Oracle Life Sciences Platform and 10g Overview

June 23 & 24Reston, VA

Charlie BergerSr. Director of Product Management, Life Sciences and Data Miningcharlie.berger@oracle.comOracle Corporation

Administrative

Thank you to our ISV Partners for sponsoring OLSUGInforSense LtdInnaPhaseWaters CorpMDLApplied BiosystemsAccelrysTom Sawyer Software, Inc.World Fusion CorpSpotfireLION bioscience, Inc.Tripos

Administrative

Auditorium—seats 120 2nd Floor—seats 70Classroom—seats 24; first come, first seating

OLSUG Agenda

Administrative

OLSUG Membership and PlansThurs at 8:30 am

Open DiscussionThurs at 4:15

Please turn in your FEEDBACK FORMS!!

Database ApplicationServer

DiscoveryDiscovery

Finance

HR Projects

Maintenance

Manage all your dataManage all your data Run all your applicationsRun all your applications

Oracle’s Solutions for Life Sciences

Manufacture/Supply Chain Management

Development& Clinical

Sales & Marketing

DiscoveryDiscovery Collaborate SecurelyCollaborate Securely

HealthcareTransactions

Life Science ChallengeTypical Research EnvironmentPublic Databases

Industrial Research

Lab

Private/Service Databases

Local Copies

Partner or Collaborator

Local Databases

Genomics

Proteomics

Pathways

Cheminformatics

Clinical

Oracle’s Platform for Life Sciences

1. Access distributed data2. Integrate a variety of data types3. Manage vast quantities of data4. Collaborate securely5. Find patterns and insights

Oracle Life Science Platform1. Access distributed data

Gateways, External Tables, SQL Loader, Streams, Oracle Gateway to Lion SRS, etc.

2. Integrate a variety of data typesXML DB, Intermedia, Text, etc.

3. Manage vast quantities of dataRAC, Partitioning, Grid, etc.

4. Collaborate securelyCollaboration Suite, iFS (Oracle FilesOnline), Portal, Security, etc.

5. Find patterns and insightsData Mining, BLAST, Statistics, Text, etc.

GenomicsGenomics

ProteomicsProteomics

PathwaysPathwaysCheminformaticsCheminformatics

ClinicalClinical

Access Distributed Data

Flat files

Distributed query

Transparent Gateway

External Sites

MySQL

Generic Connectivity

DBlinks

UltraSearch

DB2

Transparent Gateway

External Table

1. Access Distributed Data

Flat filesSRS

1. Access Distributed Data Merge StatementOracle StreamsHeterogeneous Transportable TablespacesSQL*LoaderMigration ToolkitsHigh Speed Import/ExportOracle Scheduler

Flat files MySQL

SQL*LoaderHigh-speed data loading utility

Loads data from external files into tables in an Oracle database.Accepts input data in a variety of formatsPerforms filteringLoads into multiple tables during the same load session

Three methods for loading data: Conventional Path LoadDirect Path LoadExternal Table Load

Merge StatementFast insert, update or conditional update/insert of records

MATCHED THEN insert clauseWHEN NOT

WHENSKIP ( condition )

MERGE INTO table

USING table/view/subquery

ON ( condition )

WHEN MATCHED THEN update clause

Transportable TablespacesMechanism to quickly move a tablespace between Oracle databases

Most efficient means to move bulk data between databases

Enhanced to support different hardware platforms & operating systems

sourcedatabase

targetdatabase

Oracle Data PumpHigh speed bulk data and metadata movement (Import/Export) between Oracle databasesUses high speed direct-path load/unloadAutomatically scales using parallel executionAccessible via

expdp and impdp utilitiesPL/SQL APIEnterprise Manager

Oracle SchedulerRuns PL/SQL, Java, 3GL, OS Scripts, internal utilities (RMAN)

Job classes, priorities, workload windowsIntegrated with Resource Manager & RAC service framework

Integrate Platform’s JobScheduler with Oracle databaseSingle interface for job scheduling Platform’s JobScheduler can create & schedule Oracle database jobsDatabase jobs can be incorporated into larger job flowsSchedule & use resources efficiently for combined database & computational tasks

Distributed Query OptimizationOptimized queries within and across databasesEnhanced cost based optimizerCapture complete statistics for remote tablesConsider network bandwidth & latency in deciding what parts of query plan should be remotely mappedSupport different execution cost at different nodes (e.g. based on node ownership)

Oracle StreamsEnables rule-based information sharing among multiple systems

Captures and manages eventsShares events with other databases and applicationsRoutes published information to subscribed destinationsIntegrated with new job scheduler

Capture Staging Consumption

SRS Transparent Gateway for OracleData supported by the SRS Gateway behaves as if they are in OracleOracle re-writes user’s SQL query into syntax understood by SRS, using capability table & index of GatewayThe query is executed in the SRS systemIf mapping entire query to SRS syntax is not possible, after fetching the data, Oracle will do some functions/joins locally

Integrate a Variety of Data Types

2. Integrate a Variety of Data TypesXML DB

Unite XML content & SQL/relational dataLOBs

Manage unstructured data BFILES, BLOBs, CLOBs, URIs

Files(Oracle9iFS)Central repository for structured & unstructured data

TextIndex & fast query of text content

interMediaManage audio, video & image data

Extensible indexingManage & index complex scientific data

XMLXML

XML SupportOracle Database supports XML data model

XMLType, XMLSchema, DOM Fidelity, Xpath, …

Query Language: SQL/XML and XML QueryTransparent storage optimizationsA new XML Content Repository

Hierarchical organization of the dataWebDAV compliant with indexing for fast access

Copy-based Schema Evolution for XMLTypeSQLX standards compliance

XDK Advances XML APIsXDK unifies XML APIs in/outside Database

Simplifies XML Application development in the Database, Mid-tier & Clients Eliminates multi-step processing by operating directly on XMLType Improves application performance in Java, C, and C++

XSLT performance increase up to 100%Additional XML Standards Support

DOM 3, XSLT 2, XPath 2XML Pipeline, XPointer, JAXB

Reed ElsevierLargest technical publishing conglomerate $8B annual revenueMore than 1700 scientific, technical & medical peer-reviewed journalsOver 59 million abstracts Over two million full-text scientific journal articles , another one million full-text articles via CrossRef(http://www.crossref.org/) to other publishers' platformsOracle XML DB chosen as Repository Database

Oracle TextSearch text documentsSimply text applications development via JDeveloper WizardsClassification & clustering using data mining algorithms

Theme & classification visualization

Improved FilteringMulti-part MIME for emailEncrypted PDF

Oracle Text

European Bioinformatics Institute

Manages major public databases (e.g. SwissProt, EMBL Nucleotide Sequence Database, Medline) in Oracle. (Total: > 5 TB)Uses Oracle XML DB and Oracle Text for Medline – in development.

Size: 11 million records, 200 GBUses Oracle Database and Application Server

interMediaAbility to store wide range of image types

Processing functionalityRotate/flip, brighten/darken using gamma processing, adjust contrast, change bit depth

Access through SQL, Java & Web interfacesRestrict access via security rolesConform to SQL/MM still image standardStore images as columns

Tight integration with annotations

Network Data ModelModel, store, manage & analyze generic connectivity relationships in the DB, i.e. represent data as nodes & linksCan model hierarchies, logical or spatial information, directionalityNetwork analysis at client or application level, e.g. shortest-path, tracing, within-distance analysis, minimum cost spanning tree, nearest neighborNetwork management, e.g. add, delete, modify, load

Network Data Model Reference

"Oracle 10g's Network Data Model feature is great for building asemantic work infrastructure. Oracle 10g's graphical representation

is an excellent tool for planning our Y2H protein interaction data storage needs and for building a signaling network from our Nature-

AfCS Molecule Pages Database." - Joshua Li, Sr. Computational Scientist, San Diego Supercomputer Center / UCSD

"Beyond Genomics, Inc., as a leading systems biology company, believes that Oracle 10g's network data model will significantly

advance the integration of metabolomic, proteomic, transcriptomic, and clinical data sets and the applications that derive value from

these data." – Eric Neumann, Vice President Strategic Informatics, Beyond Genomics, Inc.

Extensibility Framework

Oracle8iServer

Service Interfaces

DataCartridge

Extensibility Interfaces

TypeSystem

QueryProcessing Data

IndexingServer

Execution . . .

Database Extensibility Services

Oracle10gServer

Data CartridgesManage complex scientific data

Chemical SearchingChemistry searching requires special techniques

Chemical name is not uniqueChemists think graphically

“Viagra®”

The solution:A graphical user interface

Specialized operators such as substructuresearch (“sss”) = a chemical “contains”

“sildenafil citrate”

N

N

SO O

O

N

NN

N

O

H

H H

HHHH

H

H

Cl

Cl

O

finds

Manage Vast Quantities of Data

3. Manage Vast Quantities of DataPartitioning

Divide and conquer

Oracle 10g Application ServerProvide scalability for middle tier

Oracle Data GuardProtect data from human or system failures

Real Application Clusters (RAC)Provides high availability, performance and ease of scalability

Real Application Clusters (RAC)

Works with ALLapplicationsFail-over transparent to usersEasy to administer

Start with one server, one database and grow as you growLinear scalability out of the boxSave on Hardware and Storage costs

High-speedinterconnect

DataLoads

Sample/LabProteomics Portal

A-Z

Enterprise Grid ComputingGrid concepts provided with:

Distributed queries, External Tables, Security, RAC, etc.

Grid Access to Oracle Utilities through Globus Resource Allocation Manager (GRAM)

Export, Import, SQLPlusGrid Access to Oracle Database

Invoke PL/SQL routines specified inGlobus Resource Specification Language

Grid Resource Information Service (GRIS) for Oracle Database

Discover & monitor Oracle databases

Performance and ScalabilityDouble the performance for key OLTP workloadsOver 30 internal performance optimizationsImproved IA64 bit supportFast Interconnect support for DB/DB & DB/iASconnectivityFiber support on Windows

Ultra Large DatabasesDatabase Size Limits Raised

Millions of Terabytes (Exabytes)Unlimited size LOB columnsUltra Large data filesMultiple TEMP TablespacesHigh Speed Bulk Data Movement

Data Pump, Transportable Tablespaces

CaprionDiscover & develop innovativeproducts for the diagnosis & treatment of diseases

Scalability for a multi-TB systemIntegration of all components with existing computing environmentSecurity & protection of data integrity

Key Advantages of OracleEasy access & management of integrated informationRapid deployment of new ad hoc queryScalability necessary to accommodate growth

Oracle EnvironmentOracle DatabaseOracle9i Application ServerOracle9i Developer SuiteOracle9i AS DiscovererOracle Warehouse Builder

“The Oracle Data Warehouse is a key component of our IT

platform for proteomics analysis. The massive amount of

information we produce every day requires a system with

proven performance to effectively capture our biological

data”. - Bernard Gagnon, IT Director

ManageabilitySimplified Installation, Configuration and UpgradeImproved Manageability InfrastructureAutomated Application and SQL TuningAdaptive Instance TuningRAC Automated Workload ManagementAutomated Storage ManagementAutomated Backup and RecoveryOracle Enterprise Manager Improvements

High AvailabilitySupport for Rolling UpgradesOnline Application UpgradesFlashback Any ErrorImproved Data Guard InfrastructureImproved Backup and Recovery

Dragon Genomics Centerof Takara Bio Inc.

High-Level Project GoalsManage data throughout every step of a complicated processCreate a laboratory information management system (LIMS) enabling large scale sequencingProvide reliable back up and recovery of vast amounts of data

Key BenefitsProvided easy access and management for vast amounts of dataEnsured scalability needed to accommodate future growth

Oracle EnvironmentOracle Database Enterprise EditionOracle9iAS Enterprise Edition

"We trust Oracle in its ability to run terabyte-class

databases in clustered environments with high availability. And we're

pleased to say that Oracle has not disappointed us.“ -Toru Suzuki, Project Manager,

Dragon Genomics Center, Takara Bio Inc.

Genentech, Inc.Leading biotech company

Over 2 TBs of data in OracleOracle serves as a centralized information resource for gene searching and database cross-referencing.Oracle used for the entire pipeline from research to clinical data to manufacturing and sales applications.

Key Advantages of OracleImproved performance Greater reliability Genentech's corporate goal is 99.999% availability in a 24x7 environment

Oracle EnvironmentOracle 9i databaseReal Application Clusters

Oracle9i Real Application Clusters provide the

foundation for the scalable and highly available

database infrastructure we require to meet our growing data demands in all areas of our business.“ -Scooter Morris, Genentech, Inc.

San Diego Supercomputing Center“In the beginning, we considered using MySQL, Oracle, and another database. But when we evaluated our project needs over the next ten years and realized that our database could

grow to terabytes, we decided we needed a scalable database and one that was reliable. We didn’t want to be

forced to change databases in the middle of the project. …. “We do not need a lot of DBAs to maintain the database.”

Joshua Li, Senior Computational Scientist, University of California, San Diego, Supercomputing Center

Systemwide, SDSC relies on only three DBAs to run over 40 Oracle databases.

Bioinformatics Center Institute for Chemical Research Kyoto UniversityThe Bioinformatics Center Institute for Chemical Research Kyoto University is leading biotechnology research thanks to its comprehensive studies in various areas, including the life sciences, information sciences, chemistry and physics.

“In order to manage this massive amount of genetic information and to operate efficiently, it is essential to have a platform with paramount stability. Our web site receives accesses from all over the world continuously, 24 hours a day. In order to offer the latest information under such circumstances, performance is also an issue. In this sense, the Oracle Database was the most appropriate since it can handle this enormous amount of data in a fast and stable manner, 24 hours a day.”– Professor and Director Minoru Kanehisa, Bioinformatics Center Institute for Chemical Research Kyoto University

Collaborate Securely

4. Collaborate SecurelyOracle 10gAS Portal

Build personalized portalsOracle Workflow

Automate laboratory and business processesOracle 10gAS Files

Enable content management and collaborationRevision control, check-in/check-out, access control

Virtual Private DatabaseDifferent users have unique access privileges

AuditingCreate audit trail to facilitate FDA compliance

Oracle 10gAS Web ServicesStandard way to collaborate through the Web

Oracle PortalRich, declarative environment

Create Web interfaces, publish and manage information, access dynamic data, and customize:

extensible J2EE framework

Connect researchers and collaborators with the information they need and the flexibility to create views tailored to each community

Oracle Collaboration SuiteIntegrated communications Single enterprise search across all repositoriesFlexible access

Integrated Data and Web Services Platform

Oracle Database

iAS

Data ServicesPL/SQLJavaRelationalTextBinaryXDBStreams/AQDBMS JobsSystem Admin

eBusiness& Collaboration Services...

SOAP

SOAP

SOAP

SOAP

SOAP

ApplicationServicesJ2EEPortalBIWireless...

SOAPServiceRequestor

SOAP

SOAP = SOAP or ebXMLover HTTP-JMS-SMTP-FTP

SOAP

UDDIWSDL

Complete data protection Manage user access Detect data misuse with AuditingFacilitate regulatory compliance (HIPPA, 21 CFR PART 11)

Security Evaluations Oracle Microsoft IBMSecurity EvaluationsSecurity Evaluations OracleOracle MicrosoftMicrosoft IBMIBM

US TCSEC, Level B1

US TCSEC, Level C2

UK ITSEC, Levels E3/F-C2

UK ITSEC, Levels E3/F-B1

ISO Common Criteria, EAL-4

Russian Criteria, Levels III, IV

US FIPS 140-1, Level 2

TOTAL

US TCSEC, Level B1US TCSEC, Level B1

US TCSEC, Level C2US TCSEC, Level C2

UK ITSEC, Levels E3/FUK ITSEC, Levels E3/F--C2C2

UK ITSEC, Levels E3/FUK ITSEC, Levels E3/F--B1B1

ISO Common Criteria, EALISO Common Criteria, EAL--44

Russian Criteria, Levels III, IVRussian Criteria, Levels III, IV

US FIPS 140US FIPS 140--1, Level 21, Level 2

TOTALTOTAL

1

1

3

3

4

2

1

15

11

11

33

33

44

22

11

1515

-

1

-

-

-

-

Failed

1

--

11

--

--

--

--

FailedFailed

11

-

-

-

-

-

-

-0

--

--

--

--

--

--

--00

Oracle10g Unbreakable Security

Taratec e ComplianceTM

Built specifically to supports FDA 21 CFR Part 11 ComplianceDesigned for Life Sciences Data & File Management

FeaturesVersioning, Advance Searching, Check-in/Check-OutIntegrated storage of files from any sourceUniversal access through Web browserComplete Audit Trail of File Operations

“With Oracle as the foundation, we were able to develop a solution that can secure a vast array of file-based data with vault like security.” - Bill Gargano,

President and COO Taratec Development Corporation

Taratec e-ComplianceTM

University of California San Diego School of Medicine

The Patient Centered Access to Secure Systems Online (PCASSO)

178,000 Medical RecordsProvides trusted access to a patient’s health information from healthcare providers over the Internet Oracle Label Security & Virtual Private Database

The security is locked to the data and therefore can’t be subverted. No application coding needed to implement security.

Find Patterns and Insights

5. Discover Patterns and InsightsOracle Data Mining

Find relationships and clusters Naïve Bayes, Adaptive Bayes Networks, Attribute Importance, Association Rules, K-Means, O-Cluster, SVM, NMF algorithms

Oracle Discoverer & Oracle OLAPInteractive query & drill-down

StatisticsPerform statistics in Oracle

E.g. summary statistics, hypothesis testing, cross-tab statistics, distribution testing, correlations, linear regression

Oracle TextSearch, index, classify and cluster documents

Table FunctionsImplement complex algorithms within the database

5. Discover Patterns and Insights

Deductive Analysis

Inductive Analysis

Answer complex questions about the

relationships in genomic, clinical and

pharmacological data

Finding relationships for classification,

class discovery and prediction

Life Sciences data

Pharmacological databases

Proteomics Database

Clinical Databases

Functional Genomic

Databases

C A T G0 0 1 0 1BLAST

Implemented using a table function interfaceBLAST search functions can be placed in SQL queriesDifferent functions for match & alignSQL queries can be used to pre-filter database of sequences & post-process the search resultsCombination of SQL queries & BLAST is very powerful & flexible

Sample BLAST QueryOn the output of a BLAST search, find out how many belong to each functional class (SwissProt keyword) -- cell cycle, DNA repair etc.

select function, COUNT(seq_id) f_count from (select t.seq_id, t.score, t.expect, g.function

from SwissProt_DB g, Table(BLASTP_MATCH(‘AEQAERYDDMAAAMKRY’,

cursor (select seq_id, sequencefrom SwissProt_DB),

5)) t /* expect_value */where t.seq_id = g.seq_id)

group by function /* swissprot kw */order by f_count

BLASTP_MATCH

SwissProt_DB

seq_id, score, expect

query_sequence, parameters

seq_id, function

t.seq_id = g.seq_id

GROUP BY

function, f_count

SwissProt_DB

C A T G0 0 1 0 1

For the query sequence “ATCGCGTT”, find the top 3 matches above a similarity threshold from each organism

select seq_id, organism, score, expect from (select t.seq_id, t.score, t.expect, g.organism,

RANK() OVER (PARTITION BY organism ORDER BY score DESC) as o_rank

from SwissProt_DB g, Table(SYS_BLASTP_MATCH (‘ATCGCGTT’,cursor (select seq_id, sequence from SwissProt_DB), 5)) t /* expect_value */

where t.seq_id = g.seq_id) where o_rank <= 3

BLAST “Delighters”Queries performed in the databaseAbility to perform combinatorial queries e.g. sequence similarity AND annotation contains “Lymphoma”

SYS_BLASTP_MATCH

SwissProt_DB

seq_id, score, expect

query_sequence, parameters

Sample BLAST Query

seq_id, organism, score, expect

t.seq_id = g.seq_id

σo_rank <= 3

RANK

seq_id, organism, score, expect

SwissProt_DB

Example BLAST Application

BLAST Quote

"Oracle 10g's new BLAST feature will enable us to easily integrate multiple types of genomic and proteomic data for complicated queries used in the mining of our proprietary protein-protein

interaction and cDNA sequence datasets." - Jake Chen, Principal Bioinformatics Scientist, Myriad Proteomics

Regular Expression SearchesA powerful method of describing both simple & complex patterns for searching & manipulatingA multilingual regular expression support for SQL & PL/SQL string types Follows POSIX style Regexp syntaxSupport standard Regexp operators Includes common extensions such as case-insensitive matching, sub-expression back-references, etc.Compatible with popular Regexp implementations like GNU, Perl, Awk

Regular Expression Searches Quote

"Thanks to Oracle 10g's Regular Expressions (RE) query support, it's no longer necessary to export data from the database, process

it with a RE enabled tool and then import the data back into thedatabase. Now, RE processing can be handled with a single query." - Marcel Davidson, Head of Database Administration,

Myriad Proteomics

Quotes

“Support for regular expressions in SQL and PL/SQL is one of the most exciting features of Oracle Database 10G. Oracle has long supported the ANSI-standard LIKE predicate for rudimentary pattern matching, but regular expressions take pattern matching to a new level. They provide a powerful way to select data that matches a pattern, as well as to manipulate, rearrange, and change that data.”

Oracle Regular Expressions Pocket Reference, O’Reilly Sept. 2003

StatisticsDescriptive Statistics

mode, summary statisticsHypothesis Testing

Student t-test , F-test, Binomial test, Wilcoxon Signed Ranks test, Chi-square, Mann Whitney test, Kolmogorov-Smirnov test, One-way ANOVA

Cross TabsEnhanced with % statistics

Distribution fittingKolmogorov-Smirnov Test, Anderson-Darling Test, Chi-Squared Test, NORMAL_DIST_FIT, UNIFORM_DIST_FIT, WEIBULL_DIST_FIT, EXPONENTIAL_DIST_FIT

CorrelationsSpearmans rho coefficient, Kendals tau-b coefficient

Pareto Analysis80:20 rule, cumulative results table

10g Statistics & SQL AnalyticsRanking functions

rank, dense_rank, cume_dist, percent_rank,ntile

Window Aggregate functions (moving and cumulative)

Avg, sum, min, max, count, variance, stddev, first_value, last_value

LAG/LEAD functionsDirect inter-row reference using offsets

Reporting Aggregate functionsSum, avg, min, max, variance, stddev, count, ratio_to_report

Statistical AggregatesCorrelation, linear regression family, covariance

Linear regressionFitting of an ordinary-least-squares regression line to a set of number pairs. Frequently combined with the COVAR_POP, COVAR_SAMP, and CORR functions.

Descriptive Statisticsaverage, standard deviation, variance, min, max, median(via percentile_count), mode, group-by & roll-upDBMS_STAT_FUNCS: summarizes numerical columns of a table and returns count, min, max, range, mean, stats_mode, variance, standard deviation, median,quantile values, +/- 3 sigma values, top/bottom 5 values

CorrelationsPearson’s correlation coefficients, Spearman's and Kendall's (both nonparametric).

Cross TabsEnhanced with % statistics: chi squared, phi coefficient, Cramer's V, contingency coefficient, Cohen's kappa

Hypothesis TestingStudent t-test , F-test, Binomial test, Wilcoxon Signed Ranks test, Chi-square, Mann Whitney test, Kolmogorov-Smirnov test, One-way ANOVA

Distribution FittingKolmogorov-Smirnov Test, Anderson-Darling Test, Chi-Squared Test, Normal, Uniform, Weibull, Exponential

Pareto Analysis (documented)80:20 rule, cumulative results table

StatisticsEnables analytic pipelines without removing data to statistical packages for simple analyses (e.g. hypothesis testing)

OracleAS DiscovererAd-hoc query & reportingWeb publishingDiscoverer is included with Oracle Application Server Enterprise Edition

IEEE Floating PointSupport for industry standard treatment of numbers & precisionCritical for compute intensive operationsFaster performance

Multi-dimensional Extensions to SQLHighly scalable spreadsheet-like array computation in SQLColumns are classified into Dimensions & Measures Measures can be treated as cells in an n-dimensional arrayModels can be built & stored in the databaseSupports recursive problem solving

Oracle Data MiningPlatform for data mining applications

PL/SQL APIJava APIOracle Data Miner (GUI)

Wide range of algorithmsClassification

Support Vector Machines, Naïve Bayes, Adaptive Bayes Networks,

Attribute ImportanceAssociation RulesClustering

Enhanced K-Means, Orthogonal ClusteringNonnegative Matrix Factorization (feature extraction)BLAST (Sequence similarity search & alignment)

Data Mining Quote

“Using InforSense discovery workflows built upon the world leading Oracle data mining, text mining and R&D Database functionality,

researchers and organizations can now automate large scale and complex knowledge discovery and management activities with performance and reliability.” - Yike Guo, CEO InforSense

Biological/ Clinical

Experiments

Instruments Data Pre-Processing

Interpretation of Results

Bioinformatics Analytical Pipelines

Analytical Algorithms

New PaperNew Drug

New TreatmentNew DB Entries

Life Science Discovery Phases:• Exploratory/Prototype Analysis

• Application Development

• Production SystemFilesFilesFilesFiles

Perl Scripts

Perl Scripts AlgorithmsAlgorithms

Files

DB Files Files

AlgorithmsPerl

ScriptsFiles

DBFiles

Oracle Life Sciences Platform

C A T G0 0 1 0 1

Oracle’s Contribution to Life SciencesFind me any compound that looks like my current structure, and that has been tested on any assay in my company where the IC50>200nM, where I know that I have a unique patent position, and hasn't been published in any journal?

Find me any compound that looks like my current structure, and that has been tested on any assay in my company where the IC50>200nM, where I know that I have a unique patent position, and hasn't been published in any journal?

select c.id, p.structure, from compound c, protein p, assay awhere a.compound_id = c.idand a.protein_id = p.idand a.company = “BIO_SYS” and a.IC50 > 200nM and similar_to(p.id, “protein kinase”)and not_published(p.id, “Medline”)and extract_value(value(p.id), ‘Dgene/Protein/Id’) = p.id

select c.id, p.structure, from compound c, protein p, assay awhere a.compound_id = c.idand a.protein_id = p.idand a.company = “BIO_SYS” and a.IC50 > 200nM and similar_to(p.id, “protein kinase”)and not_published(p.id, “Medline”)and extract_value(value(p.id), ‘Dgene/Protein/Id’) = p.id

Oracle9iOracle9Oracle9ii

RelationalRelational

MessageMessage

XMLXML

TextText

ImageImage

“At the end of such testimonials, it was very difficult to see whether Oracle has a serious rival in the realm of databases for high-throughput drug discovery. With a well-known 70 percent market share, Oracle is starting to penetrate smaller labs in academia and nonprofit research institutes.”- Mark D. Uehling, Bio-IT World (online) 09/12/03

“All are among the features that make Database 10g much more than a large-scale data repository. Old 1960s labels such as "electronic brain" come to mind—Database 10g doesn't just know stuff, it also thinks about it.”- Peter Coffee, eWeek (online) 05/31/04

IDC Analysts

“Even IBM's own partners say that DB2 and DiscoveryLink have failed to gain

much ground in the life sciences despite IBM's giveaways. According to Hall,

Oracle, the "de facto standard," still holds a commanding 75 percent to 80 percent

market share in this vertical.”Mark Hall, Director of Life Sciences, IDC,

quoted in InfoWeek 12/12/2002

Oracle 10g Enables you to:Access distributed dataIntegrate a variety of data typesManage vast quantities of dataCollaborate securelyFind patterns and insights

Oracle 10g is an ideal platform for life sciences

Oracle Life Sciences Platform Summary

Oracle Consulting Services

Data Mining ServicesRichard Solari 508-477-5765630-561-9950Richard.solari@oracle.com

Patrick Hoffman 781-744-0783617-755-6740Pat.hoffman@oracle.com

Life Sciences ServicesDev Nayak781-744-0878dev.nayak@oracle.com

Life Sciences Consulting experience

JSP Struts/Blast Application Gene expression analysisSequence Analysis (blast exon/intron prediction)Clinical/Medical data analysisQSAR/Cheminformatics

Isis,Molconz, Predictive ToxAnimal StudiesProtein analysis (arrays, Mass spec)Ontology's and Text Mining

Life SciencesDM Workshop

A one day onsite technical session educating organizations on how to leverage one of their most valuable assets to provide insight in the operations of their business, the behavioral patterns of their customers and hidden relationships found deep within corporate data that can have direct impact to the bottom line.

Life SciencesDM Blueprint

A documented technical roadmap providing the organization with the strategy to integrate and deploy Life Sciences technology. This includes recommendations based on feedback from the Life Sciences workshop focusing on source data preparation, mining methodologies and supporting architecture.

Life SciencesDM Insight

A five day onsite engagement focused on providing a detailed analysis of the business problem, data preparation, model build and analysis and knowledge deployment extending the analysis of the Life Sciences workshop culminating with a technical roadmap with a strategy to integrate and deploy Life Sciences technology.

Life SciencesDMQuickstart

A thirty day engagement focused on taking a business problem and transforming into a Life Sciences solution. This includes transforming the business problem, preparing e data, creation of the mining model and knowledge deployment. Upon completion, results will be delivered mapped to the initial business problem.

Life SciencesDM Services

A series of custom services focused on delivering Life Sciences methodologies and solutions to provide insight in the operations of their business, the behavioral patterns of their customers and hidden relationships found deep within corporate data that can have direct impact to the bottom line.

Oracle Global Customer Program

S. Anand, Oracle 9:45 Thursday, 2nd Floor

Oracle Global Customer ProgramS. Anand, Oracle 9:45 Thursday, 2nd Floor

Define the Need & Budget

Define the Need & Budget

Evaluate Solution &

Target Benefits

Evaluate Solution &

Target Benefits

Select & ProcureSelect & Procure

Implement & Track

Benefits

Implement & Track

BenefitsOperate &

LearnOperate &

LearnMeasure Results

Measure Results

Build on Relationship

Build on Relationship

Buy Implement Run

Unify the “Voice of the Customer” – and Oracle’s Response

Drive Customer Business ValueBusiness Consulting

Customer InsightsCustomer Forums

Customer Communications

Customer Quality Management Evaluate Customer Success & Resolve Issues

Build ReferencesBenefits Measurement & References

Business Case

Analysis

Performance Advisory Services

Strategic Solution Planning

Executive Alignment

Surveys & Scorecards User GroupsResearch &

BenchmarksExecutive Forums

Customer Response

Field Referencing

Marketing Referencing

Benefits Realization &

ROI

Success Stories

Outreach Issue Resolution

Executive Sponsorship

Program

Q U E S T I O N SQ U E S T I O N SA N S W E R SA N S W E R S