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CONTRIBUTING.md

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Contributing to the Oral Health and Disease Ontology (OHD) Ontology

Robot and Protégé

The OHD Ontology products and subsets are built using ROBOT. Thus, you will need to have ROBOT installed on your system.

Often, you will need to view the ontology products. For this, it is best to use the Protégé ontology editor ( see Configuring Protégé for OHD contributions).

Editor's version

The top-level ontology products and subsets are built using a release process ( see Updating Ontology Products and Subsets). Changes made directly to the ontology, such as editing descriptions and managing imports, are made to the editors of this ontology: src/ontology/ohd-edit.owl.

Tracking Changes to the OHD Ontology

To track changes made to the OHD Ontology, it is best maintained by following these steps:

  1. Submit an issue detailing the problem.
  2. Create a branch to address this issue that uses the same number as the issue tracker. For example, if the issue is #50 in the issue tracker, name the branch issue-50. This allows other developers to easily know which branch needs to be checked out to contribute.
  3. Create a pull request that fixes the issue. If possible, create a draft (or WIP) branch early in the process.
  4. Merge pull request once all the necessary changes have been made. If needed, tag other developers to review the pull request.
  5. Delete the issue branch (e.g., branch issue-50).

Updating Ontology Products and Subsets

From time to time, the imports used by the OHD Ontology will need to be updated and new products (i.e., ontology products and subsets) released. The general process for updating the products is as follows:

  1. Create an issue, branch, and pull request using the steps outlined in Tracking Changes to the OHD Ontology section.
  2. Navigate to the src/ontology directory.
  3. Execute make clean. This removes all imports, ontologies, and subsets from the src/ontology directory. Note, the top-level ontology products and subsets still exist; only the files in the src/ontology directory were removed.
  4. Execute make all. This will create new ontology products and subsets in the src/ontology directory.
  5. Review the new ontology products and subsets.
  6. Once you are satisfied with the new ontology products and subsets, execute make release. This will copy the new products to the top-level directory.
  7. Finally, push your changes to the repository, make a pull request, and merge.

Configuring Protégé for OHD Contributions

Rationale

When a new entity is created using Protégé the entities are created using the default settings of Protégé. For example, using the default settings when a new entity called 'test' is created the IRI for the entity may look like this.

http://www.semanticweb.org/user/ontologies/2023/6/untitled-ontology-43#test

Ideally, we want the new entity created in the OHD ontology to look similar to the IRI below based on OBO Foundry principles:

http://purl.obolibrary.org/obo/OHD_0000024

Prerequisites

Protégé

If you do not have installed Protégé ontology editor on your machine, please download and install it from this link.

Create ORCID identifier

If you do not have an ORCID ID please create one by registering here. ORCID ID is a free-of-charge identifier for researchers.

Update Preferences

Where can I find Protégé preferences?

  • Open Protégé.
  • Go to File > Preferences.

Update user details in Protégé

  • Go to Protégé Preferences.
  • Click on the User details tab.
  • Enable Use supplied user name.
  • Enter your full name in the field indicated.
  • Enable Use Git user name when available.
  • Enter your ORCID ID in the field for ORCID.
  • Click OK to save.

user_details_edit

Update configuration for new entities

  • Go to Protégé Preferences.
  • Click the New entities tab.
  • Update Entity IRI.
    • For Start with: enable 'Specified IRI' and enter the following IRI in the field:
      • http://purl.obolibrary.org/obo
    • For Followed by: enable the forward slash option (/).
    • For End with: enable 'Auto-generated ID'.
  • Update Entity Label.
    • Enable Same as label renderer.
  • Update Auto-generated ID.
    • Enable Numeric (Iterative).
    • For Prefix: enter OHD_ in the field provided.
    • For Start: enter the lower value integer of the ID range if one has been assigned to you. For example 2,000. Most regular contributors are assigned an ID range.
    • For End: enter the upper-value integer of the ID range if one has been assigned to you. For example 2,999.
    • Enable Remember last ID between Protégé sessions.
  • Click OK to save.

new_entities

Update configuration for new entities metadata

  • Go to Protégé Preferences.
  • Click the New entities metadata tab.
  • Enable Annotate new entities with creator (user).
  • For Creator property enter the following IRI the field:
    • http://purl.org/dc/terms/contributor
  • For Creator value enable Use ORCID.
  • Enable Annotate new entities with creation date/time.
  • For Date property enter the following IRI the field:
    • http://purl.org/dc/terms/created
  • For Date property enable ISO-8601.
  • Click OK to save.

new_entities_metadata