Contents

Phenote User's Guide
What is Phenote?
Advantages to Annotation with Ontolgies
Bugs and Troubleshooting
Licensing Information
Getting Started
Phenote Webstart
Phenote from the Command Line
Ontologies included with Phenote
Running Phenote for the First Time
Exiting Phenote
The Phenote Interface
Menu Bars
Data Entry
Term Info
Annotation Spreadsheet
Changing your Configuration
Loading/Saving Annotations
Introduction to Data Adapters
Loading & Saving
The PhenoXML adapter
The PhenoSyntax Adapter
The Tag-Value Adapter
The Tab-Delimited Adapter
Creating Annotations
Editing Functions
Entering data into Free-Text fields
Entering data into Ontology Fields
Term Composition/Refinement
Changing your Autocompletion Settings
Sample Annotations
Information for Developers
Writing a Data Adapter
Connecting to a Database
Adding configurability
What to do after Phenote
I've entered my data, now what?
Other Uses for Phenote
Customizing Phenote
What is a Configuration?
How To Edit a Configuration File
Sample Configuration 1
Sample Configuration 2
XML skeleton
The <phenote-configuration> Tag
The <tab> Tag
The <dataadapter> Tag
The <master-to-local-config> Tag
The <field> Tag
The <ontology> Tag
The <auto-update-ontologies> Tag
The <update-timer> Tag
The <term-history> Tag
Appendix
An Introduction to OBO Ontologies
Basic Concepts and Vocabulary