metahq-build ontology¶

Command group for OmicIDX queries.

Usage:

metahq-build ontology [OPTIONS] COMMAND [ARGS]...

Options:

  --help  Show this message and exit.

relations¶

Extract a terms x terms ontology relations matrix.

You may interpret the output matrix as the following: For any row, column pair, if the value is 1, then the term representing that particular row is an ancestor of the term representing that particular column. If the value is 0, then there is no relationship between the terms.

Usage:

metahq-build ontology relations [OPTIONS]

Options:

  -i, --obo_file PATH  Path to ontology .obo or .obo.gz file.
  -o, --outfile PATH   Path to .parquet outfile storing ontology relations.
  --help               Show this message and exit.

search-db¶

Build the ontology search DuckDB database.

Usage:

metahq-build ontology search-db [OPTIONS]

Options:

  --mondo FILE      Path to mondo's names_synonyms.json
  --uberon-cl FILE  Path to uberon/CL's names_synonyms.json
  --out-db FILE     Output DuckDB database path
  --help            Show this message and exit.