The Text Editor panel allows you to edit all the attributes of a term. Sub-select a term in the Ontology Tree Editor Panel to load it into the text editor:
OBO-Edit does not immediately apply text edits; instead, it tries to group edits together so that the behavior of "Undo" makes more sense (you wouldn't want to have to undo each and every letter typed, for example). OBO-Edit has two modes for making text edits permanent: auto-commit mode and manual commit mode.
In auto-commit mode, text edits are applied as soon as a new term is selected or the ontology is saved. To commit edits immediately, press Command+Enter.
In manual commit mode, text edits are applied when the "Commit" button in the Text Editor is pressed. The "Commit" button is only visible in manual commit mode. Command+Enter will also commit edits in manual commit mode.
See the Text Editing section of the Configuration Manager page for information about choosing the text editing mode.
Note that you can't Undo changes made in the Text Editor until you've committed your changes as above (select a different term or click the Commit button).
The Text Editor performs text checks on the selected term. If there are any errors or warnings, this is indicated in the Text Editor title bar. To see the warnings, hover your mouse over the title bar for a few seconds; a window listing the warnings will pop up:
At the top of the Text Editor, you will see the basic attributes of the selected term.
In order to fit all of the possible editing options onto one screen, some editing options are organized into tabs. To access a tab, click the tab name. Tabs that currently contain information are marked with an asterisk.
Definition text and definition dbxrefs can be edited here. There are two fields:
See the Dbxrefs Tab section below for more information about editing dbxrefs.
The comment associated with the current term can be viewed and modified in this text area.
Cross Product Tab
Please refer to Cross Products in the Text Editor.
This tab allows the user to add, edit, and remove general dbxrefs associated with the selected term. General dbxrefs are used to provide mappings between a term and a term in another vocabulary.
To edit a dbxref, double-click it in the list. When the dbxref is selected, it will be loaded in the dbxref editor, which contains the following fields:
To add a new dbxref, click the "+" button. A new dbxref "XX:<new dbxref>" will be created. Modify the fields as desired, using tab to move between the fields. To save your new dbxref, hit return.
To remove a dbxref, select the dbxref to remove, and click the "-" button.
Synonyms are alternate names for a term. Not all terms have synonyms. If your currently selected term has synonyms, you will see them in the synonym tab.
To edit a synonym, double-click it. The synonym panel will turn into a synonym editor panel:
The interface for modifying the synonym dbxref list is exactly the same as the interface for modifying general dbxrefs (described above).
To add a new synonym, click the "Add" button. When you are done editing your new synonym, click somewhere in the gray area in the synonym editor panel to commit it and close the synonym editor.
To remove a synonym, select the synonym to remove, and click the "-" button.
Subsets are used to designate subsets of terms within an ontology. The subsets tab contains a list of the available subsets in the ontology. If the selected term is a member of a subset, the checkbox to the right will be checked. To change whether the term belongs to a particular subset, check or uncheck the appropriate checkbox.
To edit the list of available subsets, use the Subset Manager.
The display is slightly different when a relation (rather than a class) has been selected.
To specify a domain or a range for a relation using the text editor: