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