def __init__(self, id_a, id_b, mechanism, effect, direct, relation, pmid,
linenum):
self.id_a = id_a
self.id_b = id_b
self.effect = effect
self.direct = direct
self.relation = relation
self.pmid = pmid
self.linenum = linenum
self.complex_a = None
try:
if NamingConvention.is_complex(
self.id_a) and self.id_a in COMPLEXES:
self.complex_a = COMPLEXES[self.id_a]
except TypeError as err:
print(self.id_a)
raise err
self.complex_b = None
if NamingConvention.is_complex(self.id_b) and self.id_b in COMPLEXES:
self.complex_b = COMPLEXES[self.id_b]
# by default mechanism = molecular function
mechanism_term = "GO:0003674"
if self.direct == "YES":
if (mechanism):
mechanism_term = MECHANISM_GO_MAPPING[mechanism]
self.mechanism = {
"name": mechanism,
"uri": None,
"term": mechanism_term
}
self.regulated_activity = {"name": None, "uri": None, "term": None}
self.individuals = {}
self.enabled_by_stmt_a = None
def declare_entities(self, model):
uri = model.declare_individual("GO:0032991")
model.writer.writer.graph.add((uri, RDFS.label, Literal(str(self.name))))
for entity in self.entities:
entity_full_id = NamingConvention.full_id(entity)
entity_uri = model.declare_individual(entity_full_id)
part_of_stmt = model.writer.emit(uri, HAS_PART, entity_uri)
model.add_axiom(part_of_stmt)
"uri BFO:0000051 entity_uri"
return uri
def uri_in_model(self, model):
graph = model.writer.writer.graph
complex_term = "GO:0032991"
complex_uris = model.uri_list_for_individual(complex_term)
for c_uri in complex_uris:
found_entities = [] # Collect connected entities for set comparison
for entity in self.entities:
for entity_uri in model.uri_list_for_individual(NamingConvention.full_id(entity)):
if (c_uri, HAS_PART, entity_uri) in graph:
found_entities.append(entity)
if set(self.entities) == set(found_entities):
print(c_uri)
return c_uri
def b_is_complex(self):
return NamingConvention.is_complex(self.id_b)
def class_id_b(self):
return NamingConvention.class_id(self.id_b)
def full_id_b(self):
return NamingConvention.full_id(self.id_b)
def determine_entity(cls, entity_id: str, entity_name: str,
entity_type: str) -> SignorEntity:
if NamingConvention.is_complex(entity_id):
return SignorEntityFactory.complex_from_id(entity_id)
else:
return cls.entity_type_map[entity_type](entity_id, entity_name)