Difference between revisions of "OBO-Edit: Documentation Week"

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[[Category:OBO-Edit]]
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'''''NOTE: This page is obsolete.  Please visit [[OBO-Edit:_Help_document_OBO-Edit_2]] instead.'''''
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The OBO-Edit Working Group has agreed to devote the week of June 30th, 2008, to testing OBO-Edit2 and writing user documentation.  We appreciate your help!
 
The OBO-Edit Working Group has agreed to devote the week of June 30th, 2008, to testing OBO-Edit2 and writing user documentation.  We appreciate your help!
  
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Viewing Ontologies
 
Viewing Ontologies
* [http://www.oboedit.org/oe2/userguide/html/Working_with_Selections.htm Working with Selections] (Jen has done half, now handed over to Melissa)
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* [http://www.oboedit.org/oe2/userguide/html/Working_with_Selections.htm Working with Selections] (Jen has done half, now handed over to Melissa -waiting till we resolve the single OTE global panel issue-melissa)
 
* [http://www.oboedit.org/oe2/userguide/html/Perspectives.htm Perspectives] (updated by Nomi)
 
* [http://www.oboedit.org/oe2/userguide/html/Perspectives.htm Perspectives] (updated by Nomi)
 
* [http://www.oboedit.org/oe2/userguide/html/Components.htm Components] (Nomi)
 
* [http://www.oboedit.org/oe2/userguide/html/Components.htm Components] (Nomi)
 
** [http://www.oboedit.org/oe2/userguide/html/Configuration_Manager.htm Configuration Manager] (Nomi)
 
** [http://www.oboedit.org/oe2/userguide/html/Configuration_Manager.htm Configuration Manager] (Nomi)
** [http://www.oboedit.org/oe2/userguide/html/The_Term_Editor_Panel.htm The Ontology Tree Editor] (Midori - text OK; must update screenshots)
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** [http://www.oboedit.org/oe2/userguide/html/The_Term_Editor_Panel.htm The Ontology Tree Editor] (Midori - text OK; must update screenshots) (screenshots done -midori)
** [http://www.oboedit.org/oe2/userguide/html/Tree_Viewer.htm The Tree Viewer] (melissa?) note: text and screenshot don't match; if Melissa doesn't want to do this one, I can -midori
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** [http://www.oboedit.org/oe2/userguide/html/Tree_Viewer.htm The Tree Viewer] (done, but please check -Melissa)(looks good -midori)
 
** [http://www.oboedit.org/oe2/userguide/html/Graph_Viewer.htm The Graph Viewer] (Jen - done)
 
** [http://www.oboedit.org/oe2/userguide/html/Graph_Viewer.htm The Graph Viewer] (Jen - done)
 
** [http://www.oboedit.org/oe2/userguide/html/Table_of_Contents.htm Table of Contents Component] (ok)
 
** [http://www.oboedit.org/oe2/userguide/html/Table_of_Contents.htm Table of Contents Component] (ok)
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** [http://www.oboedit.org/oe2/userguide/html/Configurable_Message.htm Configurable Message] (Nomi - done)
 
** [http://www.oboedit.org/oe2/userguide/html/Configurable_Message.htm Configurable Message] (Nomi - done)
  
Filtering, Rendering & Searching (Jen)
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Filtering, Rendering & Searching
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* ('''midori''':  why don't you go ahead and reorganize these pages however you like.  I trust your judgment.  --Nomi) ('''Done!''' In fact, search docs pretty much done except for rendering. -midori)
 
* [http://www.oboedit.org/oe2/userguide/html/Filters.htm Filters] (Jen - ok)
 
* [http://www.oboedit.org/oe2/userguide/html/Filters.htm Filters] (Jen - ok)
* [http://www.oboedit.org/oe2/userguide/html/Link_Filters_vs_Term_Filters.htm Link Filters vs Term Filters] (Jen - ok)
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* [http://www.oboedit.org/oe2/userguide/html/Link_Filters_vs_Term_Filters.htm Link Filters vs Term Filters] (Jen - ok)(could be rolled into above section, both are small-melissa) (Done. --Nomi)
* [http://www.oboedit.org/oe2/userguide/html/Building_a_Filter.htm Building Filters] (Not empty--was wrong page.  Needs updating) This page is hopelessly out of date; the Attribute, Comparison, and Aspect sections should be folded into the Advanced Search (or just "Search") page; then this page should be deleted. -midori
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* [http://www.oboedit.org/oe2/userguide/html/Building_a_Filter.htm Building Filters] (Not empty--was wrong page.  Needs updating) This page is hopelessly out of date; the Attribute, Comparison, and Aspect sections should be <strike>folded into the Advanced Search (or just "Search") page; then this page should be deleted</strike>. I've changed my mind about this page; I'm now keeping it and using it as an overview of search parameters. -midori
** [http://www.oboedit.org/oe2/userguide/html/Setting_the_Filter_Mode.htm Setting the Filter Mode] (Jen - This page deleted) It still shows up in my svn checkout, but deleting it is the right thing to do. -midori
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** [http://www.oboedit.org/oe2/userguide/html/Setting_the_Filter_Mode.htm Setting the Filter Mode] (Jen - This page deleted) It still shows up in my svn checkout, but deleting it is the right thing to do. -midori (Oh, I see, it was deleted from svn but still on the wiki.  Now it's gone. --Nomi)
 
** [http://www.oboedit.org/oe2/userguide/html/Term_Filters.htm Term Filters] (Jen - part done - This documentation derails here because the filter button has not yet been added back and the ancestor/descendant menu has not been added back. I think it would make more sense to wait until this is complete to write the docs as screenshots will all soon be obsolete.) Actually, we could just lose this page. A lot of it duplicates the Building a Filter page, and both are superseded by the new search interface. -midori
 
** [http://www.oboedit.org/oe2/userguide/html/Term_Filters.htm Term Filters] (Jen - part done - This documentation derails here because the filter button has not yet been added back and the ancestor/descendant menu has not been added back. I think it would make more sense to wait until this is complete to write the docs as screenshots will all soon be obsolete.) Actually, we could just lose this page. A lot of it duplicates the Building a Filter page, and both are superseded by the new search interface. -midori
 
** [http://www.oboedit.org/oe2/userguide/html/Link_Filters.htm Link Filters] This could either be incorporated into Advanced Searching or kept separate; if we keep it separate, the screenshot and a few lines of text have to be updated. Let me know if you want me to do either. -midori
 
** [http://www.oboedit.org/oe2/userguide/html/Link_Filters.htm Link Filters] This could either be incorporated into Advanced Searching or kept separate; if we keep it separate, the screenshot and a few lines of text have to be updated. Let me know if you want me to do either. -midori
** [http://www.oboedit.org/oe2/userguide/html/Compound_Filtering.htm Compound Filtering] Delete this page - it's completely, utterly, and happily superseded by the new search interface. It might be worth keeping the last section (move to the main search doc), on search speed, because I think that's still relevant. -midori
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** [http://www.oboedit.org/oe2/userguide/html/Compound_Filtering.htm Compound Filtering] Delete this page - it's completely, utterly, and happily superseded by the new search interface. It might be worth keeping the last section (move to the main search doc), on search speed, because I think that's still relevant. -midori (Done --Nomi)
 
** [http://www.oboedit.org/oe2/userguide/html/Reusing_Filters.htm Reusing Filters] (ok -midori)
 
** [http://www.oboedit.org/oe2/userguide/html/Reusing_Filters.htm Reusing Filters] (ok -midori)
* [http://www.oboedit.org/oe2/userguide/html/Using_Filters.htm Using Filters] (empty, probably on purpose -midori)
 
 
** [http://www.oboedit.org/oe2/userguide/html/Searching.htm Searching] Out of date. Copy the last section (Saving Search Results to a File) over to the main search doc, then delete this page. -midori
 
** [http://www.oboedit.org/oe2/userguide/html/Searching.htm Searching] Out of date. Copy the last section (Saving Search Results to a File) over to the main search doc, then delete this page. -midori
 
** [http://www.oboedit.org/oe2/userguide/html/Filtering.htm Filtering] What does OE2 do about root picking algorithms (last section)? Rest of this page is out of date; I can update it, but need to know what to do with the root-picking bit. (midori)
 
** [http://www.oboedit.org/oe2/userguide/html/Filtering.htm Filtering] What does OE2 do about root picking algorithms (last section)? Rest of this page is out of date; I can update it, but need to know what to do with the root-picking bit. (midori)
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** [http://www.oboedit.org/oe2/userguide/html/Global_Filters___Renderers.htm Global Filters &amp; Renderers] (ok -midori)
 
** [http://www.oboedit.org/oe2/userguide/html/Global_Filters___Renderers.htm Global Filters &amp; Renderers] (ok -midori)
 
** [http://www.oboedit.org/oe2/userguide/html/Other_Uses_of_Filters.htm Other Uses of Filters] (ok -midori)
 
** [http://www.oboedit.org/oe2/userguide/html/Other_Uses_of_Filters.htm Other Uses of Filters] (ok -midori)
** [http://www.oboedit.org/oe2/userguide/html/Custom_Search_Buttons.htm Custom Search Buttons] It looks like this page is entirely out of date, because it depends on the old XML layout system. If so, delete it. -midori
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** [http://www.oboedit.org/oe2/userguide/html/Custom_Search_Buttons.htm Custom Search Buttons] It looks like this page is entirely out of date, because it depends on the old XML layout system. If so, delete it. -midori (Deleted --Nomi)
 
* [http://www.oboedit.org/oe2/userguide/html/Advanced_Searching.htm Advanced Searching] (Nomi made a few changes) Because this search interface supersedes so much of the OE1 search documentation, this page could be renamed just 'Searching', or it could become the new 'Building a Filter' page. In any case, "advanced" no longer makes sense. Anyway, it looks nearly done, but would benefit from a bit more explanation of  subqueries. I've added a couple of subheadings. Let me know if you want me to work on this any further. -midori
 
* [http://www.oboedit.org/oe2/userguide/html/Advanced_Searching.htm Advanced Searching] (Nomi made a few changes) Because this search interface supersedes so much of the OE1 search documentation, this page could be renamed just 'Searching', or it could become the new 'Building a Filter' page. In any case, "advanced" no longer makes sense. Anyway, it looks nearly done, but would benefit from a bit more explanation of  subqueries. I've added a couple of subheadings. Let me know if you want me to work on this any further. -midori
 
** [http://www.oboedit.org/oe2/userguide/html/HTML_Rendering.htm HTML Rendering] (Jen - done: requires one more screenshot once ancestor/descendant menu is added to global filter interface.) This page should go under Rendering. -midori
 
** [http://www.oboedit.org/oe2/userguide/html/HTML_Rendering.htm HTML Rendering] (Jen - done: requires one more screenshot once ancestor/descendant menu is added to global filter interface.) This page should go under Rendering. -midori
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Editing
 
Editing
 
* [http://www.oboedit.org/oe2/userguide/html/Undo_Redo.htm Undo/Redo] (ok)
 
* [http://www.oboedit.org/oe2/userguide/html/Undo_Redo.htm Undo/Redo] (ok)
* [http://www.oboedit.org/oe2/userguide/html/Text_Editing.htm Text Editing]
+
* [http://www.oboedit.org/oe2/userguide/html/Text_Editing.htm Text Editing] (would be nice to have bug fix for SF 2010579; otherwise ok -midori)
 
* [http://www.oboedit.org/oe2/userguide/html/Structural_Editing.htm Structural Editing] (Nomi - done (just this top-level page--not the pages in this section))
 
* [http://www.oboedit.org/oe2/userguide/html/Structural_Editing.htm Structural Editing] (Nomi - done (just this top-level page--not the pages in this section))
** [http://www.oboedit.org/oe2/userguide/html/The_Interface.htm The Interface]
+
** [http://www.oboedit.org/oe2/userguide/html/The_Interface.htm The Interface] (updated; now ok -midori)
** [http://www.oboedit.org/oe2/userguide/html/Adding_New_Terms.htm Adding New Terms]
+
** [http://www.oboedit.org/oe2/userguide/html/Adding_New_Terms.htm Adding New Terms] (ok -midori)
** [http://www.oboedit.org/oe2/userguide/html/Adding_New_Relationships.htm Adding New Relationships]
+
** [http://www.oboedit.org/oe2/userguide/html/Adding_New_Relationships.htm Adding New Relationships] (ok -midori)(maybe we should add how to create a new relation type here? or does this exist elsewhere? plus a warning about using standardized relations. I see that we have a note about why new relationship types don't show up -can also go in FAQs, but not how to add a new one.- melissa) (Adding a new relation type is essentially adding a new term, under 'relations' instead of 'classes'. I've added a bit saying so to this doc. -midori)
** [http://www.oboedit.org/oe2/userguide/html/Deleting.htm Deleting]
+
** [http://www.oboedit.org/oe2/userguide/html/Deleting.htm Deleting] (ok -midori)
** [http://www.oboedit.org/oe2/userguide/html/Destroying.htm Destroying]
+
** [http://www.oboedit.org/oe2/userguide/html/Destroying.htm Destroying] (ok -midori)
** [http://www.oboedit.org/oe2/userguide/html/Assigning_New_Roots.htm Rerooting]
+
** [http://www.oboedit.org/oe2/userguide/html/Assigning_New_Roots.htm Rerooting] (ok -midori)
** [http://www.oboedit.org/oe2/userguide/html/Cloning.htm Cloning]
+
** [http://www.oboedit.org/oe2/userguide/html/Cloning.htm Cloning] (updated -midori)
** [http://www.oboedit.org/oe2/userguide/html/Moving.htm Moving]
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** [http://www.oboedit.org/oe2/userguide/html/Moving.htm Moving] (updated -midori)
** [http://www.oboedit.org/oe2/userguide/html/Merging.htm Merging]
+
** [http://www.oboedit.org/oe2/userguide/html/Merging.htm Merging] (needs bug fix for merging with hotkey, then may need hotkey info update -midori)
** [http://www.oboedit.org/oe2/userguide/html/Changing_Relationship_Types.htm Changing Relationship Types]
+
** [http://www.oboedit.org/oe2/userguide/html/Changing_Relationship_Types.htm Changing Relationship Types] (ok -midori)
** [http://www.oboedit.org/oe2/userguide/html/Changing_Link_Attributes.htm Changing Link Attributes]
+
** [http://www.oboedit.org/oe2/userguide/html/Changing_Link_Attributes.htm Changing Link Attributes] (ok -midori)
 
** [http://www.oboedit.org/oe2/userguide/html/OBOMerge_User_Interface.htm Merging Ontology Files]
 
** [http://www.oboedit.org/oe2/userguide/html/OBOMerge_User_Interface.htm Merging Ontology Files]
* [http://www.oboedit.org/oe2/userguide/html/Graph_Editor.htm The Graph Editor] (Jen?)
+
* [http://www.oboedit.org/oe2/userguide/html/Graph_Editor.htm The Graph Editor] ('''Jen, can you update this page?''')
 
* [http://www.oboedit.org/oe2/userguide/html/Parent_Editor.htm The Parent Editor] (ok)
 
* [http://www.oboedit.org/oe2/userguide/html/Parent_Editor.htm The Parent Editor] (ok)
* [http://www.oboedit.org/oe2/userguide/html/Metadata.htm Organizing Your Ontology: Editing Metadata]
+
* [http://www.oboedit.org/oe2/userguide/html/Metadata.htm Organizing Your Ontology: Editing Metadata] (no Metadata.htm page in svn checkout ... -midori) (it's back! fixed a typo -midori)
** [http://www.oboedit.org/oe2/userguide/html/Working_with_Categories.htm Working with Categories]
+
** [http://www.oboedit.org/oe2/userguide/html/Working_with_Categories.htm Working with Categories] (ok -midori)
 
** Working with IDs
 
** Working with IDs
*** [http://www.oboedit.org/oe2/userguide/html/How_ID_Generation_Works.htm How ID Generation Works]
+
*** [http://www.oboedit.org/oe2/userguide/html/How_ID_Generation_Works.htm How ID Generation Works] (ok -midori)
*** [http://www.oboedit.org/oe2/userguide/html/The_ID_Manager_Plugin.htm The ID Manager]
+
*** [http://www.oboedit.org/oe2/userguide/html/The_ID_Manager_Plugin.htm The ID Manager] (ok -midori)
** [http://www.oboedit.org/oe2/userguide/html/Working_with_Namespaces.htm Working with Namespaces]
+
** [http://www.oboedit.org/oe2/userguide/html/Working_with_Namespaces.htm Working with Namespaces] (ok for now, but may need search link update after search/filter pages reorganized -midori)
** [http://www.oboedit.org/oe2/userguide/html/Working_with_Synonym_Categories.htm Working with Synonym Categories]
+
** [http://www.oboedit.org/oe2/userguide/html/Working_with_Synonym_Categories.htm Working with Synonym Categories] (same as namespaces -midori)
 
** Working with Obsoletes
 
** Working with Obsoletes
*** [http://www.oboedit.org/oe2/userguide/html/Editing_Obsoletes.htm Editing Obsoletes]
+
*** [http://www.oboedit.org/oe2/userguide/html/Editing_Obsoletes.htm Editing Obsoletes] (ok -midori)
*** [http://www.oboedit.org/oe2/userguide/html/Assigning_Replacement_Terms.htm Assigning Replacement Terms]
+
*** [http://www.oboedit.org/oe2/userguide/html/Assigning_Replacement_Terms.htm Assigning Replacement Terms] (ok -midori)
  
 
History (all ok)
 
History (all ok)
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Working with Data Adapters
 
Working with Data Adapters
* [http://www.oboedit.org/oe2/userguide/html/Introduction_to_Adapters.htm Introduction to Adapters]
+
* [http://www.oboedit.org/oe2/userguide/html/Introduction_to_Adapters.htm Introduction to Adapters] (ok -midori)
* [http://www.oboedit.org/oe2/userguide/html/Loading___Saving.htm Loading &amp; Saving]
+
* [http://www.oboedit.org/oe2/userguide/html/Loading___Saving.htm Loading &amp; Saving] (ok -midori)
* [http://www.oboedit.org/oe2/userguide/html/The_Basic_Flat_File_Interface.htm The Basic Flat File Interface]
+
* [http://www.oboedit.org/oe2/userguide/html/The_Basic_Flat_File_Interface.htm The Basic Flat File Interface] (ok -midori)
* [http://www.oboedit.org/oe2/userguide/html/The_OBO_Adapter.htm The OBO Adapter]
+
* [http://www.oboedit.org/oe2/userguide/html/The_OBO_Adapter.htm The OBO Adapter] (updated; filter links may need further update -midori)
* [http://www.oboedit.org/oe2/userguide/html/The_GO_Flat_File_Adapter.htm The GO Flat File Adapter]
+
* [http://www.oboedit.org/oe2/userguide/html/The_GO_Flat_File_Adapter.htm The GO Flat File Adapter] (ok -midori)
* [http://www.oboedit.org/oe2/userguide/html/The_Serial_Adapter.htm The Serial Adapter]
+
* [http://www.oboedit.org/oe2/userguide/html/The_Serial_Adapter.htm The Serial Adapter] (ok -midori)
* [http://www.oboedit.org/oe2/userguide/html/Custom_Data_Adapters.htm Custom Data Adapters]
+
* The OBO OWL Adapter '''(need new page)'''
 +
* The OWL URL Reader '''(need new page)'''
 +
* The GO Association File Adapter '''(need new page)'''
 +
* [http://www.oboedit.org/oe2/userguide/html/Custom_Data_Adapters.htm Custom Data Adapters] (ok once we add the pages needed for other adapters -midori)
  
 
The Reasoner (Amina)
 
The Reasoner (Amina)
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Ontology Verification
 
Ontology Verification
* [http://www.oboedit.org/oe2/userguide/html/Introduction_to_Verification.htm Introduction to Verification]
+
* [http://www.oboedit.org/oe2/userguide/html/Introduction_to_Verification.htm Introduction to Verification] (needs update to add during-text-edit option; I volunteer, but I'll wait for a decision on the label wording -midori)
* [http://www.oboedit.org/oe2/userguide/html/The_Verification_Plugin.htm The Verification Plugin]  
+
* [http://www.oboedit.org/oe2/userguide/html/The_Verification_Plugin.htm The Verification Plugin] (text ok; needs one more new screenshot -midori)
* [http://www.oboedit.org/oe2/userguide/html/Text_Checks.htm Text Checks]
+
* [http://www.oboedit.org/oe2/userguide/html/Text_Checks.htm Text Checks] (need info on "threaded checks", then will finish updating -midori)
* [http://www.oboedit.org/oe2/userguide/html/Definition_Check.htm Definition Check]
+
* [http://www.oboedit.org/oe2/userguide/html/Definition_Check.htm Definition Check] (ok -midori)
* [http://www.oboedit.org/oe2/userguide/html/Dangling_Intersection_Check.htm Dangling Intersection Check]
+
* [http://www.oboedit.org/oe2/userguide/html/Dangling_Intersection_Check.htm Dangling Intersection Check] (ok -midori)
* [http://www.oboedit.org/oe2/userguide/html/Dbxref_Check.htm Dbxref Check]
+
* [http://www.oboedit.org/oe2/userguide/html/Dbxref_Check.htm Dbxref Check] (ok -midori)
* [http://www.oboedit.org/oe2/userguide/html/Disjointedness_Check.htm Disjointedness Check]
+
* [http://www.oboedit.org/oe2/userguide/html/Disjointedness_Check.htm Disjointedness Check] (ok -midori)
* [http://www.oboedit.org/oe2/userguide/html/ISA_Cycle_Check.htm Cycle Check]
+
* [http://www.oboedit.org/oe2/userguide/html/ISA_Cycle_Check.htm Cycle Check] (ok -midori)
* [http://www.oboedit.org/oe2/userguide/html/Name_Redundancy_Check.htm Name Redundancy Check]
+
* [http://www.oboedit.org/oe2/userguide/html/Name_Redundancy_Check.htm Name Redundancy Check] (updated; now ok -midori)
* [http://www.oboedit.org/oe2/userguide/html/User_Defined_Checks.htm User Defined Checks]
+
* [http://www.oboedit.org/oe2/userguide/html/User_Defined_Checks.htm User Defined Checks] (new screenshots; ok -midori)
  
 
Cross Products (Karen Eilbeck)
 
Cross Products (Karen Eilbeck)
* [http://www.oboedit.org/oe2/userguide/html/Introduction_to_Cross_Products.htm Introduction to Cross Products]
+
* [http://www.oboedit.org/oe2/userguide/html/Introduction_to_Cross_Products.htm Introduction to Cross Products] (Karen--done)
* [http://www.oboedit.org/oe2/userguide/html/Cross_Products_in_the_Text_Editor.htm Cross Products in the Text Editor]
+
* [http://www.oboedit.org/oe2/userguide/html/Cross_Products_in_the_Text_Editor.htm Cross Products in the Text Editor] (Karen--done)
* [http://www.oboedit.org/oe2/userguide/html/Cross_Products_By_Hand.htm Cross Products By Hand]
+
* [http://www.oboedit.org/oe2/userguide/html/Cross_Product_Info_tab.htm Cross Product Info Tab] (Karen--done)
 +
* [http://www.oboedit.org/oe2/userguide/html/Cross_Product_Matrix_Editor.htm Cross Product Matrix Editor] (Needs text--no one's quite sure what it's supposed to do)
 +
* [http://www.oboedit.org/oe2/userguide/html/Intersection_Editor.htm Intersection Editor] (Karen--done)
  
 
Expressions
 
Expressions
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* [http://www.oboedit.org/oe2/userguide/html/Java_Options_on_the_Command_line.htm Java Options on the Command-line]
 
* [http://www.oboedit.org/oe2/userguide/html/Java_Options_on_the_Command_line.htm Java Options on the Command-line]
  
[http://www.oboedit.org/oe2/userguide/html/Frequently_Asked_Questions.htm Frequently Asked Questions]
+
Frequently Asked Questions
 
* [http://www.oboedit.org/oe2/userguide/html/How_Do_I_Make_a__Slim__Ontology_.htm How Do I Make a 'Slim' Ontology?]
 
* [http://www.oboedit.org/oe2/userguide/html/How_Do_I_Make_a__Slim__Ontology_.htm How Do I Make a 'Slim' Ontology?]
** [http://www.oboedit.org/oe2/userguide/html/Creating_Your_Own_GO_Slim_in_OBO_Edit.htm Creating Your Own GO Slim in OBO-Edit]
+
** [http://www.oboedit.org/oe2/userguide/html/Creating_Your_Own_GO_Slim_in_OBO_Edit.htm Creating Your Own GO Slim in OBO-Edit] (minor updates; filter links may also need updating after search/filter reorg -midori)
* [http://www.oboedit.org/oe2/userguide/html/How_Do_I_Find_Terms_Without_an_is_a_Parent_.htm How Do I Find Terms Without an is_a Parent?]
+
* [http://www.oboedit.org/oe2/userguide/html/How_Do_I_Find_Terms_Without_an_is_a_Parent_.htm How Do I Find Terms Without an is_a Parent?] (updated -midori)
* [http://www.oboedit.org/oe2/userguide/html/How_Do_I_Spell_Check_.htm How Do I Spell Check?]
+
* [http://www.oboedit.org/oe2/userguide/html/How_Do_I_Spell_Check_.htm How Do I Spell Check?] (what is the current status of spell check? I know it's been disabled, but was there any plan to bring it back? No pressure; just useful to know for the docs -midori) (Not sure what you mean--it automatically does spell checking of the definition and name during the Verification Checks.  What else do you want to spell-check?  --Nomi) (I think I got confused because of the problem from a while back, where some spell checking thing was really slowing down load or save ... anyway, I can do this document based on current OE2 behavior and stop fretting. -midori)
* [http://www.oboedit.org/oe2/userguide/html/How_Do_I_Not_Search_Obsoletes_.htm How Do I Not Search Obsoletes?]
+
* [http://www.oboedit.org/oe2/userguide/html/How_Do_I_Not_Search_Obsoletes_.htm How Do I Not Search Obsoletes?] (midori; done)

Latest revision as of 12:25, 30 June 2014

NOTE: This page is obsolete. Please visit OBO-Edit:_Help_document_OBO-Edit_2 instead.


The OBO-Edit Working Group has agreed to devote the week of June 30th, 2008, to testing OBO-Edit2 and writing user documentation. We appreciate your help!

Please let everyone know what you're concentrating on in your testing, and which help pages you're working on, so we don't duplicate each others' work. You can enter this information below.

Help pages

Below is the table of contents listing the current OBO-Edit2 help pages. If you are working on a page or section, please put your name after it, and commit your changes to svn (or send them to Nomi) as soon as you're done. If you've checked a page and it's up-to-date, please put "(ok)" after it. If you think we should add a new help page (or delete an existing one) please tell Nomi.

Midori has done a draft of a reorganized table of contents. Please comment!

Please note: the user guide pages linked here are not updated automatically--they are updated manually by Nomi. If you want to see your recent changes reflected here, please ask Nomi to update these pages.

OBO-Edit User's Guide (intro)

Viewing Ontologies

Filtering, Rendering & Searching

  • (midori: why don't you go ahead and reorganize these pages however you like. I trust your judgment. --Nomi) (Done! In fact, search docs pretty much done except for rendering. -midori)
  • Filters (Jen - ok)
  • Link Filters vs Term Filters (Jen - ok)(could be rolled into above section, both are small-melissa) (Done. --Nomi)
  • Building Filters (Not empty--was wrong page. Needs updating) This page is hopelessly out of date; the Attribute, Comparison, and Aspect sections should be folded into the Advanced Search (or just "Search") page; then this page should be deleted. I've changed my mind about this page; I'm now keeping it and using it as an overview of search parameters. -midori
    • Setting the Filter Mode (Jen - This page deleted) It still shows up in my svn checkout, but deleting it is the right thing to do. -midori (Oh, I see, it was deleted from svn but still on the wiki. Now it's gone. --Nomi)
    • Term Filters (Jen - part done - This documentation derails here because the filter button has not yet been added back and the ancestor/descendant menu has not been added back. I think it would make more sense to wait until this is complete to write the docs as screenshots will all soon be obsolete.) Actually, we could just lose this page. A lot of it duplicates the Building a Filter page, and both are superseded by the new search interface. -midori
    • Link Filters This could either be incorporated into Advanced Searching or kept separate; if we keep it separate, the screenshot and a few lines of text have to be updated. Let me know if you want me to do either. -midori
    • Compound Filtering Delete this page - it's completely, utterly, and happily superseded by the new search interface. It might be worth keeping the last section (move to the main search doc), on search speed, because I think that's still relevant. -midori (Done --Nomi)
    • Reusing Filters (ok -midori)
    • Searching Out of date. Copy the last section (Saving Search Results to a File) over to the main search doc, then delete this page. -midori
    • Filtering What does OE2 do about root picking algorithms (last section)? Rest of this page is out of date; I can update it, but need to know what to do with the root-picking bit. (midori)
    • Rendering Partially out of date; need decision about "render button" feature (SF 1958908) to update. -midori
    • Global Filters & Renderers (ok -midori)
    • Other Uses of Filters (ok -midori)
    • Custom Search Buttons It looks like this page is entirely out of date, because it depends on the old XML layout system. If so, delete it. -midori (Deleted --Nomi)
  • Advanced Searching (Nomi made a few changes) Because this search interface supersedes so much of the OE1 search documentation, this page could be renamed just 'Searching', or it could become the new 'Building a Filter' page. In any case, "advanced" no longer makes sense. Anyway, it looks nearly done, but would benefit from a bit more explanation of subqueries. I've added a couple of subheadings. Let me know if you want me to work on this any further. -midori
    • HTML Rendering (Jen - done: requires one more screenshot once ancestor/descendant menu is added to global filter interface.) This page should go under Rendering. -midori
    • Term Image Display Panel (Nomi - done) (Does this really belong under "Advanced Searching"? Is there a better place for it?) Hi Nomi, I wondered if it might make sense to have categories that mirror the categories under which the many components are grouped in the OBO-Edit menus. So, for example, Term Image Display Panel would be under the heading 'Viewers'. Does that seem good? (Jen) I think this should move to the "Tools" menu; it's neither an ontology viewer nor a search. (midori)

Editing

History (all ok)

Working with Data Adapters

The Reasoner (Amina)

Ontology Verification

Cross Products (Karen Eilbeck)

Expressions

Plugins

The Command Line

Frequently Asked Questions

  • How Do I Make a 'Slim' Ontology?
  • How Do I Find Terms Without an is_a Parent? (updated -midori)
  • How Do I Spell Check? (what is the current status of spell check? I know it's been disabled, but was there any plan to bring it back? No pressure; just useful to know for the docs -midori) (Not sure what you mean--it automatically does spell checking of the definition and name during the Verification Checks. What else do you want to spell-check? --Nomi) (I think I got confused because of the problem from a while back, where some spell checking thing was really slowing down load or save ... anyway, I can do this document based on current OE2 behavior and stop fretting. -midori)
  • How Do I Not Search Obsoletes? (midori; done)