The Verification Manager allows users control over all aspects of the verification system:
The Verification Manager has two tabs, the Configuration tab and the Verification Results tab.
The top half of the configuration tab contains a list of checks. Each line contains the check name, a series of checkboxes indicating the events at which this check will be run, and an optional configuration button. To specify when a check should be run, check the boxes for each event for which the check should be performed.
In the middle of the panel is a series of checkboxes labeled "Show warnings". Warnings (non-fatal error messages generated by an ontology check) are only displayed during events that are checked in this panel.
Beneath this panel is a checkbox labeled "Check obsoletes?". If this box is selected, checks are run on obsolete terms. If it is not selected, obsolete terms are ignored.
Under this is a pair of buttons labeled "Add check" and "Remove check". If "Add check" is clicked, the User Check Editor is diplayed (see below). If "Remove check" is clicked, the currently selected check will be deleted. Only user defined checks can be deleted; built in checks cannot be removed, but they can be disabled by selecting no events for that check.
At the bottom is the "Run Manual Check" button. Clicking this button triggers the manual event, and all checks that are marked "On manual?" will be run.
The following checks are built-in to OBO-Edit:
Users can create their own checks, tailored to the needs of a particular ontology. Once created, user-defined checks become available in the Verification Manager, and users can specify when the check should be run.
Whenever a verification is run for any reason, the results appear in the Verification Results tab:
Note that often the verification results will also appear in a popup window, but the results of the last verification can always be reviewed in this tab of the verification manager. Verification results appear in a popup window when the verification is triggered by a special event, such as a text edit, save, load, or reasoner-startup.
The results tab will contain a list of errors and warnings. Errors are severe problems with the ontology that must be corrected to make the ontology compliant with the OBO ontology format. Warnings are less serious problems that should be corrected, but the ontology can be saved even if these errors are not dealt with.
Warnings are preceded by a icon. Errors are preceded by a icon. Errors are generally listed first.
Warnings and error messages are grouped together by term, so that all warnings generated for a particular term appear together. If a term is mentioned in an error message or warning, the term name is a clickable hyperlink. Clicking the hyperlink causes that term to be selected. Note that these hyperlinks will not work if the verification results are displayed in an automatic popup window, but the window can be closed and the results plugin opened. The verification results will be visible in the results tab, and the hyperlinks will be clickable there.
Only the first approximately 500 warnings will be displayed (the exact number depends how many warnings are found for the last checked term). If the verification checks find more warnings, they won't be shown. To reduce the number of warnings, try fixing the problems identified in the warnings or disabling some checks.
Sometimes, a warning or error will be followed by a icon. When this icon appears, it means one or more "quick fixes" are available for the problem. When the icon is clicked, a popup menu will appear detailing the various quick fix options. To apply one of the quick fixes, select it from the menu. Normally, the fix will be applied and the verification will be at least partly re-run to reflect the changes made by the quick fix. Beware: quick fixes may modify your ontology.