Life Sciences Integrated Demo Joyce Peng Senior Product

Life Sciences Integrated Demo Joyce Peng Senior Product Manager, Life Sciences Oracle Corporation Yao-chun. Peng@oracle. com

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

Oracle Life Sciences Platform 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 Collaboration Suite Flexibly manage data Enforce security inter. Media Auditing i. FS/Files Workflow Data Mining Collaborate securely Ultra. Search external sites & repositories My. SQL Toolkit Easily move My. SQL data into Oracle Store & manage images Create audit trail to facilitate Share documents FDA compliance Extensibility Framework Automate laboratory Discover patterns & insights & business processes (Data cartridges), manage complex scientific data LOBs Manage unstructured data Text Index & query text, e. g. literature searches 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

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

Bio. Oracle Project We are scientists at a life sciences company looking to find a cure for Lymphoma

Bio. Oracle Portal Integrated data view and Single-Sign-On to many applications

Find a Cure for Lymphoma 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

Literature Search document content.

Extract Document Themes

Generate the Gist

Categorize Documents

Text Mining

Find a Cure for Lymphoma 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

Bio. Oracle Project In Oracle Files Lymphoma project workspace after adding documents

Bio. Oracle Project in Oracle Files Support revision control

Bio. Oracle Project in Oracle Files Associate metadata (Categories) to a document.

Bio. Oracle Project in Oracle Files Advanced Search

Approval Workflow

Approval Workflow

Bio. Oracle Project in Oracle Files Access Control

Bio. Oracle Project in Oracle Files Support • HTTP/Web. DAV(Web) • SMB (Windows) • NFS (UNIX) • AFP (Apple Mac) • FTP protocols

Wireless Access

Highly Scalable, Worldwide Access

Find a Cure for Lymphoma 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

Calendar Use calendar in Collaboration Suite to schedule meetings with collaborators

Internet Meeting

Protocol Sharing

Find a Cure for Lymphoma 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

Bio. Oracle Image Management Use inter. Media to manage and query Lymphoma histology data

Bio. Oracle Image Management Generate image thumbnails

Bio. Oracle Image Management Integrated search across relational data and image attributes extracted

DLBC Follicular Gene Expression Analysis for Lymphoma Biopsies Samples Instruments Filtering and Pre. Processing SQL, XML, Java Affymetrix Microarray Feature Selection Interpretation of Results SQL Molecular Pattern Recognition Oracle Data Mining Reports Feature Selection Bayesian Classifier Java Servlets Use analytical pipeline to identify the patterns that differentiate DLBC from Dataset from Golub et al Science 286: 531 -537. Follicular Lymphoma Discoverer Portals Prediction: DLBC Follicular

Find a Cure for Lymphoma 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

Oracle Data Mining Classification of Cancer Subtypes (DLBC versus Follicular) Oracle provides wizards to guide analysts through data mining model creation

Oracle Data Mining Build a classification model

Oracle Data Mining Select the target field, e. g. DLBC or Follicular Lymphoma

Oracle Data Mining Select the classification model

Oracle Data Mining Test the model on the data set of interest

Naïve Bayes has built a model that distinguishes DLBC from Folicular with 77% accuracy The confusion matrix shows the number of times the model’s predictions are accurate

Oracle Data Mining See if the Adaptive Bayes Network algorithm can build a better model

Oracle Data Mining Use wizards to define parameters for building a model

Oracle Data Mining Adaptive Bayes Network algorithm can predict Lymphoma subtype with 84% accuracy

Oracle Data Mining Adaptive Bayes Network algorithm generates rules for model interpretation

Oracle Data Mining in JDeveloper Automatically create the Java code needed to build analytical pipelines inside the database