Life Sciences Integrated Demo

Joyce Peng Senior Product Manager, Life Sciences

Oracle CorporationYao-chun.Peng@oracle.com

Access heterogeneous

Data

Access heterogeneous data

Manage vast quantities of data

Collaborate securely

Integrate a variety

of data types

Find Patterns and

insights

Informatics Challenges

Oracle Life Sciences Platform

Collaboration SuiteCollaborate securely

iFS/Files Share documents

XML DBFlexibly manage data

interMediaStore & manage images

SQL LoaderHigh performance data loader

Web ServicesStandard communication between applications

Merge/UpsertEnabling update and insert in one step

Oracle PortalBuild personalized portals

Application ServerProvide scalability for themiddle tier

Transparent GatewaysFast access using Oracle OCI

Distributed QueriesPerform searches across domains

Generic GatewaysAccess any data using ODBC

e.g. SwissProt SP-ML

Transportable Tablespaces

Rapidly exchange tables

Oracle StreamsRule-based subscription for

information sharing

Data MiningDiscover patterns & insights

BLASTSequence similarity search

Network ModelPathways Modeling

StatisticsPerform basic statistics

Table FunctionsImplement complex algorithms

OLAP & DiscovererInteractive query & drill-down

SecurityEnforce security

AuditingCreate audit trail to facilitate FDA compliance

WorkflowAutomate laboratory & business processes

Extensibility Framework (Data cartridges), manage complex scientific data LOBsManage unstructured data

TextIndex & query text, e.g. literature searches

Real Application Clusters Linear scalability

Cl

Cl

O

e.g. PubMede.g. MySQLGenBank

External TablesAbility to index and query external files

UltraSearchSearch external sites

& repositories

MySQL ToolkitEasily move MySQL

data into Oracle

Platform Features Highlighted

Collaboration SuiteCollaboration SuiteCollaborate securely

iFS/FilesiFS/Files Share documents

XML DBXML DBFlexibly manage data

interMediainterMediaStore & manage images

SQL LoaderHigh performance data loader

Web ServicesStandard communication between applications

Merge/UpsertEnabling update and insert in one step

Oracle PortalOracle PortalBuild personalized portals

Application ServerProvide scalability for themiddle tier

Transparent GatewaysTransparent GatewaysFast access using Oracle OCI

Distributed QueriesPerform searches across domains

Generic GatewaysAccess any data using ODBC

e.g. SwissProt SP-ML

Transportable Tablespaces

Rapidly exchange tables

Oracle StreamsRule-based subscription for

information sharing

Data MiningData MiningDiscover patterns & insights

BLASTBLASTSequence similarity search

Network ModelNetwork ModelPathways Modeling

StatisticsStatisticsPerform basic statistics

Table FunctionsImplement complex algorithms

OLAP & DiscovererInteractive query & drill-down

SecurityEnforce security

AuditingCreate audit trail to facilitate FDA compliance

WorkflowWorkflowAutomate laboratory & business processes

Extensibility Extensibility FrameworkFramework (Data cartridges), manage complex scientific data LOBsManage unstructured data

TextTextIndex & query text, e.g. literature searches

Real Application Clusters Linear scalability

Cl

Cl

O

e.g. PubMede.g. MySQLGenBank

External TablesExternal TablesAbility to index and query external files

UltraSearchUltraSearchSearch external sites

& repositories

MySQL ToolkitMySQL ToolkitEasily move MySQL

data into Oracle

BioOracle Project

We are scientists at a life sciences company looking to find a cure for Lymphoma

BioOracle Portal

Integrated data view and Single-Sign-On to many applications

Find a Cure for Lymphoma

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 SearchSearch document content.

Extract Document Themes

Generate the Gist

Categorize Documents

Text Mining

Find a Cure for Lymphoma

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

BioOracle Project In Oracle Files

Lymphoma project workspace after adding documents

BioOracle Project in Oracle Files

Support revision control

BioOracle Project in Oracle Files

Associate metadata (Categories) to a document.

BioOracle Project in Oracle Files

Advanced Search

Approval Workflow

Approval Workflow

BioOracle Project in Oracle Files

Access Control

BioOracle Project in Oracle Files

Support• HTTP/WebDAV(Web)• SMB (Windows)• NFS (UNIX)• AFP (Apple Mac)• FTP protocols

Wireless Access

Highly Scalable, Worldwide Access

Find a Cure for Lymphoma

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

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

BioOracle Image Management

Use interMedia to manage and query Lymphoma histology data

BioOracle Image Management

Generate image thumbnails

BioOracle Image Management

Integrated search across relational data and image attributes extracted

Interpretation of Results Discoverer

Reports

Portals

Java Servlets

Biopsies Samples

Instruments

Filtering and Pre-

Processing

SQL, XML, Java

Feature Selection

SQL

Oracle Data Mining

Feature Selection

Molecular Pattern

Recognition

Oracle Data Mining

Bayesian Classifier

Affymetrix Microarray

Dataset from Golub et al Science 286:531-537.

Gene Expression Analysis for Lymphoma

Use analytical pipeline to identify the patterns that differentiate DLBC from Follicular Lymphoma

Prediction:

DLBC Follicular

DLBC Follicular

Find a Cure for Lymphoma

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 MiningClassification 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

The confusion matrix shows the number of times the model’s predictions are accurate

Naïve Bayes has built a model that distinguishes DLBC from Folicular with 77% accuracy

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