dipper.models.Provenance module

class dipper.models.Provenance.Provenance(graph)

Bases: object

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

• Process history leading to a claim being made, including processes through which evidence is evaluated
• Processes through which information used as evidence is created.

Provenance metadata includes accounts of who conducted these processes,

what entities participated in them, and when/where they occurred.

add_agent_to_graph(agent_id, agent_label, agent_type=None, agent_description=None)

add_assay_to_graph(assay_id, assay_label, assay_type=None, assay_description=None)

add_assertion(assertion, agent, agent_label, date=None)

Add assertion to graph :param assertion: :param agent: :param evidence_line: :param date: :return: None

add_date_created(prov_type, date)

add_study_measure(study, measure)

add_study_parts(study, study_parts)

add_study_to_measurements(study, measurements)

object_properties = {'asserted_by': 'SEPIO:0000130', 'created_at_location': 'SEPIO:0000019', 'created_by': 'SEPIO:0000018', 'created_on': 'pav:createdOn', 'created_with_resource': 'SEPIO:0000022', 'date_created': 'SEPIO:0000021', 'has_agent': 'SEPIO:0000017', 'has_input': 'RO:0002233', 'has_participant': 'RO:0000057', 'has_provenance': 'SEPIO:0000011', 'has_supporting_study': 'SEPIO:0000085', 'is_asserted_in': 'SEPIO:0000015', 'is_assertion_supported_by': 'SEPIO:0000111', 'measures': 'SEPIO:0000114', 'output_of': 'RO:0002353', 'specified_by': 'SEPIO:0000041'}

provenance_types = {'assay': 'OBI:0000070', 'assertion': 'SEPIO:0000001', 'assertion_process': 'SEPIO:0000003', 'mixed_model': 'STATO:0000189', 'organization': 'foaf:organization', 'person': 'foaf:person', 'project': 'VIVO:Project', 'statistical_hypothesis_test': 'OBI:0000673', 'study': 'OBI:0000471', 'variant_classification_guideline': 'SEPIO:0000037', 'xref': 'OIO:hasdbxref'}