How do I connect a SQL database to BioCASe?

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Franck's picture
Joined: 2011-04-01
How do I connect a SQL database to BioCASe?

BioCASe is intended to work only with SQL databases that it connects by the means of a low-level softare called ‘driver’(that must be installed on the server as a prerequisite).


Configuration page of the BioCASe (version 2.6.0) provider for connecting to an SQL databases by generating the appropriate connection string. The drop-down list presents the recognized drivers for SQL databases.

Access is compatible with SQL, but unfortunately this is not the case of Excel at native state, though it is possible to connect an ODBC drivers to made it compatible with SQL (performance in network would still be very poor). Several desktop database application intended for specific biological work (curatorial management, defintion of taxonomic keys) have often very good interface allowing an easy visualisation of the scientific content on one hand, but are rarely compatible with SQL at native state on the other hand.

If you use a non-SQL database and want to publish their data with BioCASe, you will more than likey have to build a replica of your database (or of the part you want to publish) in a SQL system, and transfer the data between the two systems in tab-delimited, CSVformat (or similar)[1] [2].


Full workflow of the submission of data to OpenUp, from a source desktop database to the portal. The BioCASe provider intervene during the 2nd step

[1] CSV (comma-separated values) and tab-delimited formats are 2 way to format structured content, in order to store tabular information (field-delimited datasheet featuring rows and columns) into a simple text document that can be opened by a simple text editor. Commas, semicolon, tabs or other characters are used to represent columns in the document). Most of database systems and spreadsheets software can export and import data in this format.

[2] Difference between the encoding used in the source database, the intermediate CSV document, and the destination collected to BioCASe is a classic source of technical problems in this process (data can be published with unreadable characters replacing diacritic marks). Please ensure that the CSV documents and the database share the same encoding format (UTF-8, LATIN-1 etc…)