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Before viewing or editing the ontology, make sure you’re looking at the most current version:

1. Update the ontology trunk in your Subversion repository to get the latest changes: https://open.med.harvard.edu/svn/eagle-i-dev/datamodel/trunk.
2. Use the module scripts to generate the local ontology
   
   1. Right click on the src\isf\module-scripts folder and select ‘Open in Terminal’ to open a command window. (Note: these instructions are specific to the SmartSVN client, but a variation on this workflow should be possible from other clients. See Ontology File Structure > src/isf/module-scripts for more details.)
   2. Type ei-all.bat (for Windows) and hit enter. The script is done when the command prompt reappears. This process will take some time and potentially slow your computer down.
3. Depending on what part of the ontology you wish to view, open one of the following OWL files in Protege:
   1. eaglei-modules-top.owl — imports the source (the ISF), the module configuration, and the exclude and include files.
   2. eaglei-module-configuration.owl — shows only the source (ISF) and the module configuration.
   3. eagle-i-extended-app.owl —  shows both the eagle-i ontology generated and application OWL files.

Reminder: do not edit the generated files. Any direct edits of the generated files will not be committed to SVN (these files are SVN ignored) and they will be lost the next time the scripts are ran. Only view these files in Protégé.:

• Select Show all loaded ontologies under View settings to show terms from all files. Terms in bold are contained in the current active file. Hover over the name of unbolded terms to see their actual location.
• Show the imports closure of the active ontology shows terms both directly and indirectly imported into that file.
• Show only the active ontology shows only terms contained in the active file; no imports.

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