ontorunner.pipes package

Submodules

ontorunner.pipes.OntoRuler module

OntoRuler class for running Spacy.

class ontorunner.pipes.OntoRuler.OntoRuler(data_dir: Path = '/home/runner/work/ontorunner/ontorunner/data', settings_filepath: Path = '/home/runner/work/ontorunner/ontorunner/ontorunner/settings.ini', linker: str = 'umls', to_pickle: bool = True)

Bases: object

OntoRuler class.

extract_termlist_info(to_pickle: bool)

get_ont_terms_df(to_pickle) → DataFrame

Get Ontology terms from external source in the form of a pandas DataFrame.

Returns: Pandas DataFrame for of termlist.

get_terms_patterns(*args)

Get dictionaries of terms and patterns, along with doc format of the term.

Returns: Dictionary of terms;

Dictionary of patterns; doc object of the term

has_curies(tokens)

Check if any one token has CURIEs

Parameters: tokens – token
Returns: Boolean

Module contents

Pipelines in the project.