OBO-Edit: Documentation Week
The OBO-Edit Working Group has agreed to devote the week of June 30th, 2008, to testing OBO-Edit2 and writing user documentation. We appreciate your help!
Please let everyone know what you're concentrating on in your testing, and which help pages you're working on, so we don't duplicate each others' work. You can enter this information below.
Help pages
Below is the table of contents listing the current OBO-Edit2 help pages. If you are working on a page or section, please put your name after it, and commit your changes to svn (or send them to Nomi) as soon as you're done. If you've checked a page and it's up-to-date, please put "(ok)" after it. If you think we should add a new help page (or delete an existing one) please tell Nomi.
Please note: the user guide pages linked here are not updated automatically--they are updated manually by Nomi. If you want to see your recent changes reflected here, please ask Nomi to update these pages.
OBO-Edit User's Guide (intro)
- What is OBO-Edit? (ok)
- What is an ontology? (ok)
- Basic Concepts and Vocabulary (ok)
- An Introduction to OBO Ontologies
- Getting OBO-Edit Started (ok)
- Bugs and Troubleshooting
- Slowness
Viewing Ontologies
- Working with Selections (Jen working on this)
- Perspectives
- Components
Filtering, Rendering & Searching (Jen)
Editing
- Undo/Redo
- Text Editing
- Structural Editing
- The Graph Editor
- The Parent Plugin
- Organizing Your Ontology: Editing Metadata
- Working with Categories
- Working with IDs
- Working with Namespaces
- Working with Synonym Categories
- Working with Obsoletes
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
The Reasoner (Amina)
- The OBO-Edit Reasoner
- The Reasoner and the Interface
- The Reasoner Plugin
- The Explanation Plugin
- Reasoner Prefilters
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 (Karen Eilbeck)
Expressions
- Introduction to Expressions
- Expression Syntax
- Language Concepts
- OBO-Edit-Specific Variables
- Backtick Expressions
- Example Scripts
Plugins
- Introduction to Plugins (Jen - done)
- The GraphViz Plugin (Jen - brought up to date) (This should now be grouped with components)
- The Dbxref Library Plugin(This should now be grouped with components)
The Command Line