XPath Query View XML Data as Tables View

XPath Query

View XML Data as Tables

View the Same Data in XML

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

BLAST Search on PKC-beta

BLAST Search on PKC-beta Run BLAST in batch

BLAST Search on PKC-beta

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

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

Query the Secondary Structures A full table scan takes 1. 03 sec to complete.

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

Domain Index increases performance Now it takes 0. 09 seconds (11 times faster). Oracle Extensibility Framework enables efficient query of any specialty data.

Search of genes and genetic disorders (OMIM): Migration of OMIM from My. SQL

Migration of OMIM from My. SQL

Pathway Modeling

Zoom In

PKC-beta in the Pathway

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

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

Find a Cure for Lymphoma Cancer Ÿ Ÿ Ÿ Ÿ 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

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

Integrate a variety of data types Find Patterns and insights Manage vast quantities of data Access heterogeneo s Data

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

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