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The Uberon Build System


Uberon used to have a completely custom, ad-hoc build pipeline that only Chris Mungall knew how to run. Since 2021, the pipeline was migrated to a more standard ODK-based setup, with all the Uberon-specific bits handled by the custom src/ontology/uberon.Makefile.

The repository now uses the typical ODK layout, and the following aspects of the pipeline are managed by the ODK in a standard way:

  • the imports;
  • the production of the “variants” of the main release artifacts (-base, -full, -simple, etc.);
  • most of the reports and QC checks.

The non-standard parts of the pipeline concerns mainly:

  • the production of the main uberon.owl product;
  • the production of ontology subsets;
  • the production of the cross-species bridge files and collected/composite ontologies;
  • the production of extra QC checks and reports (notably the checks for violations of taxon constraints and all the checks involving the bridge files).

Notes about the custom pipelines

This section is not intended to provide a complete explanation of how the custom pipeline works. Not that such an explanation would not be useful, but it would be likely to become quickly out-of-sync with the actual pipeline code. Ultimately, the reference for how those pipelines work is the uberon.Makefile file. Consider this section merely as a guide to orient yourself within that Makefile.

Unless otherwise noted:

  • all filenames are relative to the src/ontology directory;
  • all steps are performed with ROBOT.

Building the main uberon.owl product

Two-steps process:

  • tmp/uberon-edit.owl: made by merging the main source file (uberon-edit.obo) along with the ODK import module and all the various components; OWL macros are expanded in that step;
  • uberon.owl: reasoning step.

The second step notably includes a materialisation phase that is particularly memory intensive and that must therefore be excluded when running the pipeline on memory-constrained machines (any machine with less than 32 GB of RAM is considered to be memory-constrained when Uberon is concerned). Run the pipeline with GH_ACTION=true to exclude that materialisation step (do not do that when trying to produce an official release!).

Building the multi-species ontologies

This is decomposed in several steps that are mostly isolated from each other, so that each step can be run independently.

  1. Building Uberon itself (sh make uberon.owl).
  2. Mirroring the taxon-specific ontologies (sh make MIR=true IMP=true all_local_imports).
  3. Mirroring the externally provided mapping sets (sh make refresh-mappings).
  4. Building the cross-species bridges (sh make refresh-bridges).
  5. Building the desired collected or composite ontology (e.g. sh make composite-metazoan.owl).

Steps 2–4 can also be run in a single command with sh make refresh-external-resources (this will also refresh the standard ODK import module).