JChem PostgreSQL Cartridge

Chemical intelligence in PostgreSQL – powerful and simple DB solution
JChem PostgreSQL Cartridge is an easy-to-deploy chemical database management and search engine. It is built on PostgreSQL relational database using native SQL language. JChem PostgreSQL Cartridge is a cost effective solution for handling chemical data-sets. Its scalability allows to manage data on individual, group or even enterprise level.
Product Type:application
Interfaces:CLIAPI ( SQL )

ChemAxon’s extension for the PostgreSQL database

ChemAxon’s JChem PostgreSQL Cartridge seamlessly integrates chemical search intelligence into PostgreSQL databases. It provides fast and scalable solution to help scientists to store, index and search chemical structures. The first release targets handling small and medium sized chemical data sets.

Rich functionality

JChem’s molecule handling and search functionality is provided by extensions created in PostgreSQL database and by running the JChem-psql service. It supports multi-user parallel execution with arbitrary number of indexed tables, and also any number of columns in the table. A custom column type, called Molecule, serves for storing chemical structures. This Molecule type can be customized according to business rules. The customization includes molecule standardization and tautomer handling. The type can contain any of the most commonly used textual chemical representations (SMILES, MDL molfile both v2000 and v3000, MDL SDF, RXN, RDF, MRV, IUPAC name, InChI).

Chemical indexing and file import

Beside of the Molecule type JChem PostgreSQL Cartridge also provides a special index type, chemindex, for speeding-up searches for molecules. The index is automatically maintained during all data operations. Chemical search on Molecule column seamlessly integrates into SQL allowing complex data mining. An import tool is offered to import SD files; line notations like SMILES or InChI files can be imported using PostgreSQL built-in functions. This enables to import a whole table with one SQL sentence.

Supported search types

  • substructure
  • full fragment
  • duplicate
  • superstructure
  • similarity search using chemical hashed fingerprints with Tanimoto metrics
Tetrahedral stereochemical features and stereochemistry around double bond are taken into account during searches. Tautomer handling is supported in all search types except for similarity search. Additionally, molecule functions are provided to create a Molecule from a string representation and vice-versa, converting a molecule between different textual representations. With the use of molecule transformation function, it is also possible to flexibly incorporate Standardizer rules in the data flow (e.g. in order to improve visualization).

Why is JChem PostgreSQL Cartridge great?

Reliable database

PostgreSQL has built good reputation for its exceptional reliability and for its wide availability in the past decade. Its key benefit is the low total cost of ownership: it is free and its maintenance and operation is much easier (and thus cheaper) than most other industry standard solutions.

Scalable chemical engine

JChem PostgreSQL Cartridge is suitable for diverse applications ranging from single user single host setups where all database management is carried out by the sole user itself, to enterprise level solutions, where it serves as the back-end of the data-warehouse of a global company accessed from multiple sites and run on a cluster of computers. Its scalability makes it particularly suitable for data back-end in web-servers where the cost of serving large number of concurrent users is the same as a single user cost.

Group level solution with low costs

In pharmaceutical research we recommend this sleek solution for small research groups that for some reason want to run their projects independently from the company IT infrastructure and manage their chemical databases themselves. Its straightforward and fast setup and maintenance-free operation makes it a viable option even for short-term projects where the infrastructure overhead must be kept low.

Architecture of JChem PostgreSQL Cartridge

System components

The system consists of three main components:
  1. the PostgreSQL database with the Cartridge
  2. the JChem-psql server providing chemical functionality
  3. a Client application using the Cartridge (not provided by ChemAxon)
The PostgreSQL database with the Cartridge and the JChem-psql server is present on the same physical or virtual machine, while the client can connect to the database through the net. The cartridge functionality is provided as an extension of the PostgreSQL database, which means that the chemical functionality is available for all users seamlessly.
Architecture Overview of JChem PostgreSQL Cartridge

Software requirements

JChem PostgreSQL Cartridge runs on Linux operating system (CentOS or RedHat), PostgreSQL version 9.4, and requires Java 8 run time environment.

Resources

Release Information
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