chemical database management with jchem base and …€¦ · chemical database management with...

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Chemical Database Management with JChem Base and Cartridge

Szabolcs Csepregi

ChemAxon European UGM Visegrad 2008

Szabolcs Csepregi

Outline

ChemAxon Chemical database productsArchitectureFeaturesFeaturesExample interfaces: JSP, ASP examplesIntegration with other CXN toolsThe coming Registration System APIWhat is coming in JCB/Cartridge 5.1

ChemAxon European UGM Visegrad 2008 2

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ChemAxon chemical database products

JChem BaseA library for adding chemical structures into relational database systems. Available in Java, JSP and .NETOpen-source web application example is available.

JChem Cartridge for OracleExtends Oracle SQL with chemical operators and index.SQL interface for ChemAxon functionality


Instant JChemAn all-in-one desktop chemical database application.

JChem Base application architectures

Web application

Cliente

Internet / Intranet

ServerCustom servlet or JSP scripts

Query structure

SQL

Hits

Web browser

Query Structures +data

JChem class library

JChem class library

JChem class library


JDBC driver

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

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JChem Base application architectures

Rich client application

Client

Internet / Intranet

ServerJDBC driver


Query structure

SQL

Hits

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

JChem class library

JChem class library

JChem class library



( , y , , , )

JChem Cartridge architecture

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

Client

Internet / Intranet

ServerOracle JChem Cartridge• PL/SQL• Java stored procedures

JChem ServerJChem Cartridge Adapter

JCh B

RMI

Client application / Application server

SQL


Java stored procedures JChem Base

Search Update

JChem core

Cache

CacheJDBC

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Compatibility and integration

Supported chemical file formats:SMILESMDL MOL/RXN/SDF/RDF (v2000 and v3000)CML, MRVetc.

Database engines:Oracle, MySQL, MS SQL Server, MS Access, PostgreSQL, IBM DB2, Derby, etc.

All operating systems through:Java API (JChem Base)


Java API (JChem Base).NET API (JChem Base + JNBridge) – for WindowsSQL (Cartridge)

Structure searching: features

Substructure, Similarity, Exact, Exact fragment, etc. Search typesWide range of query atomsWide range of query atomsQuery propertiesR-group queriesFull SMARTS supportCoordination compoundsLink nodesPseudo atoms, Lone pairs


Pseudo atoms, Lone pairsRelative stereoReaction search featuresHit coloring ...

www.chemaxon.com/conf/Structural_Search.ppt

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Structure searching: options

Some of the structure search options:Chemical Terms filter constraintTautomer searchStereo on/offIgnore charge/isotope/radical/valence/mixture bracketsVague bond matching modes: „or aromatic”; ignore bond typesInverse hit list Maximum search time / number of hits


Maximum search time / number of hits SQL SELECT statement for pre-filteringOrdering of resultsetc.

Structure search: performance

Number of compounds

Elapsed timeDuplicates not

checkedDuplicates checked

10 000 22 35

Compound registration:

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

Substructure search in a table of 3 million

compounds:


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

936 0.375 s

4,608 0.734 s

65,208 5.594 s

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Table types

Controls allowed chemical structures and available operations

Molecule

Reaction

Combinatorial Markush


Query

Any structure

Example interfaces: JSP, ASP

Example web applications: open source JSP, ASP examples

Marvin applets are used for query drawing and structurevisualization

D


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 searchTautomer duplicate filter import


p pCustom tautomer transforms or canonical tautomer using Standardizer

Query drawing and structure visualization (Marvin)Provides the most consistent interface and back-end.

Integration

Additional Cartridge functionality:JChem index (for non-JChem tables)Communication with Oracle optimizerReaction based enumeration (Reactor)Format conversions – image generation alsoMarkush 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:

C t i bl b i l iCustomizable business logicMultilevel 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)


g ( y )Pre-registration through a transitory areaBasic, customizable implementation examples

Separate examples for chemists and registrars

Web and Instant JChem interfaces will follow later

What is coming in JChem 5.1

Installation/upgrade improvements (include JDBC drivers, Cartridge configuration)

Structure searching:Position variationin Markush structures and queries

Diastereomer search option(S t t h d l t t b t


(Same tetrahedral stereo centers, but possibly different configurations.)

Check sp-hybridizationsearch option (substructure)

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What is coming in JChem 5.1

Web Services interface for JChem Base

Compound registration system APICompound registration system API

Chemical Terms calculated columns for JChem index (Cartridge – from 5.0.1)

jc_insert returns existing cd_id for duplicate


structures (Cartridge – from 5.0.3)

Under development

Further improvements of Markush handling(towards patents)

Flexible 3D pharmacophore searching

Integration of further ChemAxon functionality in the Cartridge:

R-group decompositionCustom descriptors & similarity


Custom descriptors & similarity

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


Registration system, JChem for Excel and patent Markush handling are coming.

Thank you for your attention!Tha k you for your atte tio !

For more information please visit www.chemaxon.com

ChemAxon European UGM Visegrad 2008

chemical database management with jchem base and …€¦ · chemical database management with...

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