OBO-Edit: Help document OBO-Edit 2: Difference between revisions

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There are many differences between OBO-Edit 1 and OBO-Edit 2. The OBO-Edit User Guide refers to version 1, and needs to be substantially revised before we can release OBO-Edit 2 to the public.
(Updated 19 Aug 2008)


OBO-Edit users, we need your help!  <b>Please add your name to the section or sections to which you are willing to contribute.</b>  Feel free to add new sections to the list as well--this is definitely not a complete list. Don't worry about formatting or polishing your text.  Just send whatever you have to Nomi, and she'll take care of making it pretty.
These are the help pages that still need to be updated (or, in some cases, written):
 
* Filtering.htm
* Cross-products - Jen
* The OBO OWL Adapter
* Drag and drop layout customization
* The OWL URL Reader
* Creating new layouts (and other general layout management) Jen: DONE
* The GO Association File Adapter
* The new search system
**Term search Jen: DONE
**Link search Jen: some screenshots sent in but still fairly confused about how this works. There is some good develop documentation on the link filter but I can't find it now. Still searching for it.
* The new rendering system (particularly the html expression syntax)
** html expression syntax Jen: basic stuff DONE
** would be useful also to have simpler version of [http://wiki.geneontology.org/index.php/OBO-Edit:_Arcana_for_User%27s_Guide John's Guide]
* Configurable Message Jen: DONE-ish - with rather lame example.
* Reasoner, cross products (xps): Chris M.
* Help for individual components: Nomi
* User-configurable heat maps
* Hotkey system (see [http://sourceforge.net/mailarchive/forum.php?thread_name=BEB35549-C4BB-4346-A499-8D85B22FF2AB%40berkeleybop.org&forum_name=geneontology-oboedit-working-group John's summary]): Midori DONE
* Table of Contents: Jen: DONE.
* Annotation Summary Component: Jen - I do not know how to work this.
* Term Image Display Panel: Jen: DONE


== Some references that might be useful: ==
== Some references that might be useful: ==
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* Browse the SourceForge SVN [http://geneontology.svn.sourceforge.net/viewvc/geneontology/java/ code repository] (which includes the oboedit code and also the code for the bbop and obo libraries that oboedit uses)
* Browse the SourceForge SVN [http://geneontology.svn.sourceforge.net/viewvc/geneontology/java/ code repository] (which includes the oboedit code and also the code for the bbop and obo libraries that oboedit uses)


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== Pages that can be used without changes ==
These are just my impressions; if anyone thinks any of these do need updating, speak up. -midori
*An_Introduction_to_OBO_Ontologies.htm
*Assigning_New_Roots.htm
*Backtick_Expressions.htm
*Basic_Concepts_and_Vocabulary.htm
*Cloning.htm
*Creating_Your_Own_GO_Slim_in_OBO_Edit.htm
*Cross_Products.htm
*Dangling_Intersection_Check.htm
*Dbxref_Check.htm
*Definition_Check.htm
*Deleting.htm
*Destroying.htm
*Disjointedness_Check.htm
*Editing.htm
*Editing_Obsoletes.htm
*Example_Scripts.htm
*Expression_Syntax.htm
*Filters.htm
*Frequently_Asked_Questions.htm (though of course we can add to this if we think of good Qs)
*How_ID_Generation_Works.htm
*ISA_Cycle_Check.htm
*Introduction_to_Adapters.htm
*Introduction_to_Cross_Products.htm
*Introduction_to_Expressions.htm
*Language_Concepts.htm
*Link_Filters_vs_Term_Filters.htm
*Name_Redundancy_Check.htm
*OBO_Edit_Specific_Variables.htm
*Other_Uses_of_Filters.htm
*Plugins.htm
*Reusing_Filters.htm
*Structural_Editing.htm
*Text_Checks.htm
*The_GO_Flat_File_Adapter.htm
*The_Serial_Adapter.htm
*What_is_OBO_Edit_.htm
*What_is_an_ontology_.htm
*Working_with_Obsoletes.htm
*obo2flat.htm
*obo2obo.htm
*obodiff.htm
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Revision as of 17:19, 19 August 2008

(Updated 19 Aug 2008)

These are the help pages that still need to be updated (or, in some cases, written):

  • Filtering.htm
  • The OBO OWL Adapter
  • The OWL URL Reader
  • The GO Association File Adapter

Some references that might be useful:

< Return to OBO-Edit main page