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_id_prefixes=None)

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