To load or save an ontology, use the "File" menu:
Choose "Load ontologies..." or "Save As..." (Command-S). A window like this will appear:
The top line is the same regardless of whether you are loading, saving, or doing some other operation. The drop down box contains a list of data adapters that support the current operation (some data adapters can only save data, some can only load, so not all adapters may appear for all operations). To choose a different data adapter, select it from the dropdown list. Use the "Browse" button to select a file to load or save to.
Some data adapters have two interfaces for setting options, a "Basic" interface and an "Advanced" interface. The Advanced interface will be more complex, and allow more options to be controlled by the user. If a data adapter has the option to choose between Advanced and Basic mode, the "Advanced/Basic" button will be enabled. Click the button to switch between basic and advanced modes.
The blue triangle button displays the stored profile controls. Click it to display the stored profile settings or save a new profile. Some adapters have very complex settings. The stored adapter settings allow you to save a collection of settings to reuse in the future.
To load a stored profile, click the arrow button at the right of the stored profile list and click a profile name to select it. To create a new profile, choose "<new profile>" from the list. Note that the data adapter settings will be cleared. Type a name for the new profile in the stored profile text box, and press the Enter key to save your settings.
To hide the stored profile settings, press the triangular stored profile button again.
Import a set of terms into the ontology currently being edited.
To load several ontologies at the same time, click the "File" menu and choose "Load ontologies...". Click the "Advanced" button. Then click the "Add" button to add ontology filenames (e.g., Gene Ontology and ChEBI ontology). You can add more than one ontology, but keep in mind that ontology files are very big and OBO-Edit might get really slow.
You can also create a new profile to save these file paths for later use. Enter the name of your profile (e.g., go-chebi) in the box that says "Stored adapter settings".
There's actually an easier way to load multiple ontologies if you know the full path of each ontology file. In the "Basic" file load mode, you can enter multiple ontology file paths in the "Load files" box, separated by spaces:
You can save just the ontology terms that match a particular search. The way to do this is with a filtered save.
In the File menu, choose Save As. When the 'Write ontology' window appears, click the "Advanced" button. You will see a window like this:
Click the Add button to create a new save profile.
Set the save path by typing or pasting into the text box that says "<new save path>" or choose a file path by clicking the "Browse" button. Tick the 'Filter terms' box; a set of filter controls will appear. (You may need to make the window bigger so you can see all the fields.) These filter controls work just like the searching/filtering system in the main OBO-Edit window. At this point, you can create a filter manually (use the + button to add a new filter expression) or load a filter that you have already saved by clicking the "open folder" icon to locate your filter file. Click the "OK" button at the bottom of the window to save the the filtered terms into your chosen file. (Note that saving will be slower than usual because of the filtering step.)
If you check the "Always save properties" box, the term filter will be extended so that properties (which includes Typedefs) are always saved, even if the term filter would otherwise not include them.
You can use filtered save to save two loaded ontologies in separate files. One way to do this is to set up a filter that saves terms from a specified namespace. To include all relations in the saved file, construct a compound filter that includes "OR is property" (in this context, property means relation).