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Protégé is a free, open source ontology editor and knowledge-base framework. While this document contains a few general instructions for using Protégé, it is not meant to serve as a comprehensive help document for that program. Consult the Protégé user documentation for more details: http://protegewiki.stanford.edu/wiki/Main_Page.

Setting up Protégé

Step 1: Download Protégé

    1. Download OBI-friendly Protégé 4.3 or 5: http://protege.stanford.edu/
    2. If prompted, do not install updates for the plugins, as the plugin versions contained in the download work specifically with OBI.

Step 2: Configure Protégé

If you are editing for the first time in Protégé, you will need to adjust the settings (should only need to be done once).

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Entity URI

Entity Label (for use with Auto-generated ID)

  • Select 'Same as label renderer'

Auto-generated ID

  • Select 'Numeric (iterative)'
  • Prefix: enter 'ERO_'
  • Digit count: enter '7'
  • Start: enter a four digit number one higher than that of the last ID created. To determine correct number:
    • consult the IDs.xlsx spreadsheet, located in trunk > docs to find the last ID number used
    • search for the next highest ID number in Protégé to double check no additional IDs have been created
  • End: -1

Step 4: Reasoning

The reasoner tests the logic and consistency of the asserted axioms in the ontology and computes the inferred hierarchy. The suggested reasoner for eagle-i is FaCT++. It is good practice to run the reasoner periodically before committing, to ensure nothing has been accidentally moved. The ‘Class hierarchy’ tab shows only the asserted hierarchy; the ‘Class hierarchy (inferred)’ tab shows the inferred hierarchy relationships (i.e. the hierarchy seen in the software). The inferred hierarchy is only visible after the reasoner has been run in that file.

Viewing the eagle-i ontology

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

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  • 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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