Add an Organism
After initializing the schema with 'init' command, the first task you most likely will do with PersephoneShell is to add an organism. To do this you need to use the add command (see Add) and specify the control file (see Control Files), which contains the data needed by PersephoneShell to add the organism. This section shows the steps necessary to add Oryza sativa japonica to your Persephone database.
As with many other add commands, the action pattern assumes that the particular instructions for each data loading procedure are stored in a separate control INI file that is referenced in a command by using the switch '-c', for example,
add organism -c add_japonica.ini
Review a copy of "add_japonica.ini" control file, which is included in the PersephoneShell "Samples\Organism" folder and is shown below.
; Organism ID (optional, if not specified, it will be autogenerated)
; Look up taxonomy information in http://www.ncbi.nlm.nih.gov/taxonomy
; Taxnomy ID (required)
; Alternative ID: user defined ID
; Scientific name (required)
ScientificName="Oryza sativa ssp.japonica"
; Common name (required)
;If plant, specify if the organism is monocot(0) or eudicot(1)
Copy the control file "add_japonica.ini" to the directory where you installed PersephoneShell (e.g., C:\PersephoneShell) and run a test using switch '-t':
add organism -c add_japonica.ini -t
If tests are successful, load the data into the database in verbose mode ('-v'):
add organism -c add_japonica.ini -v
AlternativeId is used in case you want to have a hyperlink to a web page with extra information about the organism. Currently, setting up this hyperlink requires manual database update, later this will be done by PersephoneShell during organism loading.
To enable the link in Persephone's form for Map Set properties, create a record in ORGANISM_CONFIG table. The URL to the external organism web page should have a placeholder %s which will be filled with the value of AlternativeId. For example, with pattern 'http://localdatabase?org=%s' and AlternativeId='a123', the generated hyperlink will be 'http://localdatabase?org=a123'
The database record should have the following fields:
The next step would be adding a map set for the newly-loaded organism.