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1. Run dbdoc_util.pl initdoc (with options) to set up dbDoc for a specified existing genomic MySQL database
2. Run dbdoc_util.pl updatedoc --dbdoc-xml-file=<file> to read XML documentation
   1. Suggestion: break up XML documentation into multiple files, such as a "core" file that does not change often, and a another file that might describe what the recent changes are. This is currently done for the HapMap databases.

Modifying documentation

• Deletions: at the moment (subversion 29) a row can be deleted from the db table and this will propagate throughout the database.
• Updates: at the moment (subversion 29) changes do not cascade well due to a circular foreign key in the process/flow_group tables. To change the name of a database the docoumentation should be re-loaded from XML.The documentation for individual databases in the runk/main/databases directory of the Subversion repository contain shell scripts for running dbdoc_util.pl. These scripts read the XML documentation files to the build the MySQL documentaiton database
• Documentation for an entire databases may be deleted by deleting row for that databases from the table db via MySQL cascade.

Locations of Documentation on Subversion

• Documentation for individual databases is in the trunk/main/databases directory of the Subversion repository.
• Global documentation on BioQ genomic features, such as the list of feature keywords and tables, can be found in web/perl/dbdoc/features.xml