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XPath Query

This tool allows users to search for protein kinase C beta secondary structures, query specific domains, and perform batch BLAST searches. It also provides efficient indexing and performance enhancements using Oracle Extensibility Framework.

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XPath Query

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  1. XPath Query

  2. View XML Data as Tables

  3. View the Same Data in XML

  4. BLAST Search on PKC-beta Query the domain 2 of PKC beta (residue 102-151)

  5. BLAST Search on PKC-beta

  6. BLAST Search on PKC-beta

  7. BLAST Search on PKC-beta Run BLAST in batch

  8. BLAST Search on PKC-beta

  9. BLAST Search on PKC-beta

  10. BLAST Search on PKC-beta

  11. Search Protein Secondary Structures Similar to PKC-beta • E : Beta Sheet • _ : Loop • H : Alpha Helix • < _ 25 40 > < E 3 3 > < _ 13 25 >

  12. Query the Secondary Structures Define an operator to match the secondary structure. Do a full table scan without domain index

  13. Query the Secondary Structures A full table scan takes 1.03 sec to complete.

  14. Query the Secondary Structures Use the domain index (Hammel L and Patel JM, VLDB 2002)

  15. Domain Index increases performance Now it takes 0.09 seconds (11 times faster). Oracle Extensibility Framework enables efficient query of any specialty data.

  16. Search of genes and genetic disorders (OMIM): Migration of OMIM from MySQL

  17. Migration of OMIM from MySQL

  18. Pathway Modeling

  19. Zoom In

  20. Zoom In

  21. PKC-beta in the Pathway

  22. Search Multiple Repositories with a Single Click Search structured and unstructured data across Web sites, email, relational tables, documents and XML

  23. BioOracle Discovery Found Protein Kinase C Beta Inhibitor is in Lilly’s pipeline for diabetes

  24. Find a Cure for Lymphoma Cancer • Literature search on Lymphoma • Set up a project workspace • Set up a meeting • Check lab protocols • Store cell histology images • Analyze gene expression results • Study the markers • Find a lead

  25. Platform Features Highlighted Transparent Gateways Fast access using Oracle OCI Distributed Queries Perform searches across domains Generic Gateways Access any data using ODBC e.g. MySQL GenBank e.g. PubMed External Tables Ability to index and query external files UltraSearch Search external sites & repositories MySQL Toolkit Easily move MySQL data into Oracle Real Application Clusters Linear scalability Oracle Portal Build personalized portals Application Server Provide scalability for themiddle tier XML DB Flexibly manage data interMedia Store & manage images Security Enforce security Auditing Create audit trail to facilitate FDA compliance Workflow Automate laboratory & business processes Collaboration Suite Collaborate securely iFS/Files Share documents e.g. SwissProt SP-ML Data Mining Discover patterns & insights BLAST Sequence similarity search Network Model Pathways Modeling Statistics Perform basic statistics Table Functions Implement complex algorithms OLAP & Discoverer Interactive query & drill-down Extensibility Framework (Data cartridges), manage complex scientific dataLOBs Manage unstructured data Text Index & query text, e.g. literature searches SQL Loader High performance data loader Web Services Standard communication between applications Merge/Upsert Enabling update and insert in one step TransportableTablespaces Rapidly exchange tables Oracle Streams Rule-based subscription for information sharing

  26. Manage vast quantities of data Accessheterogeneous data Access heterogeneous Data BioOracle Conclusions Collaborate securely Integrate a variety of data types Find Patterns and insights

  27. Charlie Berger Joyce Peng Pablo Tamayo Susie Stephens Melliyal Annamalai William.Beauregard Mark Drake Stefan Buchta Omar Alonso Scott Nichols Jack Wang Robert Haberstroh Brajesh Goyal Glen Williamson Ari Mozes Timothy Chorma Vishal Rao Vishu Krishnamurthy George Tang Neil Evans Acknowledgement: the Oracle Team

  28. Q & A Q U E S T I O N S Q U E S T I O N S A N S W E R S A N S W E R S

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