Chemical Database Management
with JChem Base and Cartridge
Szabolcs Csepregi
Solutions for Cheminformatics

Outline
• ChemAxon chemical database products
• Architecture
• Features
• Example interfaces: JSP, ASP examples
• Integration with other CXN tools
• The coming Registration System API
• What is coming in JCB/Cartridge 5.1
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Chemical database products
• JChem Base
– A library for adding chemical structures into relational
database systems. Available in Java, JSP and .NET
– Open-source web application example is available.
• JChem Cartridge for Oracle
– Extends Oracle SQL with chemical operators and index.
– SQL interface for ChemAxon functionality
• Instant JChem
– An all-in-one desktop chemical database application.
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JChem Base application architectures
Web application
Client
Web browser
Query Structures + Internet /
data Intranet
Query Server
Custom servlet structure
JChem class
JChem class
or JSP scripts Hits JChem class
library
library
library
SQL
JDBC driver
Relational database
(Oracle, MySQL, MS SQL Server, DB2, etc.)
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JChem Base application architectures
Rich client application
Rich client Query Client
structure JChem class
Rich client
application JChem class
application JChem class
library
Hits library
library
Internet /
SQL Intranet
JDBC driver Server
Relational database
(Oracle, MySQL, MS SQL Server, DB2, etc.)
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JChem Cartridge architecture
The JChem computation engine can be on a
dedicated server to balance workload.
Client
Client application / Application server
Internet /
SQL Intranet
Oracle JChem Cartridge JChem Server Server
• PL/SQL RMI JChem Cartridge Adapter
• Java stored procedures JChem Base
Search Update
Cache
JDBC Cache
JChem core
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Compatibility and integration
Supported chemical file formats:
• SMILES
• MDL MOL/RXN/SDF/RDF (v2000 and v3000)
• CML, MRV
• etc.
Database engines:
• Oracle, MySQL, MS SQL Server, MS Access,
PostgreSQL, IBM DB2, Derby, etc.
All operating systems through:
• Java API (JChem Base)
• .NET API (JChem Base + JNBridge) – for Windows
• SQL (Cartridge)
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Structure searching: features
• Substructure, Similarity,
Exact, Exact fragment, etc.
Search types
• Wide range of query atoms
• Query properties
• R-group queries
• Full SMARTS support
• Coordination compounds
• Link nodes
• Pseudo atoms, Lone pairs
• Relative stereo
• Reaction search features
• Hit coloring ...
www.chemaxon.com/conf/Structural_Search.ppt
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Structure searching: options
Some of the structure search options:
– Chemical Terms filter constraint
– Tautomer search
– Stereo on/off
– Ignore charge/isotope/radical/valence/mixture
brackets
– Vague bond matching modes: „or aromatic”;
ignore bond types
– Inverse hit list
– Maximum search time / number of hits
– SQL SELECT statement for pre-filtering
– Ordering of results
– etc. 9

Structure search: performance
Elapsed time
Compound Number of
Duplicates not Duplicates
compounds
registration: checked checked
10,000 22 s 35 s
100,000 2 min 33 s 4 min 16 s
200,000 4 min 53 s 8 min 19 s
Query Number of hits Search time
Substructure search in a
table of 3 million 12 0.219 s
compounds:
936 0.375 s
4,608 0.734 s
JChem Base 5.0, Athlon X2 2.6GHz,
4GB RAM; Oracle 9.2.0.8.0 65,208 5.594 s
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Table types
Control allowed chemical structures and available
operations
• Molecule
• Reaction
• Combinatorial Markush
• Query
• Any structure
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Example interfaces: JSP, ASP
• Example web applications: open source JSP, ASP
examples
– Marvin applets
are used for
query drawing
and structure
visualization
• Demo
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Integration
• Integration with other ChemAxon tools:
– Custom, uniform chemical representation. (Standardizer –
see separate presentation today.)
– Automatically calculated properties by Chemical Terms
Calculated columns (Calculator plugins)
– Additional similarity calculations (Screen - JChem Base
only)
– Tautomer handling:
• Tautomer search
• Tautomer duplicate filter table/index option
• Custom tautomer transforms or canonical tautomer using
Standardizer
– Query drawing and structure visualization (Marvin)
Provides the most consistent interface and back-end.
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Integration
Additional Cartridge functionality
– JChem index (for non-JChem tables)
– Communication with Oracle optimizer
– Reaction based enumeration (Reactor)
– Format conversions – image generation also
– Markush enumeration (Calculator plugins)
– Property predictions through Chemical Terms
(Calculator plugins)
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Registration system
• New component for registration system will be introduced from
summer, 2008 (API only)
• Main features:
– Customizable business logic
• Multilevel duplication control
• Customizable corporate registration ID
• Handling of salts, batches, lots, samples, and mixtures
– Identification, split and registration of salt and solvent structures
Storage of input structures in original format
– Mock registration (dry run)
– Pre-registration through a transitory area
– Basic, customizable implementation examples
• Separate examples for chemists and registrars
• Web and Instant JChem interfaces will follow later
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What is coming in JChem 5.1
Structure searching
– Position variation
in Markush structures
and queries
– Diastereomer search option
(Same tetrahedral stereo centers, but
possibly different configurations.)
– Check sp-hybridization
search option (substructure)
Cartridge installer GUI
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What is coming in JChem 5.1.X
(In a few months)
• Web Services interface for JChem Base
• Compound registration system API
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Under development
• Further improvements of Markush handling
(towards patents)
• Flexible 3D pharmacophore searching
• Integration of further ChemAxon functionality in the
Cartridge:
– R-group decomposition
– Custom descriptors & similarity measures
• Include JDBC drivers in installer
• JChem for Excel
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Summary
• JChem Base, JChem Cartridge and Instant JChem
offer comprehensive and efficient chemical
database solutions.
• They are integrated with many other ChemAxon
products and are accessible from various interfaces.
• Registration system, JChem for Excel and patent
Markush handling are coming.
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Thank you for your attention!
For more information please visit
www.chemaxon.com
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