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

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ClientClient

Internet / 

Intranet

Internet / 

Intranet

ServerServer

JDBC driver

Custom servlet

or JSP scripts

Custom servlet

or JSP scripts

Query 

structure

SQL 

Hits

Web browserWeb browser

Query Structures +

data

Relational database

(Oracle, MySQL, MS SQL  Server, DB2,  etc.)

JChem 

class library

JChem 

class library

JChem 

class library

JChem 

class library

JChem 

class library

JChem 

class library

JChem Base application architectures

Rich client application

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ClientClient

Internet / 

Intranet

Internet / 

Intranet

ServerServerJDBC driver

Rich client 

application

Rich client 

applicationQuery 

structure

SQL

Hits

Relational database

(Oracle, MySQL, MS SQL Server, DB2, 

etc.)

JChem 

class library

JChem 

class library

JChem 

class library

JChem 

class library

JChem 

class library

JChem 

class libraryRich client 

application

Rich client 

application

JChem Cartridge architecture

The JChem computation engine can be on a dedicated server to balance workload.

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ClientClient

Internet / 

Intranet

Internet / 

Intranet

ServerServerOracle JChem Cartridge• PL/SQL• Java stored procedures

JChem Cartridge• PL/SQL• Java stored procedures

JChem Server

JChem Cartridge AdapterJChem Cartridge Adapter

JChem BaseJChem Base

Search Update

JChem core

CacheCache

CacheCache

RMI

JDBC

Client application / Application serverClient application / Application server

SQL 

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.ppt8

Structure searching: optionsSome 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

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JChem Base 5.0, Athlon X2 2.6GHz, 4GB RAM; Oracle 9.2.0.8.0

Number of compounds

Elapsed timeDuplicates not

checkedDuplicates 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

12 0.219 s

936 0.375 s

4,608 0.734 s

65,208 5.594 s

Compound registration:

Substructure search in a table of 3 million

compounds:

Table typesControl allowed chemical structures and available

operations

• Molecule

• Reaction

• Combinatorial Markush

• Query

• Any structure11

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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