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 (ok)(URLS updated -midori)
- Getting OBO-Edit Started (ok)
- Bugs and Troubleshooting (Nomi - done) Do we want to use "beta" in the config directory example path? For the release, I'd think not. -midori
- Slowness (Nomi - done)
Viewing Ontologies
- Working with Selections (Jen has done half, now handed over to Melissa)
- Perspectives (updated by Nomi)
- Components (Nomi)
- Configuration Manager (Nomi)
- The Ontology Tree Editor (Midori - text OK; must update screenshots)
- The Tree Viewer (melissa?)
- The Graph Viewer (Jen - done)
- Table of Contents Component (ok)
- The Extended Info Component (ok)
- Configurable Message (Nomi - done)
Filtering, Rendering & Searching (Jen)
- Filters (Jen - ok)
- Link Filters vs Term Filters (Jen - ok)
- Building Filters (Not empty--was wrong page. Needs updating)
- Setting the Filter Mode (Jen - This page deleted)
- Term Filters (Jen - part done - This documentation derails here because the filter button has not yet been added back and the ancestor/descendant menu has not been added back. I think it would make more sense to wait until this is complete to write the docs as screenshots will all soon be obsolete.)
- Link Filters
- Compound Filtering
- Reusing Filters
- Using Filters
- Advanced Searching (Nomi made a few changes)
- HTML Rendering (Jen - done: requires one more screenshot once ancestor/descendant menu is added to global filter interface.)
- Term Image Display Panel (Nomi - done) (Does this really belong under "Advanced Searching"? Is there a better place for it?) Hi Nomi, I wondered if it might make sense to have categories that mirror the categories under which the many components are grouped in the OBO-Edit menus. So, for example, Term Image Display Panel would be under the heading 'Viewers'. Does that seem good? Jen
Editing
- Undo/Redo (ok)
- Text Editing
- Structural Editing (Nomi - done (just this top-level page--not the pages in this section))
- The Graph Editor (Jen?)
- The Parent Editor (ok)
- 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 Manager
- 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 (Jen - fixed: relative links work in Eclipse, though not in wiki.)
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