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OBO-Edit 1.000-beta6 released!
john.richter at aya.yale.edu
Thu Jun 2 23:09:22 PDT 2005
OBO-Edit version 1.000-beta6 is now available at
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
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.
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