Text Editing
When a term is sub-selected , it is loaded into the text
editor:

In this panel, you
can edit all the attributes of a term.
Committing Your Changes
OBO-Edit does not immediately apply text edits. OBO-Edit 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
Ctrl+Enter.
In manual commit mode, text edits are applied when the
"Commit" button is pressed. The "Commit" button is only visible in manual commit
mode.
See the Text Editing section
of the Configuration Plugin for information about choosing the text editing
mode.
Basic Attributes
- 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
asterick.
Dbxref Tab -

This tab allows the user to add, edit, and remove general dbxrefs. General
dbxrefs are used to provide mappings between a term and a term in another
vocabulary.
To edit a dbxref, click it on the list to left. When the dbxref is selected,
it will be loaded in the editor to the right. The editor contains the following
fields:
- Database name -
Contains the dbxref database name. The dbxref name is 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".
- Database id -
Contains the dbxref database id. The dbxref id is 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".
- Database desc - A descriptive name for the
dbxref.
To add a new dbxref, click the "Add" button. A new dbxref "XX:<new
dbxref>" will be created.
To remove a dbxref, select the dbxref to remove, click the "Del" button. The
dbxref will be removed.
Definition Tab -

Definition text and definition dbxrefs can be edited here. There are two
fields:
- Text - This
contains the definition text.
- Dbxref List
- Definition dbxrefs provide a reference explaining the origin of the
definition. To add a new dbxref, drag a dbxref
onto the list. To delete a dbxref, first click it to select the dbxref. Then
press the "Delete" key on the keyboard. To edit a dbxref, or to have the full
set of dbxref editing tools, click the "Edit" button. The following window
will appear:

The interface for modifying the definition dbxref list is
exactly the same as the interface for modifying general dbxrefs (described
above). Click "Ok" to accept the
changes.
Comment Tab -

The comment can be viewed and modified in this text area.
Cross Product Tab -
See Cross Products in the
Text Editor
Synonyms Tab -

Synonyms are alternate names for a term.
To edit a synonym, click it on the list to left. When the synonym is
selected, it will be loaded in the editor to the right. The editor contains the
following fields:
- Synonym text -
The actual synonym name.
- Synonym 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 categories have a built-in scope (for
example, a category like "UK Spelling" would have a built-in scope of "exact",
because every synonym in this category would be an exact synonym; see Working with Synonym Categories for more information). If
the synonym belongs to a category with a built-in scope, the scope cannot
be edited.
- Synonym type -
Indicates the synonym category to which this synonym belongs. Synonym
categories allow synonyms to be grouped into different types. To choose a new
synonym category, select it from the dropdown list. To add, edit, or delete a
synonym category, use the
Synonym Category Manager Plugin.
- DbXrefs - Synonym dbxrefs indicate a literature reference
that explains the origin of the synonym. To add a new dbxref, drag a dbxref
onto the list. To delete a dbxref, first click it to select the dbxref. Then
press the "Delete" key on the keyboard. To edit a dbxref, or to have the full
set of dbxref editing tools, click the "Edit" button. The following window
will appear:

The interface for modifying the synonym dbxref list is exactly
the same as the interface for modifying general dbxrefs (described above).
Click "Ok" to accept the changes.
To add a
new dbxref, click the "Add" button. A new dbxref "XX:<new dbxref>" will be
created.
To remove a dbxref, select the dbxref to remove, click the "Del" button. The
dbxref will be removed.
Category Tab -

Categories are used to designate subsets of terms within an ontology. The
category tab contains a list of the available categories in the ontology. If the
selected term is a member of a category, the checkbox to the right will be
checked. To change whether the term belongs to a particular category, check or
uncheck the appropriate checkbox.
To edit the list of available categories, use the Category Manager
Plugin
.
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 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.
- 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 that this box is marked 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.