New OE user guide TOC: Difference between revisions
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[[Category:OBO-Edit]] | |||
==Proposed OE2 User Guide Organization== | ==Proposed OE2 User Guide Organization== | ||
'''New version committed in svn July 21:''' | |||
OBO-Edit User's Guide (intro) | OBO-Edit User's Guide (intro) | ||
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** [http://www.oboedit.org/oe2/userguide/html/Components.htm Components] | ** [http://www.oboedit.org/oe2/userguide/html/Components.htm Components] | ||
** [http://www.oboedit.org/oe2/userguide/html/Perspectives.htm Perspectives] | ** [http://www.oboedit.org/oe2/userguide/html/Perspectives.htm Perspectives] | ||
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/Loading___Saving.htm Loading & Saving](perhaps this section can be split, and the loading part put up above at the beginning of viewing ontologies -melissa) (moved the whole adapters section instead because the load/save doc didn't really seem easily splittable -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_OBO_Adapter.htm The OBO Adapter] | |||
* [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_Serial_Adapter.htm The Serial Adapter] | |||
* [http://www.oboedit.org/oe2/userguide/html/The_OBO_OWL_Adapter.htm The OBO OWL Adapter] (empty new page in svn) | |||
* [http://www.oboedit.org/oe2/userguide/html/The_OWL_URL_Reader.htm The OWL URL Reader](empty new page in svn) | |||
* [http://www.oboedit.org/oe2/userguide/html/The_GO_Association_File_Adapter.htm The GO Association File Adapter] (empty new page in svn) | |||
* [http://www.oboedit.org/oe2/userguide/html/Custom_Data_Adapters.htm Custom Data Adapters] | |||
Viewing Ontologies | Viewing Ontologies | ||
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Editing | Editing | ||
:(Would it be too redundant to list the Ontology Tree Editor page again in the Editing section? --Nomi) (maybe a little, but probably outweighed by advantage of seeing it where it might be expected -midori)(I like the idea of having it here too- melissa) (done -midori) | |||
* [http://www.oboedit.org/oe2/userguide/html/Undo_Redo.htm Undo/Redo] | *Interfaces | ||
* [http://www.oboedit.org/oe2/userguide/html/Text_Editing.htm Text Editing] | **[http://www.oboedit.org/oe2/userguide/html/The_Term_Editor_Panel.htm The Ontology Tree Editor] | ||
* [http://www.oboedit.org/oe2/userguide/html/Structural_Editing.htm Structural Editing] | ** [http://www.oboedit.org/oe2/userguide/html/Graph_Editor.htm The Graph Editor] | ||
** [http://www.oboedit.org/oe2/userguide/html/The_Interface.htm The Interface] | ** [http://www.oboedit.org/oe2/userguide/html/Parent_Editor.htm The Parent Editor] | ||
** [http://www.oboedit.org/oe2/userguide/html/Adding_New_Terms.htm Adding New Terms] | *Operations | ||
** [http://www.oboedit.org/oe2/userguide/html/Adding_New_Relationships.htm Adding New Relationships] | ** [http://www.oboedit.org/oe2/userguide/html/Undo_Redo.htm Undo/Redo] | ||
** [http://www.oboedit.org/oe2/userguide/html/Deleting.htm Deleting] | ** [http://www.oboedit.org/oe2/userguide/html/Text_Editing.htm Text Editing] | ||
** [http://www.oboedit.org/oe2/userguide/html/Destroying.htm Destroying] | ** [http://www.oboedit.org/oe2/userguide/html/Structural_Editing.htm Structural Editing in the Ontology Tree Editor] | ||
** [http://www.oboedit.org/oe2/userguide/html/Assigning_New_Roots.htm Rerooting] | *** [http://www.oboedit.org/oe2/userguide/html/The_Interface.htm The Interface] | ||
** [http://www.oboedit.org/oe2/userguide/html/Cloning.htm Cloning] | *** [http://www.oboedit.org/oe2/userguide/html/Adding_New_Terms.htm Adding New Terms] | ||
** [http://www.oboedit.org/oe2/userguide/html/Moving.htm Moving] | *** [http://www.oboedit.org/oe2/userguide/html/Adding_New_Relationships.htm Adding New Relationships] | ||
** [http://www.oboedit.org/oe2/userguide/html/Merging.htm Merging] | *** [http://www.oboedit.org/oe2/userguide/html/Deleting.htm Deleting] | ||
** [http://www.oboedit.org/oe2/userguide/html/Changing_Relationship_Types.htm Changing Relationship Types] | *** [http://www.oboedit.org/oe2/userguide/html/Destroying.htm Destroying] | ||
** [http://www.oboedit.org/oe2/userguide/html/Changing_Link_Attributes.htm Changing Link Attributes] | *** [http://www.oboedit.org/oe2/userguide/html/Assigning_New_Roots.htm Rerooting] | ||
* | *** [http://www.oboedit.org/oe2/userguide/html/Cloning.htm Cloning] | ||
* [http://www.oboedit.org/oe2/userguide/html/ | *** [http://www.oboedit.org/oe2/userguide/html/Moving.htm Moving] | ||
* | *** [http://www.oboedit.org/oe2/userguide/html/Merging.htm Merging] | ||
* [http://www.oboedit.org/oe2/userguide/html/OBOMerge_User_Interface.htm Merging Ontology Files] | *** [http://www.oboedit.org/oe2/userguide/html/Changing_Relationship_Types.htm Changing Relationship Types] | ||
*** [http://www.oboedit.org/oe2/userguide/html/Changing_Link_Attributes.htm Changing Link Attributes] | |||
** [http://www.oboedit.org/oe2/userguide/html/Importing_Terms.htm Importing Terms] (empty new page in svn) | |||
** [http://www.oboedit.org/oe2/userguide/html/OBOMerge_User_Interface.htm Merging Ontology Files] | |||
[http://www.oboedit.org/oe2/userguide/html/Metadata.htm Organizing Your Ontology: Editing Metadata] (I would make this a separate section, since the Editing section is already so long) (fine by me -midori)(yes, and its really a different topic too. maybe this section should come before the editing section, since its the sort of thing you set up before you edit -melissa) (done -midori) | |||
** | * [http://www.oboedit.org/oe2/userguide/html/Working_with_Categories.htm Working with Categories] | ||
* 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/The_ID_Manager_Plugin.htm The ID Manager] | |||
** [http://www.oboedit.org/oe2/userguide/html/The_ID_Fixer.htm The ID Fixer] (empty new page) | |||
* [http://www.oboedit.org/oe2/userguide/html/Working_with_Namespaces.htm Working with Namespaces] | |||
* [http://www.oboedit.org/oe2/userguide/html/Working_with_Synonym_Categories.htm Working with Synonym Categories] | |||
* Working with Obsoletes | |||
** [http://www.oboedit.org/oe2/userguide/html/Editing_Obsoletes.htm Editing Obsoletes] | |||
** [http://www.oboedit.org/oe2/userguide/html/Assigning_Replacement_Terms.htm Assigning Replacement Terms] | |||
* [http://www.oboedit.org/oe2/userguide/html/The_Dbxref_Library_Plugin.htm The Dbxref Library] | |||
History | History | ||
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* [http://www.oboedit.org/oe2/userguide/html/Loading_a_History_File.htm Loading a History File] | * [http://www.oboedit.org/oe2/userguide/html/Loading_a_History_File.htm Loading a History File] | ||
* [http://www.oboedit.org/oe2/userguide/html/The_Change_Tracker_Plugin.htm The Ontology Change Tracker] | * [http://www.oboedit.org/oe2/userguide/html/The_Change_Tracker_Plugin.htm The Ontology Change Tracker] | ||
The Reasoner | The Reasoner | ||
| Line 90: | Line 97: | ||
* [http://www.oboedit.org/oe2/userguide/html/The_Reasoner_and_the_Interface.htm The Reasoner and the Interface] | * [http://www.oboedit.org/oe2/userguide/html/The_Reasoner_and_the_Interface.htm The Reasoner and the Interface] | ||
* [http://www.oboedit.org/oe2/userguide/html/The_Reasoner_Manager.htm The Reasoner Manager] | * [http://www.oboedit.org/oe2/userguide/html/The_Reasoner_Manager.htm The Reasoner Manager] | ||
* [http://www.oboedit.org/oe2/userguide/html/The_Explanation_Plugin.htm | * [http://www.oboedit.org/oe2/userguide/html/The_Explanation_Plugin.htm Showing Explanations] | ||
* [http://www.oboedit.org/oe2/userguide/html/Reasoner_Prefilters.htm Reasoner Prefilters] | * [http://www.oboedit.org/oe2/userguide/html/Reasoner_Prefilters.htm Reasoner Prefilters] | ||
* The Semantic Parser Manager | * [http://www.oboedit.org/oe2/userguide/html/Semantic_Parser_Manager.htm The Semantic Parser Manager] (empty new page) | ||
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] | ||
* [http://www.oboedit.org/oe2/userguide/html/The_Verification_Plugin.htm The Verification | * [http://www.oboedit.org/oe2/userguide/html/The_Verification_Plugin.htm The Verification Manager] | ||
* [http://www.oboedit.org/oe2/userguide/html/Text_Checks.htm Text Checks] | * [http://www.oboedit.org/oe2/userguide/html/Text_Checks.htm Text Checks] | ||
* [http://www.oboedit.org/oe2/userguide/html/Definition_Check.htm Definition Check] | * [http://www.oboedit.org/oe2/userguide/html/Definition_Check.htm Definition Check] | ||
| Line 109: | Line 116: | ||
* [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] | ||
* [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] | ||
* [http://www.oboedit.org/oe2/userguide/html/ | * [http://www.oboedit.org/oe2/userguide/html/Cross_Product_Info_.htm Cross Product Info Panel] | ||
* [http://www.oboedit.org/oe2/userguide/html/Cross_Product_Matrix_Editor.htm Cross Product Matrix Editor] | |||
* [http://www.oboedit.org/oe2/userguide/html/Intersection_Editor Intersection_Editor] | |||
Expressions | Expressions | ||
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* [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?] | ||
---- | |||
back to [[OBO-Edit:_Documentation_Week]] | back to [[OBO-Edit:_Documentation_Week]] | ||
[[OBO-Edit:_Adding_to_the_OBO-Edit_help_guide]] | |||
Latest revision as of 16:19, 30 June 2014
Proposed OE2 User Guide Organization
New version committed in svn July 21:
OBO-Edit User's Guide (intro)
- What is OBO-Edit?
- What is an ontology?
- Basic Concepts and Vocabulary
- An Introduction to OBO Ontologies
- Getting OBO-Edit Started
- Bugs and Troubleshooting
- Slowness
Configuring OBO-Edit
- Configuration Manager
- OBO-Edit Layout
Working with Data Adapters
- Introduction to Adapters
- Loading & Saving(perhaps this section can be split, and the loading part put up above at the beginning of viewing ontologies -melissa) (moved the whole adapters section instead because the load/save doc didn't really seem easily splittable -midori)
- The Basic Flat File Interface
- The OBO Adapter
- The GO Flat File Adapter
- The Serial Adapter
- The OBO OWL Adapter (empty new page in svn)
- The OWL URL Reader(empty new page in svn)
- The GO Association File Adapter (empty new page in svn)
- Custom Data Adapters
Viewing Ontologies
- Working with Selections
- The Ontology Tree Editor
- The Tree Viewer
- The Graph Viewer
- The GraphViz Viewer
Searching, Filtering & Rendering
- Filters
- Link Filters vs Term Filters
- The Search Interface (use the page now called Advanced Searching)
- Filtering
- Rendering
- Reusing Filters
- Global Filters & Renderers
- Other Uses of Filters
Editing
- (Would it be too redundant to list the Ontology Tree Editor page again in the Editing section? --Nomi) (maybe a little, but probably outweighed by advantage of seeing it where it might be expected -midori)(I like the idea of having it here too- melissa) (done -midori)
- Interfaces
- Operations
Organizing Your Ontology: Editing Metadata (I would make this a separate section, since the Editing section is already so long) (fine by me -midori)(yes, and its really a different topic too. maybe this section should come before the editing section, since its the sort of thing you set up before you edit -melissa) (done -midori)
- Working with Categories
- Working with IDs
- How ID Generation Works
- The ID Manager
- The ID Fixer (empty new page)
- Working with Namespaces
- Working with Synonym Categories
- Working with Obsoletes
- The Dbxref Library
History
- How OBO-Edit Understands Histories
- The History Browser
- Saving a History File
- Loading a History File
- The Ontology Change Tracker
The Reasoner
- The OBO-Edit Reasoner
- The Reasoner and the Interface
- The Reasoner Manager
- Showing Explanations
- Reasoner Prefilters
- The Semantic Parser Manager (empty new page)
Ontology Verification
- Introduction to Verification
- The Verification Manager
- Text Checks
- Definition Check
- Dangling Intersection Check
- Dbxref Check
- Disjointedness Check
- Cycle Check
- Name Redundancy Check
- User-Defined Checks
Cross Products
- Introduction to Cross Products
- Cross Products in the Text Editor
- Cross Product Info Panel
- Cross Product Matrix Editor
- Intersection_Editor
Expressions
- Introduction to Expressions
- Expression Syntax
- Language Concepts
- OBO-Edit-Specific Variables
- Backtick Expressions
- Example Scripts
Tools and Plugins
The Command Line
- How Do I Make a 'Slim' Ontology?
- How Do I Find Terms Without an is_a Parent?
- How Do I Spell Check?
- How Do I Not Search Obsoletes?
back to OBO-Edit:_Documentation_Week