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OBO-Edit 1.000-beta9 released

John Day-Richter john.richter at aya.yale.edu
Thu Sep 1 13:06:01 PDT 2005


OBO-Edit 1.000-beta9 is now available from

	http://sourceforge.net/projects/geneontology

There are a LOT of changes in this version:

	* Bug fixes
	* Added a reasoner (!)
	* Added ability to specify replacement terms and terms to consider for 
obsolete terms
	* New drag and drop operations
	* Fixed Graph Plugin
	* Added button toolbar to OBO Term Panels
	* Added the ability to split OBO-Edit panels without changing the layout

Detailed explanations of how to use the new features are included below. Check 
the README file for a complete list of changes.

Frequent users will be pleased to learn that for the next few weeks I will be 
entirely dedicated to updating the OBO-Edit documentation.

	-John

How to use the new features:

1) Using the new term panel toolbar.

There is now a small button in the bottom right corner of all term editing 
panels marked with a + icon. If this button is clicked, a toolbar will 
appear. The toolbar contains several buttons:

	* Primary selector button: When clicked, this button makes the current term 
editing panel the primary selector. Selections in this panel will be 
reflected in the term text editor, DAG Viewer, and any other component that 
responds to the selection.

	* Split horizontal button: This button splits the current term editing panel 
horizontally.

	* Split vertical button: This button splits the current term editing panel 
vertically.

	* Merge panels: This button merges to term editing panels. Term editing 
panels can also be merged by right-clicking the bar that separates the two 
panels.

	* Lock/Unlock view button: This button locks or unlocks the current term 
editing panel. When a panel is locked, the scroll bars will disappear and the 
screen will not scroll away from the currently selected term, even if the 
selection changes or the tree is expanded or collapsed.

	* Reload button: Forces a complete redraw of the term editing panel. This is 
useful if a bug has caused the screen redraw to malfunction.

	* Filter button: This button allows the user to manage filters and renderers 
that have been applied to the term editing panel. This button has the same 
function that the corner button used to have for term editing panels.

2) New drag and drop features.

* The relationship type of a link can be changed by selecting the desired 
relationship type and dragging it onto the link.

* The range and domain of a relationship type can be changed by dragging the 
desired range or domain term onto the relationship type. A menu will appear 
to allow you to specify whether you want to use the term as the range or 
domain.

* Replacement terms can be added to obsolete terms by dragging the replacement 
term onto the obsolete term. A menu will appear to allow you to specify 
whether this replacement term should always be used or whether it is just a 
term to consider. If an obsolete term has replacement terms, they will appear 
under the obsolete term in the term editor panel. Replacement terms can be 
removed by selecting them and choosing "Remove replacement term" from the 
right-click menu.

3) The Reasoner.

Open the new Reasoner Plugin. The reasoner can be enabled by checking the 
"Enable Reasoner" checkbox.

The reasoner will find redundant links in your ontology, and will display any 
links that are implied by "complete" relationships (aka intersections). The 
reasoner can take up to several minutes to run initially, but once it has 
been run, it does not need to be re-run every time a change is made. However, 
it does need to be re-run to UNDO a change, so edit carefully when the 
reasoner is enabled. The Reasoner Plugin can show you the reasoner's progress 
as it reasons over an ontology, and will give you a brief report of the 
results once the reasoner has finished running.

If the reasoner is enabled when OBO-Edit is shut down, the reasoner will be 
enabled when you restart OBO-Edit. Make sure to turn off the reasoner when 
you don't want it; OBO-Edit will run faster.

If the reasoner is running, you can get an explanation of any link in the 
ontology. To explain a link, open the Explanation Plugin. It will show you an 
explanation of the selected link.

An explanation consists of an explanation type and some evidence. The possible 
explanation types (at present) are GIVEN, TRANSITIVITY, and COMPLETENESS. 
GIVEN links are links that are user defined. Links explained by TRANSITIVITY 
are links that are derived from the transitive relationships in the graph. 
Links explained by COMPLETENESS are derived from relationships that have been 
marked "complete". The evidence for an explanation is some other collection 
of links in the graph.

Explanations are displayed in a tree view. When an explanation is expanded, 
the evidence links are shown. If an evidence link is expanded, the 
explanation for the evidence links is shown. The leaves of an evidence tree 
are always links that are GIVEN (since any derived link will be based on a 
user-defined link).

Some links may have multiple explanations. If a link has a GIVEN explanation 
AND some other explanation, that link is considered redundant, because the 
link would be implied even if it weren't explicitly stated.

Redundant and implied links can be found by using the search mechanism. Make 
sure "Link filtering" is enabled on the "Advanced" tab of the search control, 
and choose "Is Redundant" or "Is Implied" as the search criterion.

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