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OBO-Edit 1.000-beta7 now available

John Day-Richter john.richter at
Wed Jul 13 06:32:43 PDT 2005

Many, many bug fixes and feature improvements are available in OBO-Edit 
1.000-beta7. Download it from

This version integrates all the bug fixes I've written during my 
whirlwind tour of east coast labs that use OBO-Edit. Because I'm on the 
road, platform specific installers are not available. I will add them 
this weekend, once I'm back in stable surroundings.

Besides a large number of bug fixes, you might be interested in these 
feature improvements:

	* The extended info plugin now works correctly
	* The Dbxref plugin is back!
	* The OBO File Advanced Save options allow you to create arbitrary 
filters to
		decide which terms go into which files
	* obo2flat now works correctly in OBO-Edit
	* New and improved id generation system

That last one is important. There is now a plugin called the ID Manager 
Plugin, where you can configure ID generation rules, and group them 
into easily selectable profiles, so its easy to change the kind of ids 
you generate.

The ID Manager Plugin looks like a dropdown box with three buttons next 
to it. The dropdown box allows you to select the ID generation profile 
you'd like to use. You can add new profiles by clicking the "+" button, 
and remove a profile by clicking the "-" button. You can edit a profile 
by clicking the button with the gear icon.

The ID Manager Plugin allows you to create a number of ID Generation 
rules, each of which is linked to an OBO-Edit term filter. When you 
create a new term, the parent is checked against each of the ID 
generation filters. If there's a match, the associated ID generation 
rule is used. If no filter matches, the default rule (specified at the 
top of the screen) is used.

ID generation rules look like this:

	GO:$sequence(7, 10000, 20000)$

So a rule consists of some literal text and one or more variables. 
Variables are enclosed by $ characters.

There are two variables available for ID generation:

		Generates a sequence of digits LENGTH characters long. The numeric 
		of the sequence will be between MIN_VALUE and MAX_VALUE. The
		parameters are optional. If they are not specified, a default length 
of 7 and a
		default min value of 0 are used.

	* $id$
		The id of the parent term. Use of this variable is NOT RECOMMENDED,
		because it encodes ontology structure information in the ids. However,
		some projects need it, so it has been included.

When you first start OBO-Edit 1.000-beta7, your old id settings will be 
used to create a default id generation profile.

Happy bug hunting!



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