionSite and DiscoveryLink 26 Create all the relational Nicknames DecisionSite and DiscoveryLink 27 Configure Parent/Child Join DecisionSite and DiscoveryLink 28 DecisionSite and XML 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 DiscoveryLink 29 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-onDemand, Table, etc.) DecisionSite and DiscoveryLink 30 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 DecisionSite and DiscoveryLink 31 Query Optimization Great for large relational data sets such as joining assay results with a chemical compound database, etc. DecisionSite and DiscoveryLink 32 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 DecisionSite and DiscoveryLink 33 DEMO Visualize a BLAST protein similarity search against SwissProt DecisionSite and DiscoveryLink 34 Thank you. Questions? Doug Del Prete IBM Life Sciences USA [email protected]