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Maintaining the Biolink Model

The Biolink Model is under constant development with new classes and slots being added on a monthly basis. The main driver for the model is the NCATS Biomedical Data Translator.

This rapid development of the model may cause tools that directly depend on the model to break. To avoid such a scenario any tool that uses Biolink Model YAML (or it artifacts) must pin to a particular release. A full list of releases can be found on GitHub

This section will address the strategies for maintaining the Biolink Model.

Managing versions

We use the Semantic Versioning guidelines for managing our releases.

Given a version number MAJOR.MINOR.PATCH, increment the:

  • MAJOR version when you make incompatible API changes,
  • MINOR version when you add functionality in a backwards compatible manner, and
  • PATCH version when you make backwards compatible bug fixes.

Small changes to the model can be provided periodically as a new patch release.

Any structural changes to the model should be followed by a new minor release, as long as the changes are backwards compatible.

Any modification that leads to breaking changes must be followed by a new major release.

Deprecating classes and slots

BiolinkML provides slots that can be used to signify a class (or slot) as being deprecated.

Example:

  edge label:
    deprecated: >-
      This slot is deprecated in favor of 'predicate' slot.
    deprecated_element_has_exact_replacement: predicate
    is_a: association slot
    domain: association
    range: predicate type
    required: true

In the above example we use the deprecated and deprecated_element_has_exact_replacement to signify the association slot edge label as being deprecated.

  • Using the deprecated slot one can provide a human readable description of why the slot was deprecated
  • Using the deprecated_element_has_exact_replacement slot one can define what is the ideal replacement for this slot (if any)

It’s recommended that deprecated classes and slots remain in the model until the next major release.

Artifacts

BiolinkML consumes the Biolink Model YAML and generates several artifacts.

This step is automated as part of GitHub Actions.

That means no pull request to the Biolink Model repo should include updates to the artifacts themselves. In 99% of the cases any changes in a PR ought to be confined to biolink-model.yaml.

Documentation

BiolinkML consumes the Biolink Model YAML and also generates Markdown for all the classes and slots defined in the model.

This step is automated as part of GitHub Actions where changes in Markdown content are pushed to the gh-pages branch.

The Biolink Model Documentation site is driven from the gh-pages branch.

That means no pull request to the Biolink Model repo should include generated Markdown. It is advised to ensure that GitHub Actions remain disabled in the fork from which pull requests are made back to the main Biolink repository.