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.
ChemAxon’s extension for the PostgreSQL databaseChemAxon’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 functionalityJChem’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 importBeside 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
- full fragment
- similarity search using chemical hashed fingerprints with Tanimoto metrics
Why is JChem PostgreSQL Cartridge great?
Reliable databasePostgreSQL 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 engineJChem 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 costsIn 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 componentsThe system consists of three main components:
- the PostgreSQL database with the Cartridge
- the JChem-psql server providing chemical functionality
- a Client application using the Cartridge (not provided by ChemAxon)