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)

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

long strings will be converted to bnodes
Parameters:
  • type – str curie
  • label – str
Returns:

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

Add line of evidence node to association id

Parameters:
  • assoc_id – curie or iri, association id
  • evidence_line – curie or iri, evidence line
Returns:

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

Add supporting line of evidence node to association id

Parameters:
  • assoc_id – curie or iri, association id
  • evidence_line – curie or iri, evidence line
Returns:

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

<evidence> <SEPIO:0000124> <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:

data_property = {'has_measurement': 'IAO:0000004', 'has_value': 'STATO:0000129'}
data_types = {'count': 'SIO:000794', 'odds_ratio': 'STATO:0000182', 'proportional_reporting_ratio': 'OAE:0001563'}
evidence_types = {'assay': 'OBI:0000070', 'blood test evidence': 'ECO:0001016', 'effect_size': 'STATO:0000085', 'fold_change': 'STATO:0000169', 'measurement datum': 'IAO:0000109', 'percent_change': 'STATO:percent_change', 'pvalue': 'OBI:0000175', 'statistical_hypothesis_test': 'OBI:0000673', 'zscore': 'STATO:0000104'}
object_properties = {'has_evidence': 'SEPIO:0000006', 'has_significance': 'STATO:has_significance', 'has_supporting_data': 'SEPIO:0000084', 'has_supporting_evidence': 'SEPIO:0000007', 'has_supporting_reference': 'SEPIO:0000124', 'is_evidence_for': 'SEPIO:0000031', 'is_evidence_supported_by': 'SEPIO:000010', 'is_evidence_with_support_from': 'SEPIO:0000059', 'is_refuting_evidence_for': 'SEPIO:0000033', 'is_supporting_evidence_for': 'SEPIO:0000032', 'source': 'dc:source'}