New OE user guide TOC

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

Configuring OBO-Edit

• Configuration Manager
• OBO-Edit Layout
  • Components
  • Perspectives

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
  • HTML 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)
• 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) (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)
  • 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
    • Editing Obsoletes
    • Assigning Replacement Terms
  • 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(perhaps this section can be split, and the loading part put up above at the beginning of viewing ontologies -melissa)
• The Basic Flat File Interface
• The OBO Adapter
• The GO Flat File Adapter
• The Serial Adapter
• The OBO OWL Adapter (need new page)
• The OWL URL Reader (need new page)
• The GO Association File Adapter (need new page)
• 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

• Introduction to Cross Products
• Cross Products in the Text Editor
• Cross Products By Hand

Expressions

• Introduction to Expressions
• Expression Syntax
• Language Concepts
• OBO-Edit-Specific Variables
• Backtick Expressions
• Example Scripts

Tools and Plugins

• Table of Contents
• Extended Info
• Configurable Message
• Term Image Display Panel
• Plugins

The Command Line

• OBO-Edit Command-line Options
• obodiff
• obomerge
• obo2flat
• obo2obo
• Java Options on the Command-line

Frequently Asked Questions

• How Do I Make a 'Slim' Ontology?
  • Creating Your Own GO Slim in OBO-Edit
• How Do I Find Terms Without an is_a Parent?
• How Do I Spell Check?
• How Do I Not Search Obsoletes?

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