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OBO-Edit 1.000-beta7 now available
john.richter at aya.yale.edu
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
* The extended info plugin now works correctly
* The Dbxref plugin is back!
* The OBO File Advanced Save options allow you to create arbitrary
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
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:
* $sequence(LENGTH, MIN_VALUE, MAX_VALUE)$
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.
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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