This section contains general instructions for a variety of editing scenarios. Although it may not be possible to capture every possible scenario, the ones listed below should cover the most common editing situations that will arise.

Before adding new terms, you must first determine whether it should be created de novo or imported from the ISF or another ontology, and in which file to place it. Because of this, it is important to understand the underlying structure of how the eagle-i ontology is organized and generated. See the section on Ontology File Structure for more details.

General things to remember while adding terms

  • If there is more than one potential editor, always email all others before editing, in order to prevent conflicts. Include the names of the files you are locking in the email. (Example: [LOCKING] ero.owl and ero-app.owl.)
  • All de novo terms must be added to the IDs.xlsx file found in the docs folder in the eagle-i SVN. Add new terms to the row corresponding to their ERO ID, and note whether they are a class or a property.
  • Before creating a new class, make sure the correct file is active. Classes cannot be moved after they are created without manually editing the XML files or knowing how to convince protege to do this.

Scenario 1: Adding a new term to the ISF

If a term is reusable (i.e. not specific to eagle-i) and cannot be imported from an existing ontology, it can be created in the ISF. If the term is a child of an existing hierarchy in the ISF, then it should be added in the same file in the ISF. Terms should never be added directly to the generated eagle-i owl files in the public folder.

  1. Update the ontology trunk in your SVN repository to get the latest changes: https://open.med.harvard.edu/svn/eagle-i-dev/datamodel/trunk.
  2. Open the isf-dev.owl file from the ISF folder.
  3. See which file is currently used for the parent class and make that file the active ontology.
    1. Search for the parent term.
    2. Right click on the label.
    3. Select switch to the defining ontology. For example, for a technique, this will be the research-resource.owl file
  4. Add the term.
  5. Review and save changes.
  6. Commit changes to the ISF from the src\isf folder.
  7. Add the term to the IDs.xlsx file found in the docs folder in the eagle-i SVN.
  8. Use the module scripts to generate the local ontology following the steps outlined above.
  9. Open the ero-extended-app.owl file and find the corresponding app file.
    1. Search for the term. Hover over the label to see the name of the generated eagle-i file. The technique hierarchy lives in the ero.owl file.
    2. Switch to the corresponding app file (For techniques: ero-app.owl.)
  10. Add any application specific axioms that are needed.
  11. Review and save changes.
  12. Commit changes to the Harvard SVN from the trunk.

Examples:

  • Adding a new reference taxonomy sub-type (e.g. technique)
  • Adding a new resource sub-type (e.g. instrument, reagent, etc.)
  • Adding a top level resource type (e.g. Resource Collection)
  • Adding a new property that isn’t application specific
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