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.
Make sure you've already tried running the webstart edition of phenote (you can also run phenote from the command line). Running this once should leave a directory on your computer called ".phenote".
The configuration files used by Phenote are located in the ".phenote/conf " directory.
Within this directory you can store any number of configuration files. The default files that come with the webstart versions are named "flybase.cfg", "zfin-standalone.cfg", or "human.cfg", etc., depending on which version you've used in the past. Any file you create/modify should be placed in this directory.
Once you have placed or modified your configuration file in the ".phenote/conf " directory, you need to tell Phenote to use that particular file.
See Changing your Configuration for instructions.
If you have created your own custom configuration file with a ".cfg" extension, it should be listed in the list. Any changes to your configuration settings will take effect the next time Phenote is loaded.
To get a custom ontology that is local and not on SF, you'll have to copy it into ".phenote/obo-files/ ". Any reference to this ontology within your configuration file must match the filename.