Transcript Life Sciences Integrated Demo

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
BLAST Search on PKC-beta
Run BLAST in batch
BLAST Search on PKC-beta
BLAST Search on PKC-beta
BLAST Search on PKC-beta
Search Protein Secondary
Structures Similar to PKC-beta
 E : Beta Sheet
 _ : Loop
 H : Alpha Helix
 < _ 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 MySQL
Migration of OMIM from MySQL
Pathway Modeling
Zoom In
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
BioOracle Discovery
Found Protein Kinase C Beta
Inhibitor is in Lilly’s pipeline
for diabetes
Find a Cure for Lymphoma Cancer








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.
PubMed
MySQL
GenBank
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.
SwissProt
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
interMedia
Collaboration Suite
Collaborate securely
iFS/Files
Auditing
Store & manage images Create audit trail to facilitate
FDA compliance
Workflow
Extensibility
Framework
O
Cl
(Data cartridges), manage
complex scientific data
LOBs
Manage unstructured data
Index & query text,
e.g. literature
searches
Search external sites
& repositories
MySQL Toolkit
Easily move MySQL
data into Oracle
Share documents
Data Mining
Automate laboratory
Discover patterns & insights
& business processes
Cl
Text
UltraSearch
BLAST
Sequence similarity search
Network Model
Pathways Modeling
Statistics
Transportable
Tablespaces
Rapidly exchange tables
Oracle Streams
Perform basic statistics
subscription for
Table FunctionsRule-based
information sharing
Implement complex algorithms
OLAP & Discoverer
Interactive query & drill-down
BioOracle Conclusions
Access
heterogeneous
data
Integrate
a variety
of data
types
Manage
vast
quantities of
data
Find Patterns
and
insights
Collaborate
securely
Access
heterogeneous
Data
Acknowledgement: the Oracle Team










Charlie Berger
Joyce Peng
Pablo Tamayo
Susie Stephens
Melliyal Annamalai
William.Beauregard
Mark Drake
Stefan Buchta
Omar Alonso
Scott Nichols










Jack Wang
Robert Haberstroh
Brajesh Goyal
Glen Williamson
Ari Mozes
Timothy Chorma
Vishal Rao
Vishu Krishnamurthy
George Tang
Neil Evans
Q U E S T I O N S
A N S W E R S