Data cartridge

Data storage and querying are the most fundamental requirements of all informatics systems. Thanks to the Oracle Extensibility Framework (a.k.a. Oracle Data Cartridge Technology), chemical structure data can be stored and queried using direct SQL and special query operators, such as substructure search, flexmatch search, similarity search, and formula search. Also, some indexing techniques make these otherwise slow searches fast. Detailed discussions about these databases and cartridges are beyond the scope of this book. Please refer to the vendor s website and product documentation for more information. 

Molecule database and data cartridge products Similar to the above two, commercial software is available and there is no need to reinvent the wheel. 

In the case of the chemistry database, the situation is more complex. Compound data cannot be queried or updated using standard SQL. The read and write operations are encapsulated in vendor-specific Oracle data cartridges. Therefore, the Data Persistence Layer has another responsibility— hide vendor specifics with a standard interface so that the Business Layer does not care about vendor variations. 

Appendix 1 Drug, MOLECULAR REGISTRATION Systems, AND CHEMISTRY DATA Cartridges... 

Accord for Oracle—a chemical data cartridge (see Glossary)... 

This statement translates to "Select everything from the table named RXN, where the SMILES field contains the substructure string for benzoic acid as a product". The = clause is an artifact of the data cartridge implementation it does not necessarily mean that only a single occurrence of the benzoic acid substructure should be found. 

Data Cartridge. A popular term for user-customizable search "operators" that can be added to the SQL language of a relational database system. An example in chemical information is the addition of a substructure search (SSS) operator to integrate this type of search directly into a relational database search. One advantage of this approach is that the search "strategy" that the relational search program applies can take the complexity of the custom operator into account (the "cost") when performing the various search operations. 

Data Cartridge is a bundled set of tools that extends database clients and servers with new capabilities. Typically, a single data cartridge deals with a particular information domain. 

Much of this book discusses ways in which the RDBMS can be used and even extended to handle chemical structures correctly, quickly, and conveniently. Extensions of the capabilities of PostgreSQL are simply called extensions. Oracle uses the term data cartridge. There are chemical extensions or cartridges available for PostgreSQL, Oracle, and MySQL. 

O Shea, M.D. 2008. Chemoinformatics chemistry data cartridges, http // www.strychnine.co.uk/oracledatacartridges.html (accessed April 18, 2008). 

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