New OE user guide TOC: Difference between revisions
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* [http://www.oboedit.org/oe2/userguide/html/Parent_Editor.htm The Parent Editor] | * [http://www.oboedit.org/oe2/userguide/html/Parent_Editor.htm The Parent Editor] | ||
* [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/Metadata.htm Organizing Your Ontology: Editing Metadata] | * [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) | ||
** [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] | ||
** Working with IDs | ** Working with IDs | ||
Revision as of 14:43, 3 July 2008
Proposed OE2 User Guide Organization
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 (Nomi - done)
Configuring OBO-Edit
- Configuration Manager
- OBO-Edit Layout
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)
- Undo/Redo
- Text Editing
- Structural Editing
- The Interface
- Adding New Terms
- Adding New Relationships
- Deleting
- Destroying
- Rerooting
- Cloning
- Moving
- Merging
- Changing Relationship Types
- Changing Link Attributes
- Importing Terms (need new page)
- The Graph Editor
- The Parent Editor
- Merging Ontology Files
- Organizing Your Ontology: Editing Metadata (I would make this a separate section, since the Editing section is already so long)
- Working with Categories
- Working with IDs
- How ID Generation Works
- The ID Manager
- The ID Fixer (need 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
Working with Data Adapters
- Introduction to Adapters
- Loading & Saving
- The Basic Flat File Interface
- The OBO Adapter
- The GO Flat File Adapter
- The Serial Adapter
- Custom Data Adapters
The Reasoner
- The OBO-Edit Reasoner
- The Reasoner and the Interface
- The Reasoner Manager
- The Explanation Plugin
- Reasoner Prefilters
- The Semantic Parser Manager (need new page)
Ontology Verification
- Introduction to Verification
- The Verification Plugin
- Text Checks
- Definition Check
- Dangling Intersection Check
- Dbxref Check
- Disjointedness Check
- Cycle Check
- Name Redundancy Check
- User-Defined Checks
Cross Products
Expressions
- Introduction to Expressions
- Expression Syntax
- Language Concepts
- OBO-Edit-Specific Variables
- Backtick Expressions
- Example Scripts
Tools and Plugins
The Command Line