JChem Oracle Cartridge

making Oracle chemically aware

JChem Oracle Cartridge adds chemical intelligence to the Oracle platform using Oracle’s native SQL language. JChem Oracle Cartridge allows users to access the rich chemical database management and search features of JChem Base in a flexible and efficient manner from any SQL-capable platform.

Product Type:application
Interfaces:CLIAPI ( SQL )

JChem Oracle Cartridge functionality

SQL Chemistry

JChem Oracle Cartridge’s major functionality is to allow the addition, manipulation and searching of chemical data using Oracle’s native SQL language. Most industry standard chemical formats are natively handled using JChem indices. Automatically calculated physico-chemical properties and user-defined fingerprints allow users to create and search custom chemical databases. JChem Oracle Cartridge uses creative solutions to broaden the applicability of JChem’s core functions while still preserving the key benefits of the Java platform. Chemical structures can be stored and searched by superstructure, substructure and full structure. Custom similarity searches using a wide variety of molecular descriptors can also be carried out.

Rich functionality

In addition to chemical database management and search functions, JChem Oracle Cartridge provides chemical format conversions including 2D and 3D image generations. It also supports structural transformations using our Standardizer engine as well as virtual library enumeration by Reactor. Structure based predictions and property calculations via ChemAxon’s Chemical Terms language and Calculator Plugins can also be carried out in the JChem Oracle Cartridge framework. Furthermore, ChemAxon’s Markush technology, including all the structure analysis features, is also available as an add-on for JChem Oracle Cartridge.

External services via JChem Oracle Cartridge

Besides the built-in functionality of the JChem platform, Marvin Services provide the user seamless integration of third-party structure manipulations into the Cartridge framework. Marvin Services are available in JChem Oracle Cartridge through the jc_evaluate operator, ensuring easy access to external calculations and web service based operations on structures.

External services and JChem Oracle Cartridge

JChem Oracle Cartridge Architecture Overview

High performance

The chemical knowledge for JChem Oracle Cartridge comes from ChemAxon’s core Java libraries. Oracle offers the possibility to use existing Java libraries by calling them from Java Stored Procedures that run in a special Java runtime environment tightly integrated with the Oracle RDBMS. To compensate for the performance disadvantage with Oracle Java Stored Procedures JChem Oracle Cartridge performs the computation intensive functions in an external (with respect to Oracle) Java runtime environment capable of runtime byte-code compilation, the JChem Server.

JChem search technology on Oracle

At an abstract level, the JChem Server comprises two main components. JChem Base provides the core chemical functions (e.g. atom-by-atom graph search algorithms (JChem Core)) and is responsible for advanced database searches and updates (Search and Update engines which add an RDBMS-aware layer to the core JChem functions). The JChem Cartridge Adapter component translates JChem Base’s external interfaces to the needs of the JChem Oracle Cartridge in contact with the Oracle platform.

Platform independence and compatibility

JChem Oracle Cartridge works with Oracle versions 11.0 or above. It is platform independent and can be used on various operating systems including Windows, Linux, Solaris and HP-UX. JChem Oracle Cartridge works seamlessly with the most commonly used chemical representations (SMILES, MDL, molfile (v2000 and v3000), MDL SDF, RXN, RDF, MRV, IUPAC name, InChI, Markush DARC, CDX), providing great flexibility on both import and export.

Achitecture Overview of JChem Oracle Cartridge

JChem Cartridge supports Oracle

Articles in the library

What else can you do with the Markush cartridge? Tracking chemical series fo…

May 19, 2015 - Presentation
We have developed a new application that allows scientist to store and search generic scaffold structures. This was possible thanks to the Markush extension for the ChemAxon JChem Cartrid…

Consistent Stereochemical search at GlaxoSmithKline

May 19, 2015 - Presentation
GlaxoSmithKline (GSK) has recently upgraded its ChemAxon small molecule registration system to allow end-users the ability to mark-up and register molecules with complex atom based stereo…

Building a Symbiotic Informatics Platform to Support Drug Discovery

Sep 30, 2015 - Presentation
Getting heterogeneous tools to “play nicely” in the Informatics sandbox At GBT we have built an Informatics platform leveraging and integrating common, industry standard tools to pro…

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