life sciences integrated demo joyce peng senior product manager, life sciences oracle corporation
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Life Sciences Integrated Demo Joyce Peng Senior Product Manager, Life Sciences Oracle Corporation [email protected]. Manage vast quantities of data. Informatics Challenges. Access heterogeneousdata. Access heterogeneous Data. Collaborate securely. - PowerPoint PPT PresentationTRANSCRIPT
Life Sciences Integrated Demo
Joyce Peng Senior Product Manager, Life Sciences
Oracle [email protected]
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