Author image Christopher Fields
and 1 contributors


SYNOPSIS --host --dbname biosql



The arguments after the named options constitute the filelist. If there are no such files, input is read from stdin. Mandatory options are marked by (M). Default values for each parameter are shown in square brackets.

--host $URL

the host name or IP address incl. port [localhost]

--dbname $db_name

the name of the schema [biosql]

--dbuser $username

database username [root]

--dbpass $password

password [undef]

--driver $driver

the DBI driver name for the RDBMS e.g., mysql, Pg, or Oracle [mysql]

--namespace $namesp

The namespace, i.e., name of the ontology, for the terms to be associated.


don't commit anything, rollback at the end


If supplied with an integer argument n greater than zero, progress will be logged to stderr every n entries of the input file(s). Default is no progress logging.

-u, -z, or --uncompress

Uncompress the input file(s) on-the-fly by piping them through gunzip. Gunzip must be in your path for this option to work.

more args

The remaining arguments will be treated as files to parse and load. If there are no additional arguments, input is expected to come from standard input.


Hilmar Lapp <hlapp at>


 Title   : _report_progress
 Usage   :
 Function: Reports the progress to STDERR.
 Example :
 Returns : The new stopped time to be passed to the next call
 Args    : - the time at which progress was reported last
           - every how many entries progress is reported


 Title   : _find_or_create_ont
 Usage   :
 Function: Find or create the ontology entry with the given name.
 Example :
 Returns : A persistent Bio::Ontology::OntologyI object
 Args    : - the persistence adaptor factory (the $db handle)
           - the name of the ontology