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Import terms for logical axioms

Last updated 27-Mar-2024

Import terms into Mondo for use in logical axioms

This workflow is for adding classes from external ontologies (i.e., GO or CHEBI), which is much more streamlined compared to MIREOTing.

As a Mondo curator, when you have a ticket that requires a term from an external ontology, create a new git feature branch to include only the changes for the refresh of the imports following the steps below. Also, ask on Slack if other curators need other terms imported.

  1. Fetch the latest changes from master in the "mondo" repo
  2. Create a new git feature branch
  3. Open the src/ontology/imports/manual_seed.txt file
  4. Add the IRI of the term(s) you want to add to this document and save the file
    • IRIs for any entity can be added into the manual_seed.txt file, e.g. gene, NCBITaxon, etc.
  5. In the Terminal, run: export "MEMORY_GB=15"
  6. Then refresh the imports:
    • From src/ontology/ run the command: sh run.sh make refresh-merged (Note: this may take ~2 hours)
    • All the imports will be updated, which means that you might see changes in your GitHub diff in the following files:
      • src/ontology/imports/*_terms.txt
      • src/ontology/imports/merged_import.owl
    • The terms added in the manual_seed.txt file will be added to the appropriate import file (e.g human genes will be added to hgnc_terms.txt; NCBITaxon will be added to ncbitaxon_terms.txt).
  7. Close Protege and open mondo-edit.obo in Protege again and save the ontology (as .obo).
    • one needs to save the mondo-edit.obo file in order for the updates from the refresh import update process (e.g. updated names) to be visible in the ontology file
    • Therefore, changes such as updated names of imported entities might be shown in the git diff.
    • The new terms should be available for logical definitions in Protege. Therefore one can also edit the file too, but changes not manually made could be expected (see previous comment).
  8. Commit the changes to the git feature branch and create a PR.
  9. Once the PR is approved and merged, the terms imported from external ontologies can be referenced in logical definitions.

Note when importing a new NCBITaxon class

  • Check if the new NCBI Taxon identifier(s) also exist in the taxon-subset-ids.txt file in the "obophenotype/ncbitaxon/subsets" repo
    • If the identifiers are not in the file, update the taxon-subset-ids.txt file to add the identifiers and create a PR in the "obophenotype/ncbitaxon/subsets" repo to include the new identifiers
      Note: this file contains CURIEs (not IRIs) so the identifier should be added in this format NCBITaxon:1
  • This additional step is needed since we are not using NCBI Taxon directly, but the OBO slim, and the taxon-subset-ids.txt file is the seed of the NCBITaxon slim.

Alternate approaches

While there are alternate approaches to add classes from external ontologies, the instructions above are the only process that should be followed for importing external ontology classes into Mondo.