MySQL relational databases

For those who want to query PGDB data through a relational database system, the attribute-value files exported by Pathway Tools can be loaded into SRFs BioWarehouse system (14). BioWarehouse is an Oracle or MySQL-based system for integration of multiple public bioinformatics databases. PGDB data can be queried through BioWarehouse alone or in combination with other bioinformatics databases such as UniProt, Genbank, NCBI Taxonomy, ENZYME, and KEGG. 

The current project contains more than 20,000 terms for biological processes, cellular components, and molecular functions. The ontologies can be downloaded in different formats including extensible Markup Language (XML) and the open-source relational database scheme MySQL. 

Furthermore, SPARQL queries formulated for the ontology have to be translated into the query language associated with the relational database. An approach applying this architecture is for instance the Apache Jena SDB. It allows the data of the model to be stored in a relational database, like Oracle, PostgreSQL, MySQL, or HSQLDB. A Jena SDB storage can be accessed and managed with the Jena API and can be queried using SPARQL. Sesame also facilitates relational... 

An introduction to SQL is provided in Chapter 3, but with an emphasis on examples relevant to chemical information rather than business information, which is often used in other books. Chapter 4 discusses some of the RDBMS that are available, namely Oracle, MySQL, and PostgreSQL. All of them use SQL to insert, delete, update, and select data. Chapter 5 shows ways in which client programs, including Web-based applications, are used to connect to the database server. Chapter 6 examines ways in which RDBMS are typically used to handle numerical and textual chemical information using relational tables. An example of using data files from the PubChem project is included. 

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