dipper.models.assoc.G2PAssoc module

class dipper.models.assoc.G2PAssoc.G2PAssoc(graph, definedby, entity_id, phenotype_id, rel=None, entity_category=None, phenotype_category=None)

Bases: dipper.models.assoc.Association.Assoc

A specific association class for defining Genotype-to-Phenotype relationships. This assumes that a graph is created outside of this class, and nodes get added. By default, an association will assume the “has_phenotype” relationship, unless otherwise specified. Note that genotypes are expected to be created and defined outside of this association, most likely by calling methods in the Genotype() class.

add_association_to_graph(entity_category=None, phenotype_category=None)

Overrides Association by including bnode support

The reified relationship between a genotype (or any genotype part) and a phenotype is decorated with some provenance information. This makes the assumption that both the genotype and phenotype are classes.

currently hardcoded to map the annotation to the monarch namespace :param g: :param entity_category: a biolink category CURIE for self.sub :param phenotype_category: a biolink category CURIE for self.obj :return:

make_g2p_id()

Make an association id for phenotypic associations that is defined by: source of association + (Annot subject) + relationship + phenotype/disease + environment + start stage + end stage

Returns:

set_association_id(assoc_id=None)

This will set the association ID based on the internal parts of the association. To be used in cases where an external association identifier should be used.

Parameters:assoc_id – Returns:

set_environment(environment_id)

set_stage(start_stage_id, end_stage_id)