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== | ||
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*** [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] | ||
*** [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] | ||
** [http://www.oboedit.org/oe2/userguide/html/Importing_Terms.htm Importing Terms] (empty new page) | ** [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/OBOMerge_User_Interface.htm Merging Ontology Files] | ||
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** [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] | ||
** [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] | ||
** [http://www.oboedit.org/oe2/userguide/html/The_ID_Fixer.htm The ID Fixer | ** [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_Namespaces.htm Working with Namespaces] | ||
* [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] | ||
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