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insert_worm to picks up additional expression data
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Resolves #284

Searches OpenWormData/aux_data/expression_data for innexin, neuropeptide, neurotransmitter and receptor expression data not already added.
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@clbarnes
clbarnes committed Feb 3, 2017
1 parent 2764774 commit 4eb25df
Showing 1 changed file with 121 additions and 81 deletions.
202 changes: 121 additions & 81 deletions OpenWormData/scripts/insert_worm.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
import traceback
import csv
import re
import os


SQLITE_DB_LOC = '../aux_data/celegans.db'
Expand All @@ -16,6 +17,7 @@
CONNECTOME_SOURCE = "../aux_data/herm_full_edgelist.csv"
RECEPTORS_TYPES_NEUROPEPTIDES_NEUROTRANSMITTERS_INNEXINS_SOURCE = "../aux_data/Modified celegans db dump.csv"

ADDITIONAL_EXPR_DATA_DIR = '../aux_data/expression_data'


def serialize_as_n3():
Expand All @@ -26,6 +28,7 @@ def serialize_as_n3():
P.config('rdf.graph').serialize(dest, format='n3')
print('serialized to n3 file')


def upload_muscles():
""" Upload muscles and the neurons that connect to them
"""
Expand Down Expand Up @@ -158,9 +161,11 @@ def upload_neurons():
def get_altun_evidence():
return parse_bibtex_into_evidence('../aux_data/bibtex_files/altun2009.bib')


def get_wormatlas_evidence():
return parse_bibtex_into_evidence('../aux_data/bibtex_files/WormAtlas.bib')


def parse_bibtex_into_evidence(file_name):
import bibtexparser
e = None
Expand Down Expand Up @@ -197,101 +202,135 @@ def parse_bibtex_into_evidence(file_name):
pass
return e


def upload_receptors_types_neurotransmitters_neuropeptides_innexins():
""" Augment the metadata about neurons with information about receptors,
neuron types, neurotransmitters, neuropeptides and innexins.
As we go, add evidence objects to each statement."""
print ("uploading statements about types, receptors, innexins, neurotransmitters and neuropeptides")

#set up evidence objects in advance
altun_ev = get_altun_evidence()
wormatlas_ev = get_wormatlas_evidence()
_upload_receptors_types_neurotransmitters_neuropeptides_innexins_from_file(
RECEPTORS_TYPES_NEUROPEPTIDES_NEUROTRANSMITTERS_INNEXINS_SOURCE
)


def upload_additional_receptors_neurotransmitters_neuropeptides_innexins():
""" Augment the metadata about neurons with information about receptor, neurotransmitter, and neuropeptide
expression from additional sources.
"""
print ("uploading additional statements about receptors, neurotransmitters and neuropeptides")

import csv
f = open(RECEPTORS_TYPES_NEUROPEPTIDES_NEUROTRANSMITTERS_INNEXINS_SOURCE)
reader = csv.reader(f)
next(reader) #skip the header row
for root, _, filenames in sorted(os.walk(ADDITIONAL_EXPR_DATA_DIR)):
for filename in sorted(filenames):
if filename.lower().endswith('.csv'):
_upload_receptors_types_neurotransmitters_neuropeptides_innexins_from_file(os.path.join(root, filename))


def _upload_receptors_types_neurotransmitters_neuropeptides_innexins_from_file(file_path):
# set up evidence objects in advance
altun_ev = get_altun_evidence()
wormatlas_ev = get_wormatlas_evidence()

i = 0

neurons = list()
neurons = []
uris = dict()

for row in reader:
neuron_name = row[0]
relation = row[1].lower()
data = row[2]
evidence = row[3]
evidenceURL = row[4]

#prepare evidence
e = P.Evidence()

#pick correct evidence given the row
if 'altun' in evidence.lower():
e = altun_ev

elif 'wormatlas' in evidence.lower():
e = wormatlas_ev

e2 = []
try:
e2 = uris[evidenceURL]
except KeyError:
e2 = P.Evidence(uri=evidenceURL)
uris[evidenceURL] = e2

#grab the neuron object
n = NETWORK.aneuron(neuron_name)
neurons.append(n)

if relation == 'neurotransmitter':
# assign the data, grab the relation into r
r = n.neurotransmitter(data)
#assert the evidence on the relationship
e.asserts(r)
e2.asserts(r)
elif relation == 'innexin':
# assign the data, grab the relation into r
r = n.innexin(data)
#assert the evidence on the relationship
e.asserts(r)
e2.asserts(r)
elif relation == 'neuropeptide':
# assign the data, grab the relation into r
r = n.neuropeptide(data)
#assert the evidence on the relationship
e.asserts(r)
e2.asserts(r)
elif relation == 'receptor':
# assign the data, grab the relation into r
r = n.receptor(data)
#assert the evidence on the relationship
e.asserts(r)
e2.asserts(r)

if relation == 'type':
types = []
if 'sensory' in (data.lower()):
types.append('sensory')
if 'interneuron' in (data.lower()):
types.append('interneuron')
if 'motor' in (data.lower()):
types.append('motor')
if 'unknown' in (data.lower()):
types.append('unknown')
# assign the data, grab the relation into r
for t in types:
r = n.type(t)
#assert the evidence on the relationship
e.asserts(r)
e2.asserts(r)

i = i + 1
with open(file_path) as f:
reader = csv.reader(f)
next(reader) # skip the header row

for row in reader:
neuron_name = row[0]
relation = row[1].lower()
data = row[2]
evidence = row[3]
evidenceURL = row[4]

# prepare evidence
e = P.Evidence()

# pick correct evidence given the row
if 'altun' in evidence.lower():
e = altun_ev
elif 'wormatlas' in evidence.lower():
e = wormatlas_ev

e2 = []
try:
e2 = uris[evidenceURL]
except KeyError:
e2 = P.Evidence(uri=evidenceURL)
uris[evidenceURL] = e2

# grab the neuron object
n = NETWORK.aneuron(neuron_name)
neurons.append(n)

if relation == 'neurotransmitter':
if data in n.neurotransmitter():
continue
# assign the data, grab the relation into r
r = n.neurotransmitter(data)
# assert the evidence on the relationship
e.asserts(r)
e2.asserts(r)

elif relation == 'innexin':
if data in n.innexin():
continue
# assign the data, grab the relation into r
r = n.innexin(data)
# assert the evidence on the relationship
e.asserts(r)
e2.asserts(r)

elif relation == 'neuropeptide':
if data in n.neuropeptide():
continue
# assign the data, grab the relation into r
r = n.neuropeptide(data)
# assert the evidence on the relationship
e.asserts(r)
e2.asserts(r)

elif relation == 'receptor':
if data in n.receptor():
continue
# assign the data, grab the relation into r
r = n.receptor(data)
# assert the evidence on the relationship
e.asserts(r)
e2.asserts(r)

elif relation == 'type':
if data.lower() in n.type():
continue
types = []
if 'sensory' in (data.lower()):
types.append('sensory')
if 'interneuron' in (data.lower()):
types.append('interneuron')
if 'motor' in (data.lower()):
types.append('motor')
if 'unknown' in (data.lower()):
types.append('unknown')
# assign the data, grab the relation into r
for t in types:
r = n.type(t)
# assert the evidence on the relationship
e.asserts(r)
e2.asserts(r)

i += 1

for neur in neurons:
n = NETWORK.neuron(neur)
print ("uploaded " + str(i) + " statements about types, receptors, innexins, neurotransmitters and neuropeptides")
NETWORK.neuron(neur)
print(
'uploaded {} statements about types, receptors, innexins, neurotransmitters and neuropeptides from {}'.format(
i, file_path
)
)


def upload_connections():
Expand Down Expand Up @@ -510,6 +549,7 @@ def do_insert(config="default.conf", logging=False):
upload_lineage_and_descriptions()
upload_connections()
upload_receptors_types_neurotransmitters_neuropeptides_innexins()
upload_additional_receptors_neurotransmitters_neuropeptides_innexins()

print("Saving...")
WORM.save()
Expand Down

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