class om():
def __init__(self, uri_or_fp):
self.b = Brain()
self.b.learn(uri_or_fp)
self.o = self.b.getOntology()
self.bsfp = self.b.getBidiShortFormProvider(
) # uses .getEntity(<string> shortForm), .getShortForm(OWLEntity entity)
def get_OP_list(self):
s = self.o.getObjectPropertiesInSignature()
out = []
for r in s:
out.append(self.bsfp.getShortForm(r))
return out
def roll_pdm(self, id_name):
# TODO - get subsets + regular domain and range
out = {}
relations = self.get_OP_list()
local_domains = []
local_ranges = []
for r in relations:
#Assumes everything in file has a shorthand! # Better to key primary model on shortFormID and then re-key after reading.
shorthand = self.b.getAnnotation(r, "shorthand")
out[shorthand] = {}
out[shorthand]['label'] = self.b.getLabel(r)
try:
out[shorthand]['usage'] = self.b.getAnnotation(r, "usage")
out[shorthand]['defn'] = self.b.getAnnotation(r, "IAO_0000115")
local_domains = self.b.getAnnotation(r,
"local_domain").split(" ")
local_ranges = self.b.getAnnotation(r,
"local_range").split(" ")
except:
pass
if local_domains:
ldd = {}
for ld in local_domains:
if ld in id_name.keys():
ldd[ld] = id_name[ld]
else:
ldd[ld] = ''
out[shorthand]['local_domain'] = str(ldd)
if local_ranges:
lrd = {}
for lr in local_ranges:
if lr in id_name.keys():
lrd[lr] = id_name[lr]
else:
lrd[lr] = ''
out[shorthand]['local_range'] = str(lrd)
return out
class om():
def __init__(self, uri_or_fp):
self.b = Brain()
self.b.learn(uri_or_fp)
self.o = self.b.getOntology()
self.bsfp = self.b.getBidiShortFormProvider() # uses .getEntity(<string> shortForm), .getShortForm(OWLEntity entity)
def get_OP_list(self):
s = self.o.getObjectPropertiesInSignature()
out = []
for r in s:
out.append(self.bsfp.getShortForm(r))
return out
def roll_pdm(self, id_name):
# TODO - get subsets + regular domain and range
out = {}
relations = self.get_OP_list()
local_domains = []
local_ranges = []
for r in relations:
#Assumes everything in file has a shorthand! # Better to key primary model on shortFormID and then re-key after reading.
shorthand = self.b.getAnnotation(r, "shorthand")
out[shorthand] = {}
out[shorthand]['label'] = self.b.getLabel(r)
try:
out[shorthand]['usage'] = self.b.getAnnotation(r, "usage")
out[shorthand]['defn'] = self.b.getAnnotation(r, "IAO_0000115")
local_domains = self.b.getAnnotation(r, "local_domain").split(" ")
local_ranges = self.b.getAnnotation(r, "local_range").split(" ")
except:
pass
if local_domains:
ldd = {}
for ld in local_domains:
if ld in id_name.keys():
ldd[ld] = id_name[ld]
else:
ldd[ld] = ''
out[shorthand]['local_domain'] = str(ldd)
if local_ranges:
lrd = {}
for lr in local_ranges:
if lr in id_name.keys():
lrd[lr] = id_name[lr]
else:
lrd[lr] = ''
out[shorthand]['local_range'] = str(lrd)
return out
for term in tc:
oboid = term["extId"][0]
known_term_list.append(oboid)
if oboid in oboid_domId:
if "domainId" in term["domainData"]:
term["domainData"]["domainId"] = oboid_domId[oboid] # Terns that didn't formerly have domainId will not, at the point
else:
term["domainData"] = {"domainColour": [0,128,128,127],"domainId": oboid_domId[oboid],"domainSelected": "false"} # Setting default colour - will need to fix.
else:
if "domainId" in term["domainData"]:
term["domainData"]["domainId"] = '' # Remove old domain_id, if present.
owl_id = re.sub(':','_',oboid)
name = '';
if fbbt.knowsClass(owl_id):
name = fbbt.getLabel(owl_id)
print "Ignoring %s %s as , according to the mapping file, it is not a painted domain." % (oboid, name)
new_tc.append(term)
# Adding records for any new terms
for oboid, domid in oboid_domId.items():
if oboid not in known_term_list:
new_tc.append({"domainData":{"domainColour": [0,128,128,127],"domainId": domid,"domainSelected": "false"}, "extId": [oboid],"nodeState": {"open": "false", "selected": "false"} }) # Anything generated here will need a new nodeId.
update_names(new_tc, fbbt)
fbbt.sleep()
write_json(new_tc, "../json/treeContent_JFRC_BN_final.jso")
#!/usr/bin/env jython
import json
from uk.ac.ebi.brain.core import Brain
import sys
"""Takes a list of ontology URIs as args, writes a JSON lookup of ID:name."""
out = {}
for path in sys.argv[1:]:
entities = []
o = Brain()
o.learn(path)
entities.extend(list(o.getSubClasses('Thing', 0)))
entities.extend(list(o.getInstances('Thing', 0)))
for e in entities:
# Need check for if label exists. Should be able to do that by iterating over all annotations on class to check. Will slow things down a lot...
out[e] = o.getLabel(e)
o.sleep()
OUT = open('id_name.json', 'w')
OUT.write(json.dumps(out))
b.learn(v[sys.argv[1]])
# Get all classes
sc = b.getSubClasses('Thing', 0)
# set constraints
# Add nodes
statements = []
for c in sc:
label = ''
try:
label = b.getLabel(c)
label = re.sub("'", "\\'", label)
except:
pass
is_obsolete = False
try:
if b.getAnnotation(c, 'deprecated') == 'true':
is_obsolete = True
except:
pass
statements.append('MERGE (c:Class { short_form : "%s")' % c)
statements.append('MATCH (c:Class { short_form : "%s") SET c.label = "%s" SET c.is_obsolete = %r'
% (c, label, is_obsolete))
nc.commit_list(statements)
b.sleep()
from uk.ac.ebi.brain.core import Brain
import json
all_ont = Brain()
all_ont.learn = ("") # fbbi
all_ont.learn = ("") # fbbt
all_ont.learn = ("") # fbdv
classlist = all_ont.getSubClasses("Thing", 0)
id_name = {}
for c in classlist:
id_name[c] = all_ont.getLabel(c)
lookup = open("lookup", "w")
lookup.write(json.dump(id_name))
#!/usr/bin/env jython
from uk.ac.ebi.brain.core import Brain
import json
gorel = Brain()
gorel.learn("http://purl.obolibrary.org/obo/go/extensions/gorel.owl")
# Declaring AE rels as list for now.
relations = [ "GOREL_0001006" ]
# Would be better to pull list of AE rels automatically from file.
#With current structure, thus would require pulling subproperties. Can't do that with Brain.
# Iterate over list, pulling usage and saving to file named for relation:
for r in relations:
label = gorel.getLabel(r)
usage = gorel.getAnnotation(r, "usage")
usage_md = open("../.gitdown/" + label + "_usage.md", "w")
usage_md.write(usage)
usage_md.close()
gorel.sleep()
inds = vfb.getInstances("Thing", 0)
# Could grab from neo4J avoiding Brain
#statements = ["MATCH (i:Individual) RETURN i"]
#r = nc.commit_list(statements)
#inds = {some proc step here}
# Iterate over individuals, looking up types and adding them
statements = []
for i in inds:
types = vom.typeAxioms2pdm(sfid = i)
for t in types:
if t['isAnonymous']:
rel = re.sub(' ', '_', vfb.getLabel(t['relId']))
# Using related link. Can denormalise with generic edge naming script.
s = "MATCH (I:Individual), (C:Class) WHERE I.short_form = '%s'" \
"AND C.short_form = '%s' MERGE (I)-[r:Related {label: '%s', short_form: '%s' }]->(C)" \
% (i, t['objectId'], rel, t['relId']) #
statements.append(s)
facts = vom.get_triples(sfid = i)
for f in facts:
rel = re.sub(' ', '_', vfb.getLabel(f[1]))
s = "MATCH (I1:Individual), (I2:Individual) " \
"WHERE I1.short_form = '%s' and I2.short_form = '%s' " \
"MERGE (I1)-[r:Related { label: '%s', short_form: '%s' }]-(I2)" \
% (f[0], f[2], rel, f[1])
statements.append(s)
nc.commit_list_in_chunks(statements, verbose = True, chunk_length = 1000)
