RDF Utils¶

Utility methods that are used for handling RDF.

kgx.utils.rdf_utils¶

kgx.utils.rdf_utils.get_biolink_element(prefix_manager: kgx.prefix_manager.PrefixManager, predicate: Any) → Optional[linkml_runtime.linkml_model.meta.Element][source]¶

Returns a Biolink Model element for a given predicate.

Parameters

prefix_manager (PrefixManager) – An instance of prefix manager
predicate (Any) – The CURIE of a predicate

Returns

The corresponding Biolink Model element

Return type

Optional[Element]

kgx.utils.rdf_utils.infer_category(iri: rdflib.term.URIRef, rdfgraph: rdflib.graph.Graph) → Optional[List][source]¶

Infer category for a given iri by traversing rdfgraph.

Parameters

iri (rdflib.term.URIRef) – IRI
rdfgraph (rdflib.Graph) – A graph to traverse

Returns

A list of category corresponding to the given IRI

Return type

Optional[List]

kgx.utils.rdf_utils.process_predicate(prefix_manager: kgx.prefix_manager.PrefixManager, p: Union[rdflib.term.URIRef, str], predicate_mapping: Optional[Dict] = None) → Tuple[source]¶

Process a predicate where the method checks if there is a mapping in Biolink Model.

Parameters

prefix_manager (PrefixManager) – An instance of prefix manager
p (Union[URIRef, str]) – The predicate
predicate_mapping (Optional[Dict]) – Predicate mappings

Returns

A tuple that contains the Biolink CURIE (if available), the Biolink slot_uri CURIE (if available), the CURIE form of p, the reference of p

Return type

Tuple[str, str, str, str]