dipper.models.Evidence module

class dipper.models.Evidence.Evidence(graph, association)

Bases: object

To model evidence as the basis for an association. This encompasses:

  • measurements taken from the lab, and their significance.
    these can be derived from papers or other agents.
  • papers
>1 measurement may result from an assay,
each of which may have it’s own significance
add_data_individual(data_curie, label=None, ind_type=None, data_curie_category=None)

Add data individual :param data_curie: str either curie formatted or long string,

long strings will be converted to bnodes
Parameters:
  • data_curie_category – a biolink category CURIE for data_curie
  • type – str curie
  • label – str
Returns:

None
add_evidence(evidence_line, evidence_type=None, label=None)

Add line of evidence node to association id

Parameters:
  • evidence_line – curie or iri, evidence line
  • evidence_type – curie or iri, evidence type if available
Returns:

None
add_source(evidence_line, source, label=None, src_type=None, source_category=None)

Applies the triples: <evidence> <dc:source> <source> <source> <rdf:type> <type> <source> <rdfs:label> “label”

TODO this should belong in a higher level class :param evidence_line: str curie :param source: str source as curie :param label: optional, str type as curie :param type: optional, str type as curie :return: None

add_supporting_data(evidence_line, measurement_dict)

Add supporting data :param evidence_line: :param data_object: dict, where keys are curies or iris and values are measurement values for example:

{
“_:1234” : “1.53E07” “_:4567”: “20.25”

}

Note: assumes measurements are RDF:Type ‘ed elsewhere :return: None

add_supporting_evidence(evidence_line, evidence_type=None, label=None)

Add supporting line of evidence node to association id

Parameters:
  • evidence_line – curie or iri, evidence line
  • evidence_type – curie or iri, evidence type if available
Returns:

None
add_supporting_publication(evidence_line, publication, label=None, pub_type=None)

<evidence> <has_supporting_reference> <source> <source> <rdf:type> <type> <source> <rdfs:label> “label” :param evidence_line: str curie :param publication: str curie :param label: optional, str type as curie :param type: optional, str type as curie :return: