If you have ssh-askpass installed (or a variant like seahorse-ssh-askpass), you can force a prompt by adding your key to the keyring with ssh-add. Note that to get a graphical/UI prompt, you need to disable standard input, because ssh-add will read input from the connected terminal if it is available.
# will use SSH_ASKPASS, or ssh-askpass by default ssh-add ~/.ssh/id_rsa </dev/null # use seahorse's prompt utility SSH_ASKPASS=/usr/lib/seahorse/seahorse-ssh-askpass ssh-add ~/.ssh/id_rsa </dev/null
Note that seahorse itself provides a UI for managing secrets backed by gnome-keyring-daemon, but the main program is not meant for a one-shot prompt-and-save operation.