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
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)
self.ogw = OWLGraphWrapper(self.o)
self.start_auto_text = "---------------Text extracted from ontology: DO NOT EDIT---------------"
self.end_auto_text = "---------------END AUTO GENERATED SECTION---------------"
def get_valid_OP_list(self):
"""Returns a list of relations in the display_for_curators subset"""
s = self.o.getObjectPropertiesInSignature()
out = []
for r in s:
# Slightly dodgy hard-wiring of validity criterion
if 'display_for_curators' in self.ogw.getSubsets(r):
out.append(self.bsfp.getShortForm(r))
return out
def test_then_get_annotation(self, entity_sfid, AP):
content = ''
try:
content = self.b.getAnnotation(entity_sfid, AP)
except:
warnings.warn("%s has no annotations with %s" % (entity_sfid, AP))
pass
return content
def gen_includes_md(self, r, id_name):
"""Generate markdown for inclusion in wiki page
r = relation_shortFormId
id_name = and id_name dict lookup to use for domain and range
"""
# Be carful
auto_text = "%s\n" % self.start_auto_text
auto_text += "\n## %s\n" % self.test_then_get_annotation(
r, "shorthand")
auto_text += "* OWL ID: %s\n" % r
auto_text += "* label: %s\n" % self.test_then_get_annotation(
r, 'label')
auto_text += "* synonyms\n%s\n" % str(
list(self.ogw.getOBOSynonymStrings(self.bsfp.getEntity(r),
[]))) # could be prettified
auto_text += "\n### Definition\n%s\n" % self.test_then_get_annotation(
r, "IAO_0000115")
auto_text += "\n### Usage\n%s\n" % self.test_then_get_annotation(
r, "usage") #
auto_text += "\n### Comment\n%s\n" % self.test_then_get_annotation(
r, "comment") #
auto_text += "\n### Subsets\n%s\n" % str(
self.ogw.getSubsets(
self.bsfp.getEntity(r))) # Perhaps only display AE_
# Finding child and parent relations would take a reasoner object call. Better for annotators to reply on graph.
# MIght be useful to give some record of how often used in ontology
local_domain = self.test_then_get_annotation(r, "local_domain")
local_range = self.test_then_get_annotation(r, "local_range")
ldd = {}
if local_domain:
for ld in local_domain.split(" "):
if ld in id_name.keys():
ldd[ld] = id_name[ld]
else:
ldd[ld] = ''
id_name[ld] = ''
auto_text += "\n##local domain\n%s\n" % str(ldd)
lrd = {}
if local_range:
for lr in local_range.split(" "):
if lr in id_name.keys():
lrd[lr] = id_name[lr]
else:
lrd[lr] = ''
id_name[lr] = ''
auto_text += "\n## local range\n%s\n" % str(lrd)
auto_text += "\n%s\n" % self.end_auto_text
return auto_text
from owl2pdm_tools import ont_manager
from uk.ac.ebi.brain.core import Brain
from neo4j_tools import neo4j_connect
import sys
import re
"""Add typing via anonymous class expressions from OWL file.
Requires uniqueness constraint on individual & class short_form_id."""
nc = neo4j_connect(base_uri = sys.argv[1], usr = sys.argv[2], pwd = sys.argv[3])
vfb = Brain()
vfb.learn(sys.argv[4]) # Make this non-local
vom = ont_manager(vfb.getOntology())
# vom.typeAxioms2pdm(sfid = 'VFB_00005000')
# example = [{'isAnonymous': False, 'objectId': u'FBbt_00100247'},
# {'relId': u'BFO_0000050', 'isAnonymous': True, 'objectId': u'FBbt_00003624'},
# {'relId': u'BFO_0000050', 'isAnonymous': True, 'objectId': u'FBbt_00007011'},
# {'relId': u'RO_0002292', 'isAnonymous': True, 'objectId': u'FBtp0014830'}]
# Simple to use. Only issue is resolution of short_form_ids. This can be done as long as these are stored as attributes on relations. These should be added in the process of adding named relations. Check proposed schema on ticket...
# Get all inds by query
inds = vfb.getInstances("Thing", 0)
# Could grab from neo4J avoiding Brain
