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MySQL PGDBs: Creating & querying them

asked 2013-04-29 16:42:25 -0500

ptools-admin gravatar image

updated 2015-06-19 19:34:39 -0500

How can I convert my locally created file PGDB to a MySQL PGDB? If I do this, will I be able to query my PGDB using SQL?

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answered 2013-05-01 14:18:23 -0500

quang777 gravatar image

updated 2015-08-14 17:00:23 -0500

ptools-admin gravatar image

MySQL is a free, open-source relational database management system. Using MySQL to store your PGDB instead of a file enables multi-user concurrent access, change logging, and in some cases faster load and save times. Because of the format in which the data is stored, however, it will not allow you to access the data in your PGDB by writing SQL queries.

If you want to query a PGDB via SQL, you can load the PGDB into an instance of BioWarehouse using the BioCyc Loader

If you wish to programmatically access the data in Pathway Tools directly, you can use one of our Lisp, Perl or Java APIs: 

MySQL can be obtained from We do not provide any support for obtaining or installing the base MySQL software. Instructions for configuring Pathway Tools to access MySQL and for installing the Pathway Tools schema in your MySQL database can be found here. There is also a link to these instructions from the Pathway Tools Installation Guide.

Once MySQL is installed and correctly configured, start up the Pathway Tools Navigator, and invoke PathoLogic from the Tools menu. To convert a particular PGDB to use MySQL select it in PathoLogic and then invoke the command Organism->Convert File DB to MySQL DB.

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Asked: 2013-04-29 16:42:25 -0500

Seen: 12,553 times

Last updated: Aug 14 '15