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Extract Mondo terms for curation app

Extract All Mondo terms for the Delphi Curation tool

by Trish Whetzel updated Mar 14, 2025

Get all Mondo terms and the following information:

  • term ID (formatted as a CURIE)
  • label
  • definition
  • comment
  • parents (direct parents only) - the labels and CURIEs
  • synonyms (exact synonyms only)
  • xrefs to OMIM and Orphanet where there is a MONDO:equivalentTo annotation

The query is run against the mondo.owl file, which is already reasoned and corresponds to the Mondo content from the latest Mondo release.

Extract all Mondo terms

To extract all Mondo terms, run the command below from the mondo/src/ontology directory as:
sh run.sh make dump-mondo-terms

The result file is created in mondo/src/ontology/reports/mondo_term_dump.csv. This file is ignored by git so you will not see it highlighted as a changed file. NOTE: File imports into Airtable can only be done with CSV files and not TSV files.

SPARQL Queries

The query used to extract the terms is called dump-mondo-terms.ru and is in the src/sparql/reports directory.