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OBO-Edit 1.000-beta6 released!

John Day-Richter john.richter at aya.yale.edu
Thu Jun 2 23:09:22 PDT 2005


OBO-Edit version 1.000-beta6 is now available at

	http://sourceforge.net/projects/geneontology

This version fixes a number of bugs and minor issues. The most important new 
feature is an entirely overhauled search/filter/rendering system. These 
changes are meant to address feedback I received at my recent OBO-Edit demo 
at Stanford.

Documentation for the new filtering system is still forthcoming. Here are some 
tips to get you started:

	* The new default search mode is called "keyword mode". Enter a 
space-separated list of words (or ids) you want to find and click the 
"Search" button (or press enter). The search will find any term that has ALL 
the keywords you specified. If you want to use the classic OBO-Edit search 
controls, click the "Advanced" tab and unselect "Keyword filtering". If you 
want to do compound searches, select the "Compound filtering" box.

	* Keyword mode works by taking a term's name, synonyms, ids, comment, and 
definition and concatenating them into one long string. The string is then 
broken up into individual words. If any of those words contains the current 
search string, it is considered a match. The following characters are treated 
as whitespace when finding keywords: spaces, semicolons, commas, periods, 
tabs, greater than, less than, any brackets, any quotes. Note that colons are 
preserved, so that ids will behave as expected.

	* When you do a search, the search results will appear in a special tab in 
the search panel. To close the tab, press the red circle/slash button in the 
lower right corner. To make the search tab into a new window, click the 
"detach window" button in the lower right corner (just to the left of the 
close tab button). You can change the label of a set of search results by 
typing a label into the "Results label" box at the bottom of the search 
results panel and pressing enter.

	* To use your search to filter the ontology, click the filter button.

	* To use your search to create a special renderer for your ontology, click 
the "Advanced" tab and select "Rendering controls". A button labeled "Render" 
will appear on the right. Then, go back to the "Term filter" tab and set some 
rendering rules (ie click the "Bold" checkbox). Finally, click the "Render" 
button to apply your new renderer.

	* By default, the Search, Render, and Filter buttons all apply the new search 
mode to the first DAG editor on the screen. If you want to apply a search, 
filter, or renderer to some other DAG editor, instead of clicking the 
search/render/filter button, click and DRAG over the appropriate button. An 
icon will appear representing the filtering action you want to take. Drop the 
icon onto the DAG editor to which you'd like to apply the filtering action.

	* OBO-Edit now supports 2 kinds of filters, term filters and new link 
filters. Link filters allow you to filter on term relationships, rather than 
the terms themselves. To enable link filtering, choose "Link filtering" in 
the "Advanced" tab. When searching, a link filter will select a relationship 
between two terms, rather than a term itself. Link filters have their own 
rendering modes that allow you to control the appearance of the arrows drawn 
between terms and their parents.

Please email me right away with bugs.

	-John

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