Contents

OBO-Edit User's Guide What is OBO-Edit? What is an ontology? Basic Concepts and Vocabulary An Introduction to OBO Ontologies Getting OBO-Edit Started Bugs and Troubleshooting

Viewing Ontologies The Ontology Editor Panel Working with Selections

Filtering, Rendering & Searching Filters Link Filters vs Term Filters Building Filters Setting the Filter Mode Term Filters Link Filters Compound Filtering Reusing Filters Using Filters Searching Filtering Rendering Global Filters & Renderers Other Uses of Filters

Editing 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 Organizing Your Ontology Working with Namespaces Working with Categories Working with Synonym Categories The Parent Plugin Working with Obsoletes Editing Obsoletes Assigning Replacement Terms

History How OBO-Edit Understands Histories The History Plugin Saving a History File Loading a History File The Change Tracker Plugin

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

Working with IDs How ID Generation Works The ID Manager Plugin

The Reasoner The OBO-Edit Reasoner The Reasoner and the Interface The Reasoner Plugin The Explanation Plugin Reasoner Prefilters

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

Customizing OBO-Edit The Configuration Plugin Customizing the Interface Working with XML Layouts Common Parameters The <glue> Tag The <spacer> Tag The <label> Tag The <box> Tag The <grid> Tag The <panel> Tag The <compactgrid> Tag The <divider> Tag The <tabs> Tag The <window> Tag The <if> Tag The <component> Tag Example Layouts The Default Layout

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

Plugins Introduction to Plugins The DAG Viewer The Extended Info Plugin The Graph Viewer Plugin The Dbxref Library Plugin

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

How To Creating Your Own GO Slim in OBO-Edit

Frequently Asked Questions How Do I Make a %22Slim%22 Ontology? How Do I Find Terms Without an is_a Parent? How Do I Spell Check? How Do I Search a Specific Ontology? How Do I Not Search Obsoletes?