Chemical Database Management
with JChem Base and Cartridge


Szabolcs Csepregi



                     Solutions for Chemi...
Outline
• ChemAxon chemical database products
• Architecture
• Features
• Example interfaces: JSP, ASP examples
• Integrat...
Chemical database products

• JChem Base
   – A library for adding chemical structures into relational
     database syste...
JChem Base application architectures

Web application
                                                                  Cl...
JChem Base application architectures

Rich client application
             Rich client             Query                  ...
JChem Cartridge architecture
The JChem computation engine can be on a
  dedicated server to balance workload.
            ...
Compatibility and integration
Supported chemical file formats:
  •    SMILES
  •    MDL MOL/RXN/SDF/RDF (v2000 and v3000)
...
Structure searching: features
•   Substructure, Similarity,
    Exact, Exact fragment, etc.
    Search types
•   Wide rang...
Structure searching: options
Some of the structure search options:
  –   Chemical Terms filter constraint
  –   Tautomer s...
Structure search: performance
                                                              Elapsed time
          Compoun...
Table types
Control allowed chemical structures and available
                                        operations
• Molecul...
Example interfaces: JSP, ASP
• Example web applications: open source JSP, ASP
  examples
   – Marvin applets
     are used...
Integration
• Integration with other ChemAxon tools:
   – Custom, uniform chemical representation. (Standardizer –
     se...
Integration
Additional Cartridge functionality
  –   JChem index (for non-JChem tables)
  –   Communication with Oracle op...
Registration system
• New component for registration system will be introduced from
  summer, 2008 (API only)
• Main featu...
What is coming in JChem 5.1
Structure searching
  – Position variation
    in Markush structures
    and queries

  – Dias...
What is coming in JChem 5.1.X
(In a few months)
• Web Services interface for JChem Base
• Compound registration system API...
Under development
• Further improvements of Markush handling
  (towards patents)
• Flexible 3D pharmacophore searching
• I...
Summary
• JChem Base, JChem Cartridge and Instant JChem
  offer comprehensive and efficient chemical
  database solutions....
Thank you for your attention!

For more information please visit
      www.chemaxon.com



                               ...
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Chemical Database Management J Chem Base And J Chem Cartridge: US UGM 2008

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JChem Base is a chemical database management toolkit to handle chemical structures and associated data (user-defined or predicted), stored in relational databases. JChem Cartridge provides similar functionality highly integrated into Oracle as well as an Oracle interface to other ChemAxon products.
For latest developments see: http://www.chemaxon.com/product/jc_base.html

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Chemical Database Management J Chem Base And J Chem Cartridge: US UGM 2008

  1. 1. Chemical Database Management with JChem Base and Cartridge Szabolcs Csepregi Solutions for Cheminformatics
  2. 2. 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 2
  3. 3. 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. 3
  4. 4. 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.) 4
  5. 5. 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.) 5
  6. 6. 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 6
  7. 7. 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) 7
  8. 8. 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 8
  9. 9. 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
  10. 10. 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 10
  11. 11. Table types Control allowed chemical structures and available operations • Molecule • Reaction • Combinatorial Markush • Query • Any structure 11
  12. 12. Example interfaces: JSP, ASP • Example web applications: open source JSP, ASP examples – Marvin applets are used for query drawing and structure visualization • Demo 12
  13. 13. 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. 13
  14. 14. 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) 14
  15. 15. 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 15
  16. 16. 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 16
  17. 17. What is coming in JChem 5.1.X (In a few months) • Web Services interface for JChem Base • Compound registration system API 17
  18. 18. 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 18
  19. 19. 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. 19
  20. 20. Thank you for your attention! For more information please visit www.chemaxon.com 20

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