You can see sample configuration files and their corresponding Phenote screenshots in Sample Configuration 1 and Sample Configuration 2 . The easiest way to get comfortable with editing your own configuration file is to simply edit an existing configuration. You can copy the text from the sample configurations in this help file, or you can copy an existing configuration file that is distributed with Phenote. As a precaution, be sure to save your edited configuration file with a new filename to prevent any accidental overwriting by our server when you upgrade to a new Phenote version.
Before you try editing a configuration file, make sure you've launched Phenote at least once. This should create a directory on your computer called ".phenote".
The configuration files used by Phenote are located in the "conf" directory in your .phenote directory.
Within this directory you can store any number of configuration files. The configuration files that come with Phenote are named "flybase.cfg", "zfin-standalone.cfg", or "human.cfg", etc. Any configuration file you create/modify should be placed in this directory.
Once you have placed your new or modified configuration file in the .phenote/conf directory, you need to tell Phenote to use that particular configuration file.
See Changing your configuration for instructions.
If you have created your own custom configuration file with a ".cfg" extension, it should be shown in the list of known configurations. Any changes to your configuration settings will take effect the next time you launch Phenote
To use a custom ontology file in Phenote, copy the file into .phenote/obo-files/. Any reference to this ontology within your configuration file must match the filename.