oakx_oger package

Submodules

oakx_oger.cli module

Command line interface for oakx-oger.

oakx_oger.oger_implementation module

OGER Implementation.

class oakx_oger.oger_implementation.OGERImplementation(resource=None, strict=False, _multilingual=None, autosave=<factory>, exclude_owl_top_and_bottom=<factory>, ontology_metamodel_mapper=None, _converter=None, auto_relax_axioms=None, cache_lookups=False, _edge_index=None, _entailed_edge_index=None, list_of_ontologies=<factory>, **_kwargs)

Bases: TextAnnotatorInterface, OboGraphInterface

OGER Implementation.

annotate_file(text_file, configuration)

Annotate text from a file.

Parameters:

• text – Text to be annotated.

• configuration (TextAnnotationConfiguration) – TextAnnotationConfiguration , defaults to None

Yield:

Annotated result

Return type:

Iterable[TextAnnotation]

annotate_text(text, configuration)

Annotate text from a file.

Parameters:

• text (str) – Text to be annotated.

• configuration (TextAnnotationConfiguration) – TextAnnotationConfiguration , defaults to None

Yield:

Annotated result

Return type:

Iterable[TextAnnotation]

entities(filter_obsoletes=True, owl_type=None)

Yield entities from the underlying implementation.

Parameters:

• filter_obsoletes – Boolean to filter obsoletes, defaults to True

• owl_type – owl class, defaults to None

Yield:

CURIE

Return type:

Iterable[str]

entity_alias_map(curie)

Return alias map for a CURIE.

Parameters:

curie (str) – CURIE

Return type:

Dict[str, List[str]]

Returns:

Alias map.

input_dir = PosixPath('/home/runner/work/oakx-oger/oakx-oger/src/oakx_oger/input')

list_of_ontologies: List[str]

output_dir = PosixPath('/home/runner/.data/oxoger/output')

simple_mappings_by_curie(curie)

Yield a tuple o fmappings.

Parameters:

curie (str) – CURIE

Yield:

Simple mappings as a tuple.

Return type:

Iterable[Tuple[str, str]]

stopwords_dir = PosixPath('/home/runner/work/oakx-oger/oakx-oger/src/oakx_oger/stopwords')

terms_dir = PosixPath('/home/runner/.data/oxoger/terms')

Module contents

oakx_oger package.