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Importing and Defining Terms

Importing and Defining Unit Terms

This guide explains two methods for incorporating unit terms into the MOLSIM ontology:

  1. Importing Existing Terms: For terms that already exist in an ontology like the Unit Ontology (UO).
  2. Defining New Terms: For custom terms that are not available in imported ontologies.

Method 1: Importing Existing Unit Terms from UO

This method is ideal when the unit terms you need are already defined in the Unit Ontology.

1. Add Terms to the Import File

Open /src/ontology/imports/uo_terms.txt and add the unique identifiers (IRIs) of the UO terms you wish to import, each on a new line.

For example: 

UO:0000010
UO:0000109

2. Extract the Terms

Run the following ROBOT command to extract the specified terms and their related axioms from the Unit Ontology:

sh run.sh robot extract --method MIREOT \
    --input mirror/uo.owl \
    --lower-terms imports/uo_terms.txt \
    --output imports/uo_import.owl

Explanation of the command: * --method MIREOT: This specifies the "Minimum Information to Reference an External Ontology Term" method, which is recommended when you primarily need the term's hierarchy and basic information. * --input mirror/uo.owl: The source ontology from which to extract terms. * --lower-terms imports/uo_terms.txt: The file containing the list of term IDs to be extracted. * --output imports/uo_import.owl: The file where the extracted subset of the ontology will be saved.

3. Integrate the Imported Terms

Finally, run the following ODK commands to update the repository and integrate the newly imported terms into the MOLSIM ontology:

sh run.sh make update_repo         # Update the repository
sh run.sh make refresh-uo          # Refresh the Unit Ontology import
sh run.sh make prepare_release     # Integrate ontology imports with components

Method 2: Defining New Custom Unit Terms

Use this method when a required unit term is not available in the UO or other imported ontologies. This process uses ROBOT templates to create new terms within the MOLSIM ontology.

1. Modify the Template File

Open the template file at /src/ontology/templates/molsim_units_component.tsv and add a new row for each custom term you want to define. Follow the existing structure of the TSV file, providing a unique ID, Label, Alternative Term, Definition, and Parent Class.

For example, to add a new unit, you would add a line like this:

MOLSIM:010006    newton per meter    N/m    A unit of stiffness.    UO:0000111

2. Rebuild the Component and Integrate

After modifying and saving the template, run the following commands to generate the new ontology component and integrate it into the main ontology:

sh run.sh make components/molsim_units_component.owl  # Rebuild the component
sh run.sh make prepare_release     # Integrate ontology imports with components

By following these steps, you can systematically expand the MOLSIM ontology with both existing and custom unit terms to meet the specific needs of your domain.