JChem Cartridge

making Oracle chemically aware

JChem Cartridge adds chemical intelligence to the Oracle platform using Oracle’s native SQL language. JChem 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 ( Java )

JChem Cartidge functionality

SQL Chemistry

JChem 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 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 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 Cartridge framework. Furthermore, ChemAxon’s Markush technology, including all the structure analysis features, is also available as an add-on for JChem Cartridge.

External services via JChem 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 Cartridge through the jc_evaluate operator, ensuring easy access to external calculations and web service based operations on structures.

External services and JChem Cartridge

JChem Cartridge Architecture Overview

High performance

The chemical knowledge for JChem 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 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 Cartridge in contact with the Oracle platform.

Platform independence and compatibility

JChem Cartridge works with Oracle versions 10.2 or above. It is platform independent and can be used on various operating systems including Windows, Linux, Solaris and HP-UX. JChem 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 Cartridge

JChem Cartridge supports Oracle

Articles in the library

ChemAxon US User Group Meeting, September 25-26, Cambridge Massachusetts

Dec 18, 2014 - Report
Conclusion Attendees and Social Events Overview of ChemAxon by Alex Drijver The ChemAxon Product Profile Biomolecule Toolkit Plexus Suite …

Searching Project Team Documents with D2DB

Sep 26, 2014 - Presentation
At Genentech as in many other biotechnology and pharmaceutical companies, therapeutic project teams generate many documents

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

Sep 26, 2014 - Presentation
In a collaboration with ChemAxon we have developed a web-based interface for searching, browsing and managing chemical information.

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