The Verification Plugin allows users control over all aspects of the verification system:
The Verification Plugin is based around 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:
Each user-defined check is associated with a term filter. If the filter matches any term in the ontology, the check fails and an error is reported to the verification system.
To create a user-defined filter, click the "Add check" button. When the "Add Check" button is clicked, the User Check Editor appears:
The "Check name" field contains the name of the user-defined check.
Below the "Check name" field is a filter editor. This editor contains the filter that will be used to determine whether a term passes or fails this check. The filter should be designed so that any term that matches this filter fails the check.
Beneath this is the "Message suffix" text field. This field contains the ending of the error message that will be generated for terms that fail this check. The error message has the form "Term <term name> <message suffix>".
The final control is the "Is fatal" checkbox. If this box is selected, errors generated by this check are treated as fatal errors. An ontology that generates fatal errors when checked cannot be saved until the errors are corrected. If this box is not selected, error messages are treated as non-fatal warnings.
Once the check is configured, save the new configuration by clicking "Ok".
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 plugin. 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.
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.