bionty.base.Ontology

class bionty.base.Ontology(handle=None, import_depth=-1, timeout=100, threads=None, prefix='')

Bases: Ontology

Interface with ontologies via pronto.

Also see: https://pronto.readthedocs.io/en/stable/api/pronto.Ontology.html

Parameters:

  • handle (str | Path | BinaryIO | None, default: None) – Path to an ontology source file.

  • import_depth (int, default: -1) – The maximum depth of imports to resolve in the ontology tree.

  • timeout (int, default: 100) – The timeout in seconds to use when performing network I/O.

  • threads (int | None, default: None) – The number of threads to use when parsing.

  • url – The url of the ontology.

  • prefix (str, default: '') – Dev only -> prefix for get_term.

Methods

get_term(term)

Search an ontology by its id.

to_df(source=None, include_rel=None, include_id_prefixes=None)

Convert pronto.Ontology to a DataFrame with columns id, name, parents, definition, and synonyms.

Parameters:

  • source (str | None, default: None) – The source of the ontology terms to include. If None, all terms are included.

  • include_rel (str | None, default: None) – The relationship ID to include when gathering parent relationships. If provided, it extends the superclasses with the specified relationship.

  • include_id_prefixes (dict[str, list[str]] | None, default: None) – A dictionary mapping sources to lists of ID prefixes. Only terms with IDs starting with these prefixes will be included for the specified source.

Returns:

A DataFrame containing the filtered ontology terms with columns –

  • ontology_id (index): The unique identifier for each term.

  • name: The name of the term.

  • definition: The definition of the term (None if not available).

  • synonyms: A pipe-separated string of exact synonyms (None if no synonyms).

  • parents: A list of parent term IDs, including superclasses and optionally the specified relationship.