Text Editing

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:

Committing Your Changes

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).

Text Checking

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:

Basic Term Attributes

At the top of the Text Editor, you will see the basic attributes of the selected term.

• ID - The id of the term. The id cannot be edited.
• Namespace - The namespace (aka the ontology name) of this term. The namespace can be changed by selecting a different namespace from the dropdown list. The list of available namespaces can be edited using the Namespace Manager Plugin.
• Term Name - The term's display name can be edited in this text box.

Tabs

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 Tab

Definition text and definition dbxrefs can be edited here. There are two fields:

• Definition - This contains the definition text.
• Dbxrefs - Definition dbxrefs provide a reference explaining the origin of the definition. To add a new dbxref, click the + button. To delete a dbxref, first click it to select the dbxref, and then click the - button. To edit a dbxref, or to have the full set of dbxref editing tools, double-click the dbxref id. A dbxref editing panel will appear:
  

  

See the Dbxrefs Tab section below for more information about editing dbxrefs.

Comment Tab

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.

Dbxrefs Tab

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:

• Database name - Contains the dbxref database name--the part of the dbxref that appears to the left of the colon. For example, in the dbxref "EC:1.8.1.7", the database name is "EC".
• ID - Contains the dbxref database id--the part of the dbxref that appears to the right of the colon. For example, in the dbxref "EC:1.8.1.7", the database id is "1.8.1.7".
• Description - A descriptive name for the dbxref.

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 Tab

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:

• Name - The actual synonym name.
• Scope - The synonym scope indicates how specific this synonym is. To choose a new scope, select it from the drop down list. The possible values are:
  • Related synonym - The catch-all scope. This means that this synonym has a slightly different meaning than the term name, so it can't be said to be more or less specific in scope. Related synonyms are often phrases that a user might use when searching for a term. For example, sometimes the Gene Ontology will specify a well-known gene product name as a related synonym of the associated function or process term to aid in searching. 
  • Exact synonym - Indicates that this synonym means exactly the same thing as the term name.
  • Narrow synonym - Indicates that this synonym means something more specific than the term name.
  • Broad synonym - Indicates that this synonym means something less specific than the term name.
  Note that some synonym types have a built-in scope (for example, a type like "UK Spelling" would have a built-in scope of "exact", because every synonym in this type would be an exact synonym; see Working with Synonym Types for more information). If the synonym belongs to a type with a built-in scope, the scope cannot be edited.
• Synonym type - Indicates the synonym type to which this synonym belongs. Synonym types allow synonyms to be grouped into different types. To choose a new synonym type, select it from the dropdown list. To add, edit, or delete a synonym type, use the Synonym Type Manager Plugin.
• DbXrefs - Synonym dbxrefs indicate a literature reference that explains the origin of the synonym. To add a new dbxref to this synonym, click the "+" button next to the Scope pulldown:

  

  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 Tab

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.

Relation-Specific Attributes

The display is slightly different when a relation (rather than a class) has been selected.

• Range - The relation range restricts the possible parents for any relationship that uses this relation. If this relation is listed as a relationship type in a given relationship, the parent of that relationship must be a subclass of this relation's range. To set a new range, drag a term onto the blue range button. To clear the range, click the blue range button. See An Introduction to OBO Ontologies for more information about range.
• Domain - The relation domain restricts the possible children for any relationship that uses this relation. If this relation is listed as a relationship type in a given relationship, the child of that relationship must be a subclass of this relation's domain. To set a new domain, drag a term onto the blue domain button. To clear the domain, click the blue domain button. See An Introduction to OBO Ontologies for more information about domain.
• Is transitive - If this box is checked, the relationship type is transitive. It is very important to that this box is marked correctly; the OBO-Edit reasoner makes extensive use of this information. If the transitive status of a relation is incorrectly indicated, the reasoner may make many incorrect inferences.
• Is symmetric - If this box is checked, the relationship type is symmetric. It is very important to mark this box correctly; the OBO-Edit reasoner makes extensive use of this information. If the symmetric status of a relation is incorrectly indicated, the reasoner may make many incorrect inferences.
• Is cyclic - If this box is checked, it is legal to create cycles out of this relationship type. That is, it is legal to say that a term has a relationship to itself over this relation. Note that if "Is cyclic" isn't selected, even indirect cycles (that is, cycles that are made of implied relationships) are illegal.

To specify a domain or a range for a relation using the text editor:

• Open both the text editor and the ontology tree editor.
• Set the ontology tree editor to Local Mode.
• Drag the ontology term from the tree editor to the <no domain specified> or <no range specified> bubble in the text editor. The corners of the bubble will momentarily turn square, and when you release the curser, the domain or range term should show up in the bubble.