OBO-Edit: Documentation Week: Difference between revisions
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* [http://www.oboedit.org/oe2/userguide/html/Loading_a_History_File.htm Loading a History File] | * [http://www.oboedit.org/oe2/userguide/html/Loading_a_History_File.htm Loading a History File] | ||
* [http://www.oboedit.org/oe2/userguide/html/The_Change_Tracker_Plugin.htm The Change Tracker Plugin] | * [http://www.oboedit.org/oe2/userguide/html/The_Change_Tracker_Plugin.htm The Change Tracker Plugin] | ||
Working with Data Adapters | |||
* [http://www.oboedit.org/oe2/userguide/html/Introduction_to_Adapters.htm Introduction to Adapters] | * [http://www.oboedit.org/oe2/userguide/html/Introduction_to_Adapters.htm Introduction to Adapters] | ||
* [http://www.oboedit.org/oe2/userguide/html/Loading___Saving.htm Loading & Saving] | * [http://www.oboedit.org/oe2/userguide/html/Loading___Saving.htm Loading & Saving] | ||
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* [http://www.oboedit.org/oe2/userguide/html/The_Serial_Adapter.htm The Serial Adapter] | * [http://www.oboedit.org/oe2/userguide/html/The_Serial_Adapter.htm The Serial Adapter] | ||
* [http://www.oboedit.org/oe2/userguide/html/Custom_Data_Adapters.htm Custom Data Adapters] | * [http://www.oboedit.org/oe2/userguide/html/Custom_Data_Adapters.htm Custom Data Adapters] | ||
The Reasoner | |||
* [http://www.oboedit.org/oe2/userguide/html/The_OBO_Edit_Reasoner.htm The OBO-Edit Reasoner] | * [http://www.oboedit.org/oe2/userguide/html/The_OBO_Edit_Reasoner.htm The OBO-Edit Reasoner] | ||
* [http://www.oboedit.org/oe2/userguide/html/The_Reasoner_and_the_Interface.htm The Reasoner and the Interface] | * [http://www.oboedit.org/oe2/userguide/html/The_Reasoner_and_the_Interface.htm The Reasoner and the Interface] | ||
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* [http://www.oboedit.org/oe2/userguide/html/The_Explanation_Plugin.htm The Explanation Plugin] | * [http://www.oboedit.org/oe2/userguide/html/The_Explanation_Plugin.htm The Explanation Plugin] | ||
* [http://www.oboedit.org/oe2/userguide/html/Reasoner_Prefilters.htm Reasoner Prefilters] | * [http://www.oboedit.org/oe2/userguide/html/Reasoner_Prefilters.htm Reasoner Prefilters] | ||
Ontology Verification | |||
* [http://www.oboedit.org/oe2/userguide/html/Introduction_to_Verification.htm Introduction to Verification] | * [http://www.oboedit.org/oe2/userguide/html/Introduction_to_Verification.htm Introduction to Verification] | ||
* [http://www.oboedit.org/oe2/userguide/html/The_Verification_Plugin.htm The Verification Plugin] | * [http://www.oboedit.org/oe2/userguide/html/The_Verification_Plugin.htm The Verification Plugin] | ||
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* [http://www.oboedit.org/oe2/userguide/html/Name_Redundancy_Check.htm Name Redundancy Check] | * [http://www.oboedit.org/oe2/userguide/html/Name_Redundancy_Check.htm Name Redundancy Check] | ||
* [http://www.oboedit.org/oe2/userguide/html/User_Defined_Checks.htm User Defined Checks] | * [http://www.oboedit.org/oe2/userguide/html/User_Defined_Checks.htm User Defined Checks] | ||
Cross Products (Karen Eilbeck) | |||
* [http://www.oboedit.org/oe2/userguide/html/Introduction_to_Cross_Products.htm Introduction to Cross Products] | * [http://www.oboedit.org/oe2/userguide/html/Introduction_to_Cross_Products.htm Introduction to Cross Products] | ||
* [http://www.oboedit.org/oe2/userguide/html/Cross_Products_in_the_Text_Editor.htm Cross Products in the Text Editor] | * [http://www.oboedit.org/oe2/userguide/html/Cross_Products_in_the_Text_Editor.htm Cross Products in the Text Editor] | ||
* [http://www.oboedit.org/oe2/userguide/html/Cross_Products_By_Hand.htm Cross Products By Hand] | * [http://www.oboedit.org/oe2/userguide/html/Cross_Products_By_Hand.htm Cross Products By Hand] | ||
Expressions | |||
* [http://www.oboedit.org/oe2/userguide/html/Introduction_to_Expressions.htm Introduction to Expressions] | * [http://www.oboedit.org/oe2/userguide/html/Introduction_to_Expressions.htm Introduction to Expressions] | ||
* [http://www.oboedit.org/oe2/userguide/html/Expression_Syntax.htm Expression Syntax] | * [http://www.oboedit.org/oe2/userguide/html/Expression_Syntax.htm Expression Syntax] | ||
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* [http://www.oboedit.org/oe2/userguide/html/Backtick_Expressions.htm Backtick Expressions] | * [http://www.oboedit.org/oe2/userguide/html/Backtick_Expressions.htm Backtick Expressions] | ||
* [http://www.oboedit.org/oe2/userguide/html/Example_Scripts.htm Example Scripts] | * [http://www.oboedit.org/oe2/userguide/html/Example_Scripts.htm Example Scripts] | ||
Plugins | |||
* [http://www.oboedit.org/oe2/userguide/html/Introduction_to_Plugins.htm Introduction to Plugins] | * [http://www.oboedit.org/oe2/userguide/html/Introduction_to_Plugins.htm Introduction to Plugins] | ||
* [http://www.oboedit.org/oe2/userguide/html/The_GraphViz_Plugin.htm The GraphViz Plugin] | * [http://www.oboedit.org/oe2/userguide/html/The_GraphViz_Plugin.htm The GraphViz Plugin] | ||
* [http://www.oboedit.org/oe2/userguide/html/The_Dbxref_Library_Plugin.htm The Dbxref Library Plugin] | * [http://www.oboedit.org/oe2/userguide/html/The_Dbxref_Library_Plugin.htm The Dbxref Library Plugin] | ||
The Command Line | |||
* [http://www.oboedit.org/oe2/userguide/html/OBO_Edit_Command_line_Options.htm OBO-Edit Command-line Options] | * [http://www.oboedit.org/oe2/userguide/html/OBO_Edit_Command_line_Options.htm OBO-Edit Command-line Options] | ||
* [http://www.oboedit.org/oe2/userguide/html/obodiff.htm obodiff] | * [http://www.oboedit.org/oe2/userguide/html/obodiff.htm obodiff] | ||
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* [http://www.oboedit.org/oe2/userguide/html/obo2obo.htm obo2obo] | * [http://www.oboedit.org/oe2/userguide/html/obo2obo.htm obo2obo] | ||
* [http://www.oboedit.org/oe2/userguide/html/Java_Options_on_the_Command_line.htm Java Options on the Command-line] | * [http://www.oboedit.org/oe2/userguide/html/Java_Options_on_the_Command_line.htm Java Options on the Command-line] | ||
[http://www.oboedit.org/oe2/userguide/html/Frequently_Asked_Questions.htm Frequently Asked Questions] | |||
* [http://www.oboedit.org/oe2/userguide/html/How_Do_I_Make_a__Slim__Ontology_.htm How Do I Make a 'Slim' Ontology?] | * [http://www.oboedit.org/oe2/userguide/html/How_Do_I_Make_a__Slim__Ontology_.htm How Do I Make a 'Slim' Ontology?] | ||
* [http://www.oboedit.org/oe2/userguide/html/Creating_Your_Own_GO_Slim_in_OBO_Edit.htm Creating Your Own GO Slim in OBO-Edit] | ** [http://www.oboedit.org/oe2/userguide/html/Creating_Your_Own_GO_Slim_in_OBO_Edit.htm Creating Your Own GO Slim in OBO-Edit] | ||
* [http://www.oboedit.org/oe2/userguide/html/How_Do_I_Find_Terms_Without_an_is_a_Parent_.htm How Do I Find Terms Without an is_a Parent?] | * [http://www.oboedit.org/oe2/userguide/html/How_Do_I_Find_Terms_Without_an_is_a_Parent_.htm How Do I Find Terms Without an is_a Parent?] | ||
* [http://www.oboedit.org/oe2/userguide/html/How_Do_I_Spell_Check_.htm How Do I Spell Check?] | * [http://www.oboedit.org/oe2/userguide/html/How_Do_I_Spell_Check_.htm How Do I Spell Check?] | ||
* [http://www.oboedit.org/oe2/userguide/html/How_Do_I_Not_Search_Obsoletes_.htm How Do I Not Search Obsoletes?] | * [http://www.oboedit.org/oe2/userguide/html/How_Do_I_Not_Search_Obsoletes_.htm How Do I Not Search Obsoletes?] |
Revision as of 17:06, 30 June 2008
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
Here is a list of all the current OBO-Edit help pages. If you are working on one, 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 one 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?
- What is an ontology?
- Basic Concepts and Vocabulary
- An Introduction to OBO Ontologies
- Getting OBO-Edit Started
- Bugs and Troubleshooting
- Slowness
Viewing Ontologies
Filtering, Rendering & Searching (Amina)
Editing
- Undo/Redo
- Text Editing
- Structural Editing
- The Graph Editor (Jen)
- The Parent Plugin
- Organizing Your Ontology: Editing Metadata
- Working with Categories
- Working with IDs
- Working with Namespaces
- Working with Synonym Categories
- 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
The Reasoner
- 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
The Command Line