Skip to content

Commit

Permalink
Fixes for issues #3, #4, #5, and #6.
Browse files Browse the repository at this point in the history
  • Loading branch information
@dustine32
dustine32 committed Mar 30, 2018
1 parent 44bf9ac commit 4fb735e
Show file tree
Hide file tree
Showing 2 changed files with 135 additions and 91 deletions.
120 changes: 70 additions & 50 deletions pathway_connections.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -77,7 +77,6 @@ def __init__(self, id_a, id_b, mechanism, effect, direct, relation, pmid, linenu

self.individuals = {}
self.enabled_by_stmt_a = None
self.regulated_activity_uris = []

def print(self):
print("[UniProtKB:{ida}] <- enabled_by – [{mechanism}] – [{relation}]-> [{regulated_activity}] – enabled_by-> [UniProtKB:{idb}]".format(ida=self.id_a,
Expand All @@ -98,15 +97,17 @@ def declare_a(self, model):
model.declare_class(self.full_id_a())

# Individuals
if self.full_id_a() not in self.individuals:
# if self.full_id_a() not in self.individuals:
if self.full_id_a() not in model.individuals:
if self.a_is_complex():
uri_a = self.complex_a.declare_entities(model)
else:
uri_a = model.declare_individual(self.full_id_a())
self.individuals[self.full_id_a()] = uri_a
# self.individuals[self.full_id_a()] = uri_a
self.individuals[self.full_id_a()] = model.individuals[self.full_id_a()]

self.mechanism["uri"] = model.declare_individual(self.mechanism["term"])
self.individuals[self.mechanism["term"]] = self.mechanism["uri"]
# self.mechanism["uri"] = model.declare_individual(self.mechanism["term"]) # Segregate from singular entity declaration
# self.individuals[self.mechanism["term"]] = self.mechanism["uri"]

return model

Expand Down Expand Up @@ -183,53 +184,54 @@ def full_statement_bnode_in_model(self, model):
return candidate_reg_triple

class PathwayConnectionSet():
def __init__(self, filename):
def __init__(self, filename=None):
self.connections = []
linenum = 0

with open(filename, "r") as f:
data = list(csv.DictReader(f, delimiter="\t"))
for line in data:
linenum += 1

# If up-regulates (including any variants of this), use RO:0002629 if DIRECT, and use RO:0002213 if not DIRECT
relation = None
if line["EFFECT"].startswith("up-regulates"):
if line["DIRECT"] == "YES":
relation = "RO:0002629"
elif line["DIRECT"] == "NO":
relation = "RO:0002213"
# If down-regulates (including any variants of this), use RO:0002630 if DIRECT, and use RO:0002212 if not DIRECT
if line["EFFECT"].startswith("down-regulates"):
if line["DIRECT"] == "YES":
relation = "RO:0002630"
elif line["DIRECT"] == "NO":
relation = "RO:0002212"
# If unknown, use RO:0002211
if line["EFFECT"] == "unknown":
relation = "RO:0002211"
# If form_complex, ignore these lines for now
if line["EFFECT"] == "form_complex":
continue

pc = PathwayConnection(
line["IDA"],
line["IDB"],
line["MECHANISM"],
line["EFFECT"],
line["DIRECT"],
relation,
[line["PMID"]],
linenum
)

# if not (pc.id_a.startswith("SIGNOR") or pc.id_b.startswith("SIGNOR") or line["TYPEA"] == "phenotype" or line["TYPEB"] == "phenotype"):
acceptable_types = ['protein','complex']
if line["TYPEA"] in acceptable_types and line["TYPEB"] in acceptable_types:
if self.find(pc):
self.append_reference(pc)
else:
self.append(pc)
if filename:
with open(filename, "r") as f:
data = list(csv.DictReader(f, delimiter="\t"))
for line in data:
linenum += 1

# If up-regulates (including any variants of this), use RO:0002629 if DIRECT, and use RO:0002213 if not DIRECT
relation = None
if line["EFFECT"].startswith("up-regulates"):
if line["DIRECT"] == "YES":
relation = "RO:0002629"
elif line["DIRECT"] == "NO":
relation = "RO:0002213"
# If down-regulates (including any variants of this), use RO:0002630 if DIRECT, and use RO:0002212 if not DIRECT
if line["EFFECT"].startswith("down-regulates"):
if line["DIRECT"] == "YES":
relation = "RO:0002630"
elif line["DIRECT"] == "NO":
relation = "RO:0002212"
# If unknown, use RO:0002211
if line["EFFECT"] == "unknown":
relation = "RO:0002211"
# If form_complex, ignore these lines for now
if line["EFFECT"] == "form_complex":
continue

pc = PathwayConnection(
line["IDA"],
line["IDB"],
line["MECHANISM"],
line["EFFECT"],
line["DIRECT"],
relation,
[line["PMID"]],
linenum
)

# if not (pc.id_a.startswith("SIGNOR") or pc.id_b.startswith("SIGNOR") or line["TYPEA"] == "phenotype" or line["TYPEB"] == "phenotype"):
acceptable_types = ['protein','complex']
if line["TYPEA"] in acceptable_types and line["TYPEB"] in acceptable_types:
if self.find(pc):
self.append_reference(pc)
else:
self.append(pc)


def append(self, pathway_connection):
Expand Down Expand Up @@ -264,4 +266,22 @@ def find_other_regulated_activity(self, id_b):
if pc.mechanism["term"] != "GO:0003674":
filtered_reg_pcs.append(pc)
if len(filtered_reg_pcs) > 0:
return filtered_reg_pcs[0]
return filtered_reg_pcs[0]

def find_all_by_id_a_and_id_b(self, pathway_connection):
found_connections = PathwayConnectionSet()
for pc in self.connections:
if pc.id_a == pathway_connection.id_a and pc.id_b == pathway_connection.id_b:
found_connections.append(pc)
return found_connections

def find_by_mech_term(self, term):
for pc in self.connections:
if pc.mechanism["term"] == term:
return pc

def remove_list(self, pc_list):
new_connection_list = self.connections
for dead_pc in pc_list:
new_connection_list = [pc for pc in new_connection_list if not pc.equals(dead_pc)]
self.connections = new_connection_list
106 changes: 65 additions & 41 deletions pathway_importer.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@

ro = OboRO()
ENABLED_BY = URIRef(expand_uri(ro.enabled_by))
HAS_INPUT = URIRef(expand_uri("RO:0002233"))

parser = argparse.ArgumentParser()
parser.add_argument('-f', "--filename", type=str, required=True,
Expand Down Expand Up @@ -42,11 +43,18 @@ def test_label_finding(model):
print(labels)
axiom_counter += 1


def main():

## Organize connection objects
## Declare entity A GPs and MFs
## Add "Has_input" relations between MF and entity B GPs
## If entity B not declared, declare it
## Connect regulation relations to all MF's enabled by entity B
## If no MF for entity B, add root MF enabled by B

args = parser.parse_args()

model = GoCamModel("connect_all_genes.ttl")
model = GoCamModel("delete_uncertain_multi_activities.ttl")
# p_connections = PathwayConnectionSet("SIGNOR-G2-M_trans_02_03_18.tsv")
p_connections = PathwayConnectionSet(args.filename)
linenum = 1
Expand All @@ -57,6 +65,25 @@ def main():
print(total_pcs)
skipped_count = 0

# Toss out connections according to precedence rules:
# protein kinase activity should be chosen over protein binding
# This should be separate from/before any OWL individuals are declared
for pc in p_connections.connections:
# Get list of all pcs with pc.id_a and pc.id_b
# If len of list is > 1
# Look for protein kinase activity (GO:0004672), delete others if remaining are all protein binding (GO:0005515)
pc_list = p_connections.find_all_by_id_a_and_id_b(pc)
if len(pc_list.connections) > 1:
the_good_one = pc_list.find_by_mech_term("GO:0004672")
the_bad_one = pc_list.find_by_mech_term("GO:0005515")
# adfkafkeae # WHY IS THIS NOT CATCHING ATM TO ABL1 MFs?
if the_good_one is not None and the_bad_one is not None:
pc_list.connections.remove(the_good_one)
p_connections.remove_list(pc_list.connections)
elif the_good_one is not None:
[uncertain_pc.print() for uncertain_pc in pc_list.connections]
p_connections.remove_list(pc_list.connections)

# fill in regulated activities
for pc in p_connections.connections:
regulated_activity_pc = p_connections.find_other_regulated_activity(pc.id_b)
Expand All @@ -74,38 +101,36 @@ def main():
else:
pc.regulated_activity["term"] = regulated_activity_term
pc.regulated_activity["uri"] = regulated_activity_term_uri
# pc.individuals[pc.regulated_activity["term"]] = regulated_activity_term_uri

# model = pc.declare_entities(model)

# enabled_by_stmt_a = model.writer.emit(model.individuals[pc.mechanism_go_term], ENABLED_BY, model.individuals[pc.full_id_a()])
# if pc.mechanism["term"] in pc.individuals and not model_contains_statement(model, pc.individuals[pc.mechanism["term"]], ENABLED_BY, pc.full_id_a()):
# full_statement = pc.full_statement_bnode_in_model(model)
# if pc.mechanism["term"] in pc.individuals and full_statement is None:
# if full_statement is None:
# print("Hey " + pc.full_id_a())
# if pc.id_a == "Q13315" and pc.id_b == "P38398":
# print("Dang " + pc.pmid[0])
# model = pc.declare_entities(model)

# enabled_by_stmt_a_triple = (pc.mechanism["uri"], ENABLED_BY, pc.individuals[pc.full_id_a()])
if pc.a_is_complex():
entity_a = pc.complex_a.uri_in_model(model)
else:
entity_a = pc.full_id_a()
if entity_a is not None:
enabled_by_stmt_a_triples = model.triples_by_ids(pc.mechanism["term"], ENABLED_BY, entity_a)
else:
enabled_by_stmt_a_triples = []
if len(enabled_by_stmt_a_triples) == 0:
# If triple A doesn't exist for entities, declare individuals and create it
# enabled_by_stmt_a = model.writer.emit(pc.mechanism["term"], ENABLED_BY, pc.full_id_a())
model = pc.declare_a(model)
pc.enabled_by_stmt_a = model.writer.emit(pc.mechanism["uri"], ENABLED_BY, pc.individuals[pc.full_id_a()])
model.add_axiom(pc.enabled_by_stmt_a)
# Don't care about existing "statements", just look for existing entity A GP and always create new enabled by statement
# if entity_a is not None:
# enabled_by_stmt_a_triples = model.triples_by_ids(pc.mechanism["term"], ENABLED_BY, entity_a)
# else:
# enabled_by_stmt_a_triples = []
# if len(enabled_by_stmt_a_triples) == 0:

# If triple A doesn't exist for entities, declare individuals and create it
# enabled_by_stmt_a = model.writer.emit(pc.mechanism["term"], ENABLED_BY, pc.full_id_a())
if entity_a is None or not isinstance(entity_a, URIRef):
for uri_a in model.uri_list_for_individual(pc.full_id_a()):
pc.individuals[pc.full_id_a()] = uri_a
if pc.full_id_a() not in pc.individuals:
model = pc.declare_a(model)
else:
pc.enabled_by_stmt_a = enabled_by_stmt_a_triples[0]
pc.individuals[pc.full_id_a()] = entity_a
pc.mechanism["uri"] = model.declare_individual(pc.mechanism["term"])
pc.individuals[pc.mechanism["term"]] = pc.mechanism["uri"]
pc.enabled_by_stmt_a = model.writer.emit(pc.mechanism["uri"], ENABLED_BY, pc.individuals[pc.full_id_a()])
axiom_a = model.add_axiom(pc.enabled_by_stmt_a)
model.add_evidence(axiom_a, "EXP", ["PMID:" + pmid for pmid in pc.pmid])

# else:
# pc.enabled_by_stmt_a = enabled_by_stmt_a_triples[0]

# Now that the a's are declared, go check on the b's.
for pc in p_connections.connections:
Expand All @@ -118,28 +143,29 @@ def main():
enabled_by_stmt_b_triples = model.triples_by_ids(None, ENABLED_BY, entity_b)
else:
enabled_by_stmt_b_triples = []
# If pointing to activity
regulated_activity_uris = []
for b_triple in enabled_by_stmt_b_triples:
regulated_activity_uris.append(b_triple[0])
# If pointing to GP
entity_b_uris = model.uri_list_for_individual(pc.full_id_b())
if len(regulated_activity_uris) == 0:
model = pc.declare_b(model)
enabled_by_stmt_b = model.writer.emit(pc.regulated_activity["uri"], ENABLED_BY,
pc.individuals[pc.full_id_b()])
model.add_axiom(enabled_by_stmt_b)
axiom_b = model.add_axiom(enabled_by_stmt_b)
# model.add_evidence(axiom_b, "EXP", ["PMID:" + pmid for pmid in pc.pmid]) # Maybe don't want to add evidence to B since we're assuming these statements?
regulated_activity_uris.append(enabled_by_stmt_b[0])
# if enabled_by_stmt_b_triple in model.writer.writer.graph:
# enabled_by_stmt_b = next(model.writer.writer.graph.triples(enabled_by_stmt_b_triple))
# else:
# enabled_by_stmt_b = model.writer.emit(enabled_by_stmt_b_triple[0], enabled_by_stmt_b_triple[1], enabled_by_stmt_b_triple[2])
# axiom_b = model.add_axiom(enabled_by_stmt_b)
entity_b_uris.append(pc.individuals[pc.full_id_b()])

for entity_b_uri in entity_b_uris:
model.writer.emit(pc.enabled_by_stmt_a[0], HAS_INPUT, entity_b_uri)
relation_axiom = model.writer.emit_axiom(pc.enabled_by_stmt_a[0], HAS_INPUT, entity_b_uri)

# Connect the two activities
# Decouple this from ENABLED_BY statements to allow multiple regulation relations from one GP-MF node - issue #2
# source_id = model.individuals[pc.mechanism_go_term]
source_id = pc.enabled_by_stmt_a[0]
property_id = URIRef(expand_uri(pc.relation))
# target_id = model.individuals[pc.regulated_activity_term]
# target_id = pc.regulated_activity["uri"] # This should be an array of target activities (individual_list)
# if not model_contains_statement(model, source_id, property_id, pc.regulated_activity["term"]): # Make into for loop
for reg_activity_uri in regulated_activity_uris:
target_id = reg_activity_uri
Expand All @@ -148,16 +174,14 @@ def main():
# Add axiom (Source=MF term URI, Property=relation code, Target=MF term URI)
relation_axiom = model.writer.emit_axiom(source_id, property_id, target_id)
model.add_evidence(relation_axiom, "EXP", ["PMID:" + pmid for pmid in pc.pmid])
# else:
# print("2")

# pc.print()

with open(model.filepath, 'wb') as f:
model.writer.writer.serialize(destination=f)

print(skipped_count)

grouped = map(lambda x:x.id_a, p_connections.connections)
print(grouped)

if __name__ == '__main__':
main()
print("hey")
main()

0 comments on commit 4fb735e

Please sign in to comment.