def get_cpt_id(procedure, user=None):
for iden in procedure.identifiers:
if iden["identifier_type"].lower() in ["umls concept uid", "umls concept unique id", "umls concept unique identifier", "umls cui", "umls id", "umls identifier"]:
if user is not None:
proc_array = []
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/search/current?string=" + iden["identifier"] + "inputType=sourceUi&searchType=exact&sabs=MTH"
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"string": query, "ticket": tick, "pageNumber": page_num}
r = requests.get(base+ext, params=query)
r.encoding = 'utf-8'
print(r.text)
items = json.loads(r.text)
json_data = items["result"]
for rep in json_data["results"]:
if rep["ui"] not in proc_array and rep["ui"] != "NONE":
proc_array.append(rep["ui"])
if json_data["results"][0]["ui"] == "NONE":
break
return proc_array
def get_loc_sh(anat, user=None, source="umls"):
loc_array = []
for ident in anat.identifiers:
if ident["identifier_type"].lower() in [
"lch", "lcsh", "library of congress sh",
"library of congress subject heading", "loc sh"
] and ident["identifier"] not in loc_array:
loc_array.append(ident["identifier"])
if loc_array:
return loc_array
for iden in anat.identifiers:
if iden["identifier_type"].lower() in [
"neu", "neu id", "neu identifier",
"neuronames brain hierarchy id",
"neuronames brain hierarchy identifier"
]:
if source.lower() in ["umls", "all"]:
anat_array = []
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/crosswalk/current/source/NEU/" + iden["identifier"]
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"ticket": tick, "pageNumber": page_num}
r = requests.get(base + ext, params=query)
r.encoding = 'utf-8'
items = json.loads(r.text)
json_data = items["result"]
for rep in json_data:
if rep["ui"] not in loc_array and rep["ui"] != "NONE":
# Library of Congress.
if rep["rootSource"] == "LCH":
loc_array.append(rep["ui"])
gnomics.objects.anatomical_structure.AnatomicalStructure.add_identifier(
anat,
identifier=rep["ui"],
identifier_type=
"Library of Congress Subject Heading",
language=None,
source="UMLS Metathesaurus")
if not json_data:
break
return loc_array
def get_loc_sh(anat, user=None, source="umls"):
loc_array = []
for ident in anat.identifiers:
if ident["identifier_type"].lower() in ["lch", "lcsh", "library of congress sh", "library of congress subject heading", "loc sh"] and ident["identifier"] not in loc_array:
loc_array.append(ident["identifier"])
if loc_array:
return loc_array
for iden in anat.identifiers:
if iden["identifier_type"].lower() in ["neu", "neu id", "neu identifier", "neuronames brain hierarchy id", "neuronames brain hierarchy identifier"]:
if source.lower() in ["umls", "all"]:
anat_array = []
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/crosswalk/current/source/NEU/" + iden["identifier"]
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"ticket": tick, "pageNumber": page_num}
r = requests.get(base+ext, params=query)
r.encoding = 'utf-8'
items = json.loads(r.text)
json_data = items["result"]
for rep in json_data:
if rep["ui"] not in loc_array and rep["ui"] != "NONE":
# Library of Congress.
if rep["rootSource"] == "LCH":
loc_array.append(rep["ui"])
gnomics.objects.anatomical_structure.AnatomicalStructure.add_identifier(anat, identifier=rep["ui"], identifier_type="Library of Congress Subject Heading", language=None, source="UMLS Metathesaurus")
if not json_data:
break
return loc_array
def get_snomed_ct_id(phen, user = None):
if user is not None:
umls_tgt = User.umls_tgt(user)
phen_array = []
for ident in phen.identifiers:
if ident["identifier_type"].lower() in ["sct id", "sct identifier", "sctid", "snomed ct", "snomed ct concept id", "snomed id", "snomed identifier", "snomed-ct", "snomed-ct concept id", "snomed-ct id", "snomed-ct identifier"]:
phen_array.append(ident["identifier"])
if phen_array:
return phen_array
ids_completed = []
for ident in phen.identifiers:
if (ident["identifier_type"].lower() in ["hp code", "hp id", "hp identifier", "hpo code", "hpo id", "hpo identifier", "human phenotype ontology code", "human phenotype ontology id", "human phenotype ontology identifier", "hp", "hpo", "human phenotype ontology"]) and user is not None:
stringy = ident["identifier"]
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/crosswalk/current/source/HPO/" + ident["identifier"] + "?targetSource=SNOMEDCT_US"
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"ticket": tick, "pageNumber": page_num}
r = requests.get(base+ext, params=query)
r.encoding = 'utf-8'
items = json.loads(r.text)
json_data = items["result"]
for er in json_data:
if er["ui"] not in phen_array and er["ui"] != "NONE":
snomedct = er["ui"]
phen_array.append(snomedct)
if not json_data:
break
elif (ident["identifier_type"].lower() in ["hp code", "hp id", "hp identifier", "hpo code", "hpo id", "hpo identifier", "human phenotype ontology code", "human phenotype ontology id", "human phenotype ontology identifier", "hp", "hpo", "human phenotype ontology"]) and user is None:
if ident["identifier"] not in ids_completed:
ids_completed.append(ident["identifier"])
hpo_id = ident["identifier"]
if ":" in hpo_id:
hpo_id = hpo_id.replace(":", "_")
url = "https://www.ebi.ac.uk/ols/api/ontologies"
ext = "/hp/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252F" + hpo_id
r = requests.get(url+ext, headers={"Content-Type": "application/json"})
if not r.ok:
print("Something went wrong.")
else:
decoded = r.json()
for xref in decoded["annotation"]["database_cross_reference"]:
if "SNOMEDCT_US:" in xref:
snomed_id = xref.split("SNOMEDCT_US:")[1]
phen_array.append(snomed_id)
gnomics.objects.phenotype.Phenotype.add_identifier(phen, identifier = snomed_id, identifier_type = "SNOMED-CT ID", source = "OLS")
return phen_array
def get_fma_id(anat, user=None, source="umls"):
fma_array = []
for ident in anat.identifiers:
if ident["identifier_type"].lower() in ["fma", "fma id", "fma identifier", "fmaid", "foundational model of anatomy", "foundational model of anatomy id", "foundational model of anatomy identifier"] and ident["identifier"] not in fma_array:
fma_array.append(ident["identifier"])
if fma_array:
return fma_array
for iden in anat.identifiers:
if iden["identifier_type"].lower() in ["neu", "neu id", "neu identifier", "neuronames brain hierarchy id", "neuronames brain hierarchy identifier"]:
if source.lower() in ["umls", "all"] and user is not None:
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/crosswalk/current/source/NEU/" + iden["identifier"]
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"ticket": tick, "pageNumber": page_num}
r = requests.get(base+ext, params=query)
r.encoding = 'utf-8'
items = json.loads(r.text)
json_data = items["result"]
for rep in json_data:
if rep["ui"] not in anat_array and rep["ui"] != "NONE":
# FMA ID.
if rep["rootSource"] == "FMA":
fma_array.append(rep["ui"])
gnomics.objects.anatomical_structure.AnatomicalStructure.add_identifier(anat, identifier=rep["ui"], identifier_type="FMA ID", language=None, source="UMLS Metathesaurus", name=rep["name"])
if not json_data:
break
elif iden["identifier_type"].lower() in ["uwda", "uwda id", "uwda identifier"]:
if source.lower() in ["umls", "all"] and user is not None:
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/crosswalk/current/source/UWDA/" + iden["identifier"]
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"ticket": tick, "pageNumber": page_num}
r = requests.get(base+ext, params=query)
r.encoding = 'utf-8'
items = json.loads(r.text)
json_data = items["result"]
for rep in json_data:
if rep["ui"] not in anat_array and rep["ui"] != "NONE":
# FMA ID.
if rep["rootSource"] == "FMA":
fma_array.append(rep["ui"])
gnomics.objects.anatomical_structure.AnatomicalStructure.add_identifier(anat, identifier=rep["ui"], identifier_type="FMA ID", language=None, source="UMLS Metathesaurus", name=rep["name"])
if not json_data:
break
if iden["identifier_type"].lower() in ["wikidata", "wikidata accession", "wikidata id", "wikidata identifier"]:
for stuff in gnomics.objects.anatomical_structure.AnatomicalStructure.wikidata(anat):
for prop_id, prop_dict in stuff["claims"].items():
base = "https://www.wikidata.org/w/api.php"
ext = "?action=wbgetentities&ids=" + prop_id + "&format=json"
r = requests.get(base+ext, headers={"Content-Type": "application/json"})
if not r.ok:
r.raise_for_status()
sys.exit()
decoded = json.loads(r.text)
en_prop_name = decoded["entities"][prop_id]["labels"]["en"]["value"]
if en_prop_name.lower() == "foundational model of anatomy id":
for x in prop_dict:
if x["mainsnak"]["datavalue"]["value"] not in fma_array:
gnomics.objects.anatomical_structure.AnatomicalStructure.add_identifier(anat, identifier = x["mainsnak"]["datavalue"]["value"], identifier_type = "Foundational Model of Anatomy ID", language = None, source = "Wikidata")
fma_array.append(x["mainsnak"]["datavalue"]["value"])
elif (ident["identifier_type"].lower() in ["wikipedia", "wikipedia accession", "wikipedia article"]) and ident["language"].lower() == "en":
for stuff in gnomics.objects.anatomical_structure.AnatomicalStructure.wikidata(anat):
for prop_id, prop_dict in stuff["claims"].items():
base = "https://www.wikidata.org/w/api.php"
ext = "?action=wbgetentities&ids=" + prop_id + "&format=json"
r = requests.get(base+ext, headers={"Content-Type": "application/json"})
if not r.ok:
r.raise_for_status()
sys.exit()
decoded = json.loads(r.text)
en_prop_name = decoded["entities"][prop_id]["labels"]["en"]["value"]
if en_prop_name.lower() == "foundational model of anatomy id":
for x in prop_dict:
if x["mainsnak"]["datavalue"]["value"] not in fma_array:
gnomics.objects.anatomical_structure.AnatomicalStructure.add_identifier(anat, identifier = x["mainsnak"]["datavalue"]["value"], identifier_type = "Foundational Model of Anatomy ID", language = None, source = "Wikidata")
fma_array.append(x["mainsnak"]["datavalue"]["value"])
elif ident["identifier_type"].lower() in ["uberon", "uberon id", "uberon identifier"]:
gnomics.objects.anatomical_structure.AnatomicalStructure.wikipedia_accession(anat, language = "en")
anat_array = []
for stuff in gnomics.objects.anatomical_structure.AnatomicalStructure.wikidata(anat):
for prop_id, prop_dict in stuff["claims"].items():
base = "https://www.wikidata.org/w/api.php"
ext = "?action=wbgetentities&ids=" + prop_id + "&format=json"
r = requests.get(base+ext, headers={"Content-Type": "application/json"})
if not r.ok:
r.raise_for_status()
sys.exit()
decoded = json.loads(r.text)
en_prop_name = decoded["entities"][prop_id]["labels"]["en"]["value"]
if en_prop_name.lower() == "foundational model of anatomy id":
for x in prop_dict:
if x["mainsnak"]["datavalue"]["value"] not in fma_array:
gnomics.objects.anatomical_structure.AnatomicalStructure.add_identifier(anat, identifier = x["mainsnak"]["datavalue"]["value"], identifier_type = "Foundational Model of Anatomy ID", language = None, source = "Wikidata")
fma_array.append(x["mainsnak"]["datavalue"]["value"])
return fma_array
def get_meddra_obj(adverse_event, user=None, source="umls"):
obj_array = []
for ae_obj in adverse_event.adverse_event_objects:
if 'object_type' in com_obj:
if ae_obj['object_type'].lower() in ['mdr', 'mdr code', 'mdr id', 'mdr identifier', 'meddra', 'meddra code', 'meddra id', 'meddra identifier', 'meddra label', 'meddra object', 'meddra term']:
return ae_obj['object']
if obj_array:
return obj_array
ids_completed = []
if user is not None:
for meddra_term in get_meddra_term(adverse_event):
if source.lower() in ["umls", "all"] and meddra_term not in ids_completed and user.umls_api_key is not None:
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/search/current?sabs=MDR&searchType=exact&returnIdType=code"
id_array = []
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"string": str(meddra_term), "ticket": tick, "pageNumber": page_num}
r = requests.get(base+ext, params=query)
r.encoding = 'utf-8'
if not r.ok:
break
else:
items = json.loads(r.text)
json_data = items["result"]
if json_data["results"][0]["ui"] == "NONE":
break
else:
id_array.append(json_data)
if id_array:
gnomics.objects.adverse_event.AdverseEvent.add_object(adverse_event, obj = id_array, object_type = "MedDRA Object")
obj_array.append(id_array)
if source.lower() != "all":
ids_completed.append(meddra_term)
if source.lower() in ["ncbo", "all"] and meddra_term not in ids_completed and user.ncbo_api_key is not None:
base = "http://data.bioontology.org/search"
ext = "?q=" + str(meddra_term) + "&ontologies=MEDDRA&require_exact_match=true&roots_only=true/?apikey=" + user.ncbo_api_key
r = requests.get(base+ext, headers={"Content-Type": "application/json", "Authorization": "apikey token="+ user.ncbo_api_key})
if not r.ok:
continue
else:
decoded = json.loads(r.text)
id_array = []
for result in decoded["collection"]:
id_array.append(result)
if id_array:
gnomics.objects.adverse_event.AdverseEvent.add_object(adverse_event, obj = id_array, object_type = "MedDRA Object")
obj_array.append(id_array)
if source.lower() != "all":
ids_completed.append(meddra_term)
return obj_array
else:
print("MedDRA object cannot be obtained without valid user object (with valid UMLS API key or NCBO API key).")
def get_hpo_term(phen, user=None):
hpo_term_array = []
for ident in phen.identifiers:
if ident["identifier_type"].lower() in [
"hp label", "hp term", "hpo label", "hpo term",
"human phenotype ontology label",
"human phenotype ontology term"
]:
if ident["identifier"] not in hpo_id_array:
hpo_id_array.append(ident["identifier"])
if hpo_term_array:
return hpo_term_array
for ident in phen.identifiers:
if ident["identifier_type"].lower() in [
"hp code", "hp id", "hp identifier", "hpo code", "hpo id",
"hpo identifier", "human phenotype ontology code",
"human phenotype ontology id",
"human phenotype ontology identifier", "hp", "hpo",
"human phenotype ontology"
]:
if user:
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/content/current/source/HPO/" + ident["identifier"]
umls_tgt = User.umls_tgt(user)
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"ticket": tick, "pageNumber": page_num}
r = requests.get(base + ext, params=query)
r.encoding = 'utf-8'
try:
items = json.loads(r.text)
json_data = items["result"]
if "name" in json_data:
if json_data["name"] not in hpo_term_array:
hpo_term = json_data["name"]
gnomics.objects.phenotype.Phenotype.add_identifier(
phen,
identifier=hpo_term,
identifier_type="HPO Term",
source="UMLS",
taxon="H**o sapiens")
hpo_term_array.append(hpo_term)
else:
break
except:
break
break
else:
proc_id = ident["identifier"]
if ":" in proc_id:
proc_id = proc_id.replace(":", "_")
url = "https://www.ebi.ac.uk/ols/api/ontologies"
ext = "/hp/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252F" + proc_id
r = requests.get(url + ext,
headers={"Content-Type": "application/json"})
if not r.ok:
print("Something went wrong.")
else:
new_decoded = r.json()
if new_decoded["label"] not in hpo_term_array:
gnomics.objects.phenotype.Phenotype.add_identifier(
phen,
identifier=new_decoded["label"],
identifier_type="HPO Term",
source="OLS",
taxon="H**o sapiens")
hpo_term_array.append(new_decoded["label"])
return hpo_term_array
def search(query,
user=None,
source="ebi",
search_type="exact",
return_id_type="sourceUi"):
anat_list = []
anat_id_array = []
if source.lower() in ["ebi", "all"]:
url = "http://www.ebi.ac.uk/ols/api/"
ext = "search?q=" + str(
query
) + "&ontology=aeo,caro,fma,uberon,ceph,ehdaa2,emap,emapa,fbbt,hao,ma,mfmo,plana,tads,tgma,wbbt,xao,zfa,fao"
r = requests.get(url + ext,
headers={"Content-Type": "application/json"})
if not r.ok:
print("An error occurred in the EBI OLS API.")
else:
decoded = r.json()
# See here:
# https://www.ebi.ac.uk/ols/ontologies
for doc in decoded["response"]["docs"]:
if "obo_id" in doc:
# Taxon agnostic (I think)
if "AEO" in doc["obo_id"]:
new_id = doc["obo_id"]
if new_id not in anat_id_array:
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=new_id,
identifier_type="AEO ID",
source="Ontology Lookup Service",
name=doc["label"])
anat_list.append(anat_temp)
anat_id_array.append(new_id)
elif "CARO" in doc["obo_id"]:
new_id = doc["obo_id"]
if new_id not in anat_id_array:
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=new_id,
identifier_type="CARO ID",
source="Ontology Lookup Service",
name=doc["label"])
anat_list.append(anat_temp)
anat_id_array.append(new_id)
elif "FAO" in doc["obo_id"]:
new_id = doc["obo_id"]
if new_id not in anat_id_array:
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=new_id,
identifier_type="FAO ID",
source="Ontology Lookup Service",
name=doc["label"])
anat_list.append(anat_temp)
anat_id_array.append(new_id)
elif "UBERON" in doc["obo_id"]:
new_id = doc["obo_id"]
if new_id not in anat_id_array:
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=new_id,
identifier_type="UBERON ID",
source="Ontology Lookup Service",
name=doc["label"])
anat_list.append(anat_temp)
anat_id_array.append(new_id)
# Taxon specific (I think)
elif "CEPH" in doc["obo_id"]:
new_id = doc["obo_id"]
if new_id not in anat_id_array:
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=new_id,
identifier_type="CEPH ID",
source="Ontology Lookup Service",
taxon="Cephalopoda",
name=doc["label"])
anat_list.append(anat_temp)
anat_id_array.append(new_id)
elif "EHDAA2" in doc["obo_id"]:
new_id = doc["obo_id"]
if new_id not in anat_id_array:
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=new_id,
identifier_type="EHDAA2 ID",
source="Ontology Lookup Service",
taxon="H**o sapiens",
name=doc["label"])
anat_list.append(anat_temp)
anat_id_array.append(new_id)
elif "EMAP" in doc["obo_id"]:
new_id = doc["obo_id"]
if new_id not in anat_id_array:
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=new_id,
identifier_type="EMAP ID",
source="Ontology Lookup Service",
taxon="Mus",
name=doc["label"])
anat_list.append(anat_temp)
anat_id_array.append(new_id)
elif "EMAPA" in doc["obo_id"]:
new_id = doc["obo_id"]
if new_id not in anat_id_array:
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=new_id,
identifier_type="EMAPA ID",
source="Ontology Lookup Service",
taxon="Mus",
name=doc["label"])
anat_list.append(anat_temp)
anat_id_array.append(new_id)
elif "FBbt" in doc["obo_id"]:
new_id = doc["obo_id"]
if new_id not in anat_id_array:
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=new_id,
identifier_type="FBbt ID",
source="Ontology Lookup Service",
taxon="Drosophila melanogaster",
name=doc["label"])
anat_list.append(anat_temp)
anat_id_array.append(new_id)
elif "FMA" in doc["obo_id"]:
new_id = doc["obo_id"]
if new_id not in anat_id_array:
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=new_id,
identifier_type="FMA ID",
source="Ontology Lookup Service",
name=doc["label"],
taxon="H**o sapiens")
anat_list.append(anat_temp)
anat_id_array.append(new_id)
elif "HAO" in doc["obo_id"]:
new_id = doc["obo_id"]
if new_id not in anat_id_array:
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=new_id,
identifier_type="HAO ID",
source="Ontology Lookup Service",
taxon="Hymenoptera",
name=doc["label"])
anat_list.append(anat_temp)
anat_id_array.append(new_id)
elif "MA" in doc["obo_id"]:
new_id = doc["obo_id"]
if new_id not in anat_id_array:
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=new_id,
identifier_type="MA ID",
source="Ontology Lookup Service",
taxon="Mus",
name=doc["label"])
anat_list.append(anat_temp)
anat_id_array.append(new_id)
elif "MFMO" in doc["obo_id"]:
new_id = doc["obo_id"]
if new_id not in anat_id_array:
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=new_id,
identifier_type="MFMO ID",
source="Ontology Lookup Service",
taxon="Mammalia",
name=doc["label"])
anat_list.append(anat_temp)
anat_id_array.append(new_id)
elif "PLANA" in doc["obo_id"]:
new_id = doc["obo_id"]
if new_id not in anat_id_array:
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=new_id,
identifier_type="PLANA ID",
source="Ontology Lookup Service",
taxon="Schmidtea mediterranea",
name=doc["label"])
anat_list.append(anat_temp)
anat_id_array.append(new_id)
elif "TADS" in doc["obo_id"]:
new_id = doc["obo_id"]
if new_id not in anat_id_array:
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=new_id,
identifier_type="FBbt ID",
source="Ontology Lookup Service",
taxon=["Ixodidae", "Argassidae"],
name=doc["label"])
anat_list.append(anat_temp)
anat_id_array.append(new_id)
elif "TGMA" in doc["obo_id"]:
new_id = doc["obo_id"]
if new_id not in anat_id_array:
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=new_id,
identifier_type="TGMA ID",
source="Ontology Lookup Service",
taxon="Culicidae",
name=doc["label"])
anat_list.append(anat_temp)
anat_id_array.append(new_id)
elif "WBBT" in doc["obo_id"]:
new_id = doc["obo_id"]
if new_id not in anat_id_array:
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=new_id,
identifier_type="WBBT ID",
source="Ontology Lookup Service",
taxon="Caenorhabditis elegans",
name=doc["label"])
anat_list.append(anat_temp)
anat_id_array.append(new_id)
elif "XAO" in doc["obo_id"]:
new_id = doc["obo_id"]
if new_id not in anat_id_array:
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=new_id,
identifier_type="XAO ID",
source="Ontology Lookup Service",
taxon="Xenopus laevis",
name=doc["label"])
anat_list.append(anat_temp)
anat_id_array.append(new_id)
elif "ZFA" in doc["obo_id"]:
new_id = doc["obo_id"]
if new_id not in anat_id_array:
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=new_id,
identifier_type="ZFA ID",
source="Ontology Lookup Service",
taxon="Danio rerio",
name=doc["label"])
anat_list.append(anat_temp)
anat_id_array.append(new_id)
if source.lower() in ["umls", "all"] and user is not None:
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/search/current?string=" + query + "&inputType=sourceUi&searchType=words&returnIdType=" + return_id_type
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"string": query, "ticket": tick, "pageNumber": page_num}
r = requests.get(base + ext, params=query)
r.encoding = 'utf-8'
# print(r.text)
items = json.loads(r.text)
json_data = items["result"]
for rep in json_data["results"]:
if rep["ui"] not in anat_id_array and rep["ui"] != "NONE":
# Foundational Model of Anatomy.
if rep["rootSource"] == "FMA":
temp_anat = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=rep["ui"],
identifier_type="FMA ID",
language=None,
source="UMLS Metathesaurus",
name=rep["name"],
taxon="H**o sapiens")
anat_list.append(temp_anat)
anat_id_array.append(rep["ui"])
# Neuronames Brain Hierarchy.
elif rep["rootSource"] == "NEU":
temp_anat = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=rep["ui"],
identifier_type="NEU ID",
language=None,
source="UMLS Metathesaurus",
name=rep["name"])
anat_list.append(temp_anat)
anat_id_array.append(rep["ui"])
# Digital Anatomist.
elif rep["rootSource"] == "UWDA":
temp_anat = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=rep["ui"],
identifier_type="UWDA ID",
language=None,
source="UMLS Metathesaurus",
name=rep["name"],
taxon="H**o sapiens")
anat_list.append(temp_anat)
anat_id_array.append(rep["ui"])
if json_data["results"][0]["ui"] == "NONE":
break
if source.lower() in ["ncbo", "all"] and user.ncbo_api_key is not None:
base = "http://data.bioontology.org/search"
ext = "?q=" + str(
query
) + "&ontologies=FMA,PAE,XAO,UBERON,ZEA,FB-BT,FAO,WB-BT,ZFA,HAO,TGMA,ICD11-BODYSYSTEM,DDANAT,SPD,TADS,VHOG,CARO,MA,MOOCCUADO,EMAPA,CTENO,MOOCCIADO,AAO,PHMAMMADO,CEPH,PHFUMIADO,HAROREADO,CISAVIADO,MAT,EHDA,MFMO,CIINTEADO,EHDAA,EMAP,BSAO,PLANA,MFO,EHDAA2,AEO,PORO,MOOCULADO,TAO,VSAO&roots_only=true/?apikey=" + user.ncbo_api_key
r = requests.get(base + ext,
headers={
"Content-Type": "application/json",
"Authorization":
"apikey token=" + user.ncbo_api_key
})
if not r.ok:
r.raise_for_status()
sys.exit()
else:
decoded = json.loads(r.text)
for result in decoded["collection"]:
# Foundational Model of Anatomy
if "FMA" in result["@id"]:
fma_id = result["@id"].split("/obo/")[1]
if fma_id not in anat_id_array:
anat_id_array.append(fma_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=fma_id,
identifier_type="FMA ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="H**o sapiens")
anat_list.append(anat_temp)
# Vertebrate Skeletal Anatomy Ontology
elif "VSAO" in result["@id"]:
vsao_id = result["@id"].split("/obo/")[1]
if vsao_id not in anat_id_array:
anat_id_array.append(vsao_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=vsao_id,
identifier_type="VSAO ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="Vertebrata")
anat_list.append(anat_temp)
# Teleost Anatomy Ontology
elif "TAO" in result["@id"]:
tao_id = result["@id"].split("/obo/")[1]
if tao_id not in anat_id_array:
anat_id_array.append(tao_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=tao_id,
identifier_type="TAO ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="Teleostei")
anat_list.append(anat_temp)
# Molgula oculata Anatomy and Development Ontology
elif "MOOCULADO" in result["@id"]:
mooculado_id = result["@id"].split("/obo/")[1]
if mooculado_id not in anat_id_array:
anat_id_array.append(mooculado_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=mooculado_id,
identifier_type="MOOCULADO ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="Molgula oculata")
anat_list.append(anat_temp)
# Porifera Ontology
elif "PORO" in result["@id"]:
poro_id = result["@id"].split("/obo/")[1]
if poro_id not in anat_id_array:
anat_id_array.append(poro_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=poro_id,
identifier_type="PORO ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="Porifera")
anat_list.append(anat_temp)
# Anatomical Entity Ontology
elif "AEO" in result["@id"]:
aeo_id = result["@id"].split("/obo/")[1]
if aeo_id not in anat_id_array:
anat_id_array.append(aeo_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=aeo_id,
identifier_type="AEO ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon=None)
anat_list.append(anat_temp)
# Human Developmental Anatomy Ontology, abstract version 2
elif "EHDAA2" in result["@id"]:
ehdaa2_id = result["@id"].split("/obo/")[1]
if ehdaa2_id not in anat_id_array:
anat_id_array.append(ehdaa2_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=ehdaa2_id,
identifier_type="EHDAA2 ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="H**o sapiens")
anat_list.append(anat_temp)
# Medaka Fish Anatomy and Development Ontology
elif "MFO" in result["@id"]:
mfo_id = result["@id"].split("/obo/")[1]
if mfo_id not in anat_id_array:
anat_id_array.append(mfo_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=mfo_id,
identifier_type="MFO ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="Oryzias latipes")
anat_list.append(anat_temp)
# Planarian Anatomy and Developmental Stage Ontology
elif "PLANA" in result["@id"]:
plana_id = result["@id"].split("/obo/")[1]
if plana_id not in anat_id_array:
anat_id_array.append(plana_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=plana_id,
identifier_type="PLANA ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="Schmidtea mediterranea")
anat_list.append(anat_temp)
# Botryllus schlosseri anatomy and development Ontology
elif "BSAO" in result["@id"]:
bsao_id = result["@id"].split("/obo/")[1]
if bsao_id not in anat_id_array:
anat_id_array.append(bsao_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=bsao_id,
identifier_type="BSAO ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="Botryllus schlosseri")
anat_list.append(anat_temp)
# Mouse Gross Anatomy and Development Ontology
elif "EMAP" in result["@id"]:
emap_id = result["@id"].split("/obo/")[1]
if emap_id not in anat_id_array:
anat_id_array.append(emap_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=emap_id,
identifier_type="EMAP ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="Mus")
anat_list.append(anat_temp)
# Human Developmental Anatomy Ontology, abstract version 1
elif "EHDAA" in result["@id"]:
ehdaa_id = result["@id"].split("/obo/")[1]
if ehdaa_id not in anat_id_array:
anat_id_array.append(ehdaa_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=ehdaa_id,
identifier_type="EHDAA ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="H**o sapiens")
anat_list.append(anat_temp)
# Ciona intestinalis Anatomy and Development Ontology
elif "CIINTEADO" in result["@id"]:
ciinteado_id = result["@id"].split("/obo/")[1]
if ciinteado_id not in anat_id_array:
anat_id_array.append(ciinteado_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=ciinteado_id,
identifier_type="CIINTEADO ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="Ciona intestinalis")
anat_list.append(anat_temp)
# Mammalian Feeding Muscle Ontology
elif "MFMO" in result["@id"]:
mfmo_id = result["@id"].split("/obo/")[1]
if mfmo_id not in anat_id_array:
anat_id_array.append(mfmo_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=mfmo_id,
identifier_type="MFMO ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="Mammalia")
anat_list.append(anat_temp)
# Human Developmental Anatomy Ontology, timed version
elif "EHDA" in result["@id"]:
ehda_id = result["@id"].split("/obo/")[1]
if ehda_id not in anat_id_array:
anat_id_array.append(ehda_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=ehda_id,
identifier_type="EHDA ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="H**o sapiens")
anat_list.append(anat_temp)
# Minimal Anatomical Terminology
elif "MAT" in result["@id"]:
mat_id = result["@id"].split("/obo/")[1]
if mat_id not in anat_id_array:
anat_id_array.append(mat_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=mat_id,
identifier_type="MAT ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon=None)
anat_list.append(anat_temp)
# Ciona savignyi Anatomy and Development Ontology
elif "CISAVIADO" in result["@id"]:
cisaviado_id = result["@id"].split("/obo/")[1]
if cisaviado_id not in anat_id_array:
anat_id_array.append(cisaviado_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=cisaviado_id,
identifier_type="CISAVIADO ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="Ciona savignyi")
anat_list.append(anat_temp)
# Halocynthia roretzi Anatomy and Development Ontology
elif "HAROREADO" in result["@id"]:
haroreado_id = result["@id"].split("/obo/")[1]
if haroreado_id not in anat_id_array:
anat_id_array.append(haroreado_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=haroreado_id,
identifier_type="HAROREADO ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="Halocynthia roretzi")
anat_list.append(anat_temp)
# Phallusia fumigata Anatomy and Development Ontology
elif "PHFUMIADO" in result["@id"]:
phfumiado_id = result["@id"].split("/obo/")[1]
if phfumiado_id not in anat_id_array:
anat_id_array.append(phfumiado_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=caro_id,
identifier_type="PHFUMIADO ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="Phallusia fumigata")
anat_list.append(anat_temp)
# Cephalopod Ontology
elif "CEPH" in result["@id"]:
ceph_id = result["@id"].split("/obo/")[1]
if ceph_id not in anat_id_array:
anat_id_array.append(ceph_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=ceph_id,
identifier_type="CEPH ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon=None)
anat_list.append(anat_temp)
# Anatomy Gross Anatomy Ontology
elif "AAO" in result["@id"]:
aao_id = result["@id"].split("/obo/")[1]
if aao_id not in anat_id_array:
anat_id_array.append(aao_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=aao_id,
identifier_type="AAO ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="Amphibia")
anat_list.append(anat_temp)
# Phallusia mammillata Anatomy and Development Ontology
elif "PHMAMMADO" in result["@id"]:
phmammado_id = result["@id"].split("/obo/")[1]
if phmammado_id not in anat_id_array:
anat_id_array.append(phmammado_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=phmammado_id,
identifier_type="PHMAMMADO ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="Phallusia mammillata")
anat_list.append(anat_temp)
# Molgula occidentalis Anatomy and Development Ontology
elif "MOOCCIADO" in result["@id"]:
moocciado_id = result["@id"].split("/obo/")[1]
if moocciado_id not in anat_id_array:
anat_id_array.append(moocciado_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=moocciado_id,
identifier_type="MOOCCIADO ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="Molgula occidentalis")
anat_list.append(anat_temp)
# Ctenophore Ontology
elif "CTENO" in result["@id"]:
cteno_id = result["@id"].split("/obo/")[1]
if cteno_id not in anat_id_array:
anat_id_array.append(cteno_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=cteno_id,
identifier_type="CTENO ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="Ctenophora")
anat_list.append(anat_temp)
# Mouse gross anatomy and development, timed
elif "EMAPA" in result["@id"]:
emapa_id = result["@id"].split("/obo/")[1]
if emapa_id not in anat_id_array:
anat_id_array.append(emapa_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=emapa_id,
identifier_type="EMAPA ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="Mus musculus")
anat_list.append(anat_temp)
# Molgula occulta Anatomy and Development Ontology
elif "MOOCCUADO" in result["@id"]:
mooccuado_id = result["@id"].split("/obo/")[1]
if mooccuado_id not in anat_id_array:
anat_id_array.append(mooccuado_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=mooccuado_id,
identifier_type="MOOCCUADO ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="Molgula occulta")
anat_list.append(anat_temp)
# Common Anatomy Reference Ontology
elif "CARO" in result["@id"]:
caro_id = result["@id"].split("/obo/")[1]
if caro_id not in anat_id_array:
anat_id_array.append(caro_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=caro_id,
identifier_type="CARO ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon=None)
anat_list.append(anat_temp)
# Vertebrate Homologous Organ Group Ontology
elif "VHOG" in result["@id"]:
vhog_id = result["@id"].split("/obo/")[1]
if vhog_id not in anat_id_array:
anat_id_array.append(vhog_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=vhog_id,
identifier_type="VHOG ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="Vertebrata")
anat_list.append(anat_temp)
# Tick Gross Anatomy Ontology
elif "TADS" in result["@id"]:
tads_id = result["@id"].split("/obo/")[1]
if tads_id not in anat_id_array:
anat_id_array.append(tads_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=tads_id,
identifier_type="TADS ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon=["Ixodidae", "Argassidae"])
anat_list.append(anat_temp)
# Spider Ontology
elif "SPD" in result["@id"]:
spd_id = result["@id"].split("/obo/")[1]
if spd_id not in anat_id_array:
anat_id_array.append(spd_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=spd_id,
identifier_type="SPD ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="Araneae")
anat_list.append(anat_temp)
# Dictyostelium Discoideum Anatomy Ontology
elif "DDANAT" in result["@id"]:
ddanat_id = result["@id"].split("/obo/")[1]
if ddanat_id not in anat_id_array:
anat_id_array.append(ddanat_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=ddanat_id,
identifier_type="DDANAT ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="Dictyostelium discoideum")
anat_list.append(anat_temp)
# Body System Terms from ICD-11
elif "ICD11-BODYSYSTEM" in result["@id"]:
icd11_id = result["@id"].split("/obo/")[1]
if icd11_id not in anat_id_array:
anat_id_array.append(icd11_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=icd11_id,
identifier_type="ICD11-BODYSYSTEM Code",
source="NCBO BioPortal",
name=result["prefLabel"])
anat_list.append(anat_temp)
# Mosquito Gross Anatomy Ontology
elif "TGMA" in result["@id"]:
tgma_id = result["@id"].split("/obo/")[1]
if tgma_id not in anat_id_array:
anat_id_array.append(tgma_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=tgma_id,
identifier_type="TGMA ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="Culicidae")
anat_list.append(anat_temp)
# Mouse Adult Gross Anatomy Ontology
elif "MA" in result["@id"]:
ma_id = result["@id"].split("/obo/")[1]
if ma_id not in anat_id_array:
anat_id_array.append(ma_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=ma_id,
identifier_type="MA ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="Mus")
anat_list.append(anat_temp)
# Hymenoptera Anatomy Ontology
elif "HAO" in result["@id"]:
hao_id = result["@id"].split("/obo/")[1]
if hao_id not in anat_id_array:
anat_id_array.append(hao_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=hao_id,
identifier_type="HAO ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="Hymenoptera")
anat_list.append(anat_temp)
# Zebrafish Anatomy and Development Ontology
elif "ZFA" in result["@id"]:
zfa_id = result["@id"].split("/obo/")[1]
if zfa_id not in anat_id_array:
anat_id_array.append(zfa_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=zfa_id,
identifier_type="ZFA ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="Danio rerio")
anat_list.append(anat_temp)
# Plant Anatomy
elif "PAE" in result["@id"]:
pae_id = result["@id"].split("/obo/")[1]
if pae_id not in anat_id_array:
anat_id_array.append(pae_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=pae_id,
identifier_type="PAE ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="Plantae")
anat_list.append(anat_temp)
# Xenopus Anatomy and Development Ontology
elif "XAO" in result["@id"]:
xao_id = result["@id"].split("/obo/")[1]
if xao_id not in anat_id_array:
anat_id_array.append(xao_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=xao_id,
identifier_type="XAO ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="Xenopus laevis")
anat_list.append(anat_temp)
# Uber Anatomy Ontology
elif "UBERON" in result["@id"]:
uberon_id = result["@id"].split("/obo/")[1]
if uberon_id not in anat_id_array:
anat_id_array.append(uberon_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=uberon_id,
identifier_type="UBERON ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon=None)
anat_list.append(anat_temp)
# Maize Gross Anatomy Ontology
elif "ZEA" in result["@id"]:
zea_id = result["@id"].split("/obo/")[1]
if zea_id not in anat_id_array:
anat_id_array.append(zea_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=zea_id,
identifier_type="ZEA ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="Zea mays")
anat_list.append(anat_temp)
# Drosophila Gross Anatomy Ontology
elif "FB-BT" in result["@id"]:
fbbt_id = result["@id"].split("/obo/")[1]
if fbbt_id not in anat_id_array:
anat_id_array.append(fbbt_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=fbbt_id,
identifier_type="FB-BT ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="Drosophila melanogaster")
anat_list.append(anat_temp)
# Fungal Gross Anatomy Ontology
elif "FAO" in result["@id"]:
fao_id = result["@id"].split("/obo/")[1]
if fao_id not in anat_id_array:
anat_id_array.append(fao_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=fao_id,
identifier_type="FAO ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="Fungi")
anat_list.append(anat_temp)
# C. elegans Gross Anatomy Ontology
elif "WB-BT" in result["@id"]:
wbbt_id = result["@id"].split("/obo/")[1]
if wbbt_id not in anat_id_array:
anat_id_array.append(wbbt_id)
anat_temp = gnomics.objects.anatomical_structure.AnatomicalStructure(
identifier=wbbt_id,
identifier_type="WB-BT ID",
source="NCBO BioPortal",
name=result["prefLabel"],
taxon="Caenorhabditis elegans")
anat_list.append(anat_temp)
return anat_list
def get_fma_id(anat, user=None, source="umls"):
fma_array = []
for ident in anat.identifiers:
if ident["identifier_type"].lower() in [
"fma", "fma id", "fma identifier", "fmaid",
"foundational model of anatomy",
"foundational model of anatomy id",
"foundational model of anatomy identifier"
] and ident["identifier"] not in fma_array:
fma_array.append(ident["identifier"])
if fma_array:
return fma_array
for iden in anat.identifiers:
if iden["identifier_type"].lower() in [
"neu", "neu id", "neu identifier",
"neuronames brain hierarchy id",
"neuronames brain hierarchy identifier"
]:
if source.lower() in ["umls", "all"] and user is not None:
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/crosswalk/current/source/NEU/" + iden["identifier"]
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"ticket": tick, "pageNumber": page_num}
r = requests.get(base + ext, params=query)
r.encoding = 'utf-8'
items = json.loads(r.text)
json_data = items["result"]
for rep in json_data:
if rep["ui"] not in anat_array and rep["ui"] != "NONE":
# FMA ID.
if rep["rootSource"] == "FMA":
fma_array.append(rep["ui"])
gnomics.objects.anatomical_structure.AnatomicalStructure.add_identifier(
anat,
identifier=rep["ui"],
identifier_type="FMA ID",
language=None,
source="UMLS Metathesaurus",
name=rep["name"])
if not json_data:
break
elif iden["identifier_type"].lower() in [
"uwda", "uwda id", "uwda identifier"
]:
if source.lower() in ["umls", "all"] and user is not None:
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/crosswalk/current/source/UWDA/" + iden["identifier"]
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"ticket": tick, "pageNumber": page_num}
r = requests.get(base + ext, params=query)
r.encoding = 'utf-8'
items = json.loads(r.text)
json_data = items["result"]
for rep in json_data:
if rep["ui"] not in anat_array and rep["ui"] != "NONE":
# FMA ID.
if rep["rootSource"] == "FMA":
fma_array.append(rep["ui"])
gnomics.objects.anatomical_structure.AnatomicalStructure.add_identifier(
anat,
identifier=rep["ui"],
identifier_type="FMA ID",
language=None,
source="UMLS Metathesaurus",
name=rep["name"])
if not json_data:
break
if iden["identifier_type"].lower() in [
"wikidata", "wikidata accession", "wikidata id",
"wikidata identifier"
]:
for stuff in gnomics.objects.anatomical_structure.AnatomicalStructure.wikidata(
anat):
for prop_id, prop_dict in stuff["claims"].items():
base = "https://www.wikidata.org/w/api.php"
ext = "?action=wbgetentities&ids=" + prop_id + "&format=json"
r = requests.get(
base + ext,
headers={"Content-Type": "application/json"})
if not r.ok:
r.raise_for_status()
sys.exit()
decoded = json.loads(r.text)
en_prop_name = decoded["entities"][prop_id]["labels"][
"en"]["value"]
if en_prop_name.lower(
) == "foundational model of anatomy id":
for x in prop_dict:
if x["mainsnak"]["datavalue"][
"value"] not in fma_array:
gnomics.objects.anatomical_structure.AnatomicalStructure.add_identifier(
anat,
identifier=x["mainsnak"]["datavalue"]
["value"],
identifier_type=
"Foundational Model of Anatomy ID",
language=None,
source="Wikidata")
fma_array.append(
x["mainsnak"]["datavalue"]["value"])
elif (ident["identifier_type"].lower() in [
"wikipedia", "wikipedia accession", "wikipedia article"
]) and ident["language"].lower() == "en":
for stuff in gnomics.objects.anatomical_structure.AnatomicalStructure.wikidata(
anat):
for prop_id, prop_dict in stuff["claims"].items():
base = "https://www.wikidata.org/w/api.php"
ext = "?action=wbgetentities&ids=" + prop_id + "&format=json"
r = requests.get(
base + ext,
headers={"Content-Type": "application/json"})
if not r.ok:
r.raise_for_status()
sys.exit()
decoded = json.loads(r.text)
en_prop_name = decoded["entities"][prop_id]["labels"][
"en"]["value"]
if en_prop_name.lower(
) == "foundational model of anatomy id":
for x in prop_dict:
if x["mainsnak"]["datavalue"][
"value"] not in fma_array:
gnomics.objects.anatomical_structure.AnatomicalStructure.add_identifier(
anat,
identifier=x["mainsnak"]["datavalue"]
["value"],
identifier_type=
"Foundational Model of Anatomy ID",
language=None,
source="Wikidata")
fma_array.append(
x["mainsnak"]["datavalue"]["value"])
elif ident["identifier_type"].lower() in [
"uberon", "uberon id", "uberon identifier"
]:
gnomics.objects.anatomical_structure.AnatomicalStructure.wikipedia_accession(
anat, language="en")
anat_array = []
for stuff in gnomics.objects.anatomical_structure.AnatomicalStructure.wikidata(
anat):
for prop_id, prop_dict in stuff["claims"].items():
base = "https://www.wikidata.org/w/api.php"
ext = "?action=wbgetentities&ids=" + prop_id + "&format=json"
r = requests.get(
base + ext,
headers={"Content-Type": "application/json"})
if not r.ok:
r.raise_for_status()
sys.exit()
decoded = json.loads(r.text)
en_prop_name = decoded["entities"][prop_id]["labels"][
"en"]["value"]
if en_prop_name.lower(
) == "foundational model of anatomy id":
for x in prop_dict:
if x["mainsnak"]["datavalue"][
"value"] not in fma_array:
gnomics.objects.anatomical_structure.AnatomicalStructure.add_identifier(
anat,
identifier=x["mainsnak"]["datavalue"]
["value"],
identifier_type=
"Foundational Model of Anatomy ID",
language=None,
source="Wikidata")
fma_array.append(
x["mainsnak"]["datavalue"]["value"])
return fma_array
def get_snomed_ct_id(phen, user=None):
if user is not None:
umls_tgt = User.umls_tgt(user)
phen_array = []
for ident in phen.identifiers:
if ident["identifier_type"].lower() in [
"sct id", "sct identifier", "sctid", "snomed ct",
"snomed ct concept id", "snomed id", "snomed identifier",
"snomed-ct", "snomed-ct concept id", "snomed-ct id",
"snomed-ct identifier"
]:
phen_array.append(ident["identifier"])
if phen_array:
return phen_array
ids_completed = []
for ident in phen.identifiers:
if (ident["identifier_type"].lower() in [
"hp code", "hp id", "hp identifier", "hpo code", "hpo id",
"hpo identifier", "human phenotype ontology code",
"human phenotype ontology id",
"human phenotype ontology identifier", "hp", "hpo",
"human phenotype ontology"
]) and user is not None:
stringy = ident["identifier"]
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/crosswalk/current/source/HPO/" + ident[
"identifier"] + "?targetSource=SNOMEDCT_US"
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"ticket": tick, "pageNumber": page_num}
r = requests.get(base + ext, params=query)
r.encoding = 'utf-8'
items = json.loads(r.text)
json_data = items["result"]
for er in json_data:
if er["ui"] not in phen_array and er["ui"] != "NONE":
snomedct = er["ui"]
phen_array.append(snomedct)
if not json_data:
break
elif (ident["identifier_type"].lower() in [
"hp code", "hp id", "hp identifier", "hpo code", "hpo id",
"hpo identifier", "human phenotype ontology code",
"human phenotype ontology id",
"human phenotype ontology identifier", "hp", "hpo",
"human phenotype ontology"
]) and user is None:
if ident["identifier"] not in ids_completed:
ids_completed.append(ident["identifier"])
hpo_id = ident["identifier"]
if ":" in hpo_id:
hpo_id = hpo_id.replace(":", "_")
url = "https://www.ebi.ac.uk/ols/api/ontologies"
ext = "/hp/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252F" + hpo_id
r = requests.get(url + ext,
headers={"Content-Type": "application/json"})
if not r.ok:
print("Something went wrong.")
else:
decoded = r.json()
for xref in decoded["annotation"][
"database_cross_reference"]:
if "SNOMEDCT_US:" in xref:
snomed_id = xref.split("SNOMEDCT_US:")[1]
phen_array.append(snomed_id)
gnomics.objects.phenotype.Phenotype.add_identifier(
phen,
identifier=snomed_id,
identifier_type="SNOMED-CT ID",
source="OLS")
return phen_array
def get_cpm(anat, user=None, source="umls"):
cpm_array = []
for iden in anat.identifiers:
if iden["identifier_type"].lower() in [
"cpm", "cpm code", "cpm id", "cpm identifier", "med",
"med code", "med id", "med identifier"
] and iden["identifier"] not in cpm_array:
cpm_array.append(iden["identifier"])
if cpm_array:
return cpm_array
for iden in anat.identifiers:
if iden["identifier_type"].lower() in [
"neu id", "neu identifier", "neu",
"neuronames brain hierarchy id",
"neuronames brain hierarchy identifier"
]:
if source.lower() in ["umls", "all"]:
anat_array = []
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/crosswalk/current/source/NEU/" + iden["identifier"]
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"ticket": tick, "pageNumber": page_num}
r = requests.get(base + ext, params=query)
r.encoding = 'utf-8'
items = json.loads(r.text)
json_data = items["result"]
with open("sample_2.txt", "a", encoding="utf8") as f:
f.write(str(items))
for rep in json_data:
if rep["ui"] != "NONE":
# CPM ID.
if rep["rootSource"] == "CPM" and rep[
"ui"] not in cpm_array:
cpm_array.append(rep["ui"])
gnomics.objects.anatomical_structure.AnatomicalStructure.add_identifier(
anat,
identifier=rep["ui"],
identifier_type="CPM ID",
language=None,
source="UMLS Metathesaurus")
if not json_data:
break
elif iden["identifier_type"].lower() in [
"uwda id", "uwda identifier", "uwda"
]:
if source.lower() in ["umls", "all"]:
anat_array = []
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/crosswalk/current/source/UWDA/" + iden["identifier"]
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"ticket": tick, "pageNumber": page_num}
r = requests.get(base + ext, params=query)
r.encoding = 'utf-8'
items = json.loads(r.text)
json_data = items["result"]
with open("sample_2.txt", "a", encoding="utf8") as f:
f.write(str(items))
for rep in json_data:
if rep["ui"] != "NONE":
# CPM ID.
if rep["rootSource"] == "CPM" and rep[
"ui"] not in cpm_array:
cpm_array.append(rep["ui"])
gnomics.objects.anatomical_structure.AnatomicalStructure.add_identifier(
anat,
identifier=rep["ui"],
identifier_type="CPM ID",
language=None,
source="UMLS Metathesaurus")
if not json_data:
break
elif iden["identifier_type"].lower() in [
"rcd", "rcd id", "rcd identifier", "read code",
"read code clinical terms version 3", "read code ctv3",
"read code, clinical terms version 3", "read code, ctv3"
]:
if source == "umls":
anat_array = []
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/crosswalk/current/source/RCD/" + iden["identifier"]
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"ticket": tick, "pageNumber": page_num}
r = requests.get(base + ext, params=query)
r.encoding = 'utf-8'
items = json.loads(r.text)
json_data = items["result"]
for rep in json_data:
if rep["ui"] != "NONE":
# CPM ID.
if rep["rootSource"] == "CPM" and rep[
"ui"] not in cpm_array:
cpm_array.append(rep["ui"])
gnomics.objects.anatomical_structure.AnatomicalStructure.add_identifier(
anat,
identifier=rep["ui"],
identifier_type="CPM ID",
language=None,
source="UMLS Metathesaurus",
name=rep["name"])
if not json_data:
break
elif iden["identifier_type"].lower() in [
"alcohol and other drug", "alcohol and other drug id",
"alcohol and other drug identifier", "aod", "aod id",
"aod identifier"
]:
if source == "umls":
anat_array = []
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/crosswalk/current/source/AOD/" + iden["identifier"]
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"ticket": tick, "pageNumber": page_num}
r = requests.get(base + ext, params=query)
r.encoding = 'utf-8'
items = json.loads(r.text)
json_data = items["result"]
for rep in json_data:
if rep["ui"] not in anat_array and rep["ui"] != "NONE":
# CPM ID.
if rep["rootSource"] == "CPM" and rep[
"ui"] not in cpm_array:
cpm_array.append(rep["ui"])
gnomics.objects.anatomical_structure.AnatomicalStructure.add_identifier(
anat,
identifier=rep["ui"],
identifier_type="CPM ID",
language=None,
source="UMLS Metathesaurus",
name=rep["name"])
if not json_data:
break
return cpm_array
def get_meddra_obj(adverse_event, user=None, source="umls"):
obj_array = []
for ae_obj in adverse_event.adverse_event_objects:
if 'object_type' in com_obj:
if ae_obj['object_type'].lower() in [
'mdr', 'mdr code', 'mdr id', 'mdr identifier', 'meddra',
'meddra code', 'meddra id', 'meddra identifier',
'meddra label', 'meddra object', 'meddra term'
]:
return ae_obj['object']
if obj_array:
return obj_array
ids_completed = []
if user is not None:
for meddra_term in get_meddra_term(adverse_event):
if source.lower() in [
"umls", "all"
] and meddra_term not in ids_completed and user.umls_api_key is not None:
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/search/current?sabs=MDR&searchType=exact&returnIdType=code"
id_array = []
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {
"string": str(meddra_term),
"ticket": tick,
"pageNumber": page_num
}
r = requests.get(base + ext, params=query)
r.encoding = 'utf-8'
if not r.ok:
break
else:
items = json.loads(r.text)
json_data = items["result"]
if json_data["results"][0]["ui"] == "NONE":
break
else:
id_array.append(json_data)
if id_array:
gnomics.objects.adverse_event.AdverseEvent.add_object(
adverse_event,
obj=id_array,
object_type="MedDRA Object")
obj_array.append(id_array)
if source.lower() != "all":
ids_completed.append(meddra_term)
if source.lower() in [
"ncbo", "all"
] and meddra_term not in ids_completed and user.ncbo_api_key is not None:
base = "http://data.bioontology.org/search"
ext = "?q=" + str(
meddra_term
) + "&ontologies=MEDDRA&require_exact_match=true&roots_only=true/?apikey=" + user.ncbo_api_key
r = requests.get(base + ext,
headers={
"Content-Type":
"application/json",
"Authorization":
"apikey token=" + user.ncbo_api_key
})
if not r.ok:
continue
else:
decoded = json.loads(r.text)
id_array = []
for result in decoded["collection"]:
id_array.append(result)
if id_array:
gnomics.objects.adverse_event.AdverseEvent.add_object(
adverse_event,
obj=id_array,
object_type="MedDRA Object")
obj_array.append(id_array)
if source.lower() != "all":
ids_completed.append(meddra_term)
return obj_array
else:
print(
"MedDRA object cannot be obtained without valid user object (with valid UMLS API key or NCBO API key)."
)
def get_phenotypes(adverse_event, user=None):
phen_array = []
ids_completed = []
for iden in gnomics.objects.auxiliary_files.identifier.filter_identifiers(
adverse_event.identifiers, [
"meddra term", "mdr label", "mdr name", "mdr term",
"meddra label", "meddra name"
]):
if iden["identifier"] not in ids_completed and user is not None:
ids_completed.append(iden["identifier"])
if user.ncbo_api_key is not None:
# Map MedDRA term to MedDRA ID.
meddra_id_array = gnomics.objects.adverse_event.AdverseEvent.meddra_id(
adverse_event, user)
hpo_id_array = []
for iden in meddra_id_array:
base = "http://data.bioontology.org/ontologies/"
ext = "MEDDRA/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F" + str(
iden) + "/mappings/?apikey=" + user.ncbo_api_key
r = requests.get(
base + ext,
headers={"Content-Type": "application/json"})
if not r.ok:
continue
else:
decoded = json.loads(r.text)
for result in decoded:
for subresult in result["classes"]:
if "http://purl.obolibrary.org/obo/HP_" in subresult[
"@id"]:
hpo_id = subresult["@id"].split("/obo/")[1]
if hpo_id not in hpo_id_array:
hpo_id_array.append(hpo_id)
temp_phen = gnomics.objects.phenotype.Phenotype(
identifier=hpo_id,
identifier_type="HPO ID",
source="NCBO BioPortal",
taxon="H**o sapiens")
phen_array.append(temp_phen)
if not hpo_id_array:
mesh_uid_array = []
mesh_uids = gnomics.objects.adverse_event.AdverseEvent.mesh_uid(
adverse_event, user)
mesh_uid_array.extend(mesh_uids)
for iden in mesh_uid_array:
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/crosswalk/current/source/MSH/" + iden + "?targetSource=HPO"
try:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"ticket": tick, "pageNumber": page_num}
r = requests.get(base + ext, params=query)
r.encoding = 'utf-8'
if not r.ok:
print("No mapping from MeSH to HPO found.")
else:
items = json.loads(r.text)
json_data = items["result"]
for er in json_data:
if er["ui"] not in hpo_id_array and er[
"ui"] != "NONE":
hpo_id = er["ui"]
hpo_id_array.append(hpo_id)
temp_phen = gnomics.objects.phenotype.Phenotype(
identifier=hpo_id,
identifier_type="HPO ID",
source="UMLS",
taxon="H**o sapiens")
phen_array.append(temp_phen)
if not json_data:
continue
except:
continue
else:
print(
"A valid NCBO API key is necessary to access the NCBO Bioontology API. Please provide a valid user object with such a key."
)
else:
print(
"A valid user object with an NCBO API key is necessary to access the NCBO Bioontology API. Please provide such an object."
)
return phen_array
def get_mesh_uid(adverse_event, user=None):
mesh_array = []
for iden in gnomics.objects.auxiliary_files.identifier.filter_identifiers(
adverse_event.identifiers, [
"mesh", "mesh uid", "mesh unique id", "mesh unique identifier",
"msh", "msh uid", "msh unique id", "msh unique identifier"
]):
if iden["identifier"] not in mesh_array:
mesh_array.append(iden["identifier"])
if mesh_array:
return mesh_array
ids_completed = []
for iden in gnomics.objects.auxiliary_files.identifier.filter_identifiers(
adverse_event.identifiers, [
"mdr", "mdr code", "mdr id", "mdr identifier", "meddra",
"meddra code", "meddra id", "meddra identifier"
]):
if iden["identifier"] not in ids_completed and user is not None:
ids_completed.append(iden["identifier"])
if user.umls_api_key is not None:
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/crosswalk/current/source/MDR/" + str(
iden["identifier"]) + "?targetSource=MSH"
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"ticket": tick, "pageNumber": page_num}
r = requests.get(base + ext, params=query)
r.encoding = 'utf-8'
if not r.ok:
break
else:
items = json.loads(r.text)
json_data = items["result"]
for er in json_data:
if er["ui"] not in mesh_array and er[
"ui"] != "NONE":
mesh_uid = er["ui"]
mesh_name = er["name"]
mesh_array.append(mesh_uid)
gnomics.objects.adverse_event.AdverseEvent.add_identifier(
adverse_event,
identifier=mesh_uid,
identifier_type="MeSH UID",
source="UMLS",
name=mesh_name)
if not json_data:
break
if user.ncbo_api_key is not None:
base = "http://data.bioontology.org/ontologies/"
ext = "MEDDRA/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F" + str(
iden["identifier"]
) + "/mappings/?apikey=" + user.ncbo_api_key
r = requests.get(base + ext,
headers={
"Content-Type":
"application/json",
"Authorization":
"apikey token=" + user.ncbo_api_key
})
if not r.ok:
continue
else:
decoded = json.loads(r.text)
for result in decoded:
for subresult in result["classes"]:
if "http://purl.bioontology.org/ontology/MESH" in subresult[
"@id"]:
mesh_uid = subresult["@id"].split("/MESH/")[1]
if mesh_uid not in mesh_array:
mesh_array.append(mesh_uid)
gnomics.objects.adverse_event.AdverseEvent.add_identifier(
adverse_event,
identifier=mesh_uid,
identifier_type="MeSH UID",
source="NCBO BioPortal",
name=subresult["prefLabel"])
elif user is None:
print(
"A valid user with a valid UMLS API Key or valid NCBO BioPortal API Key is necessary for this transaction."
)
return mesh_array
def get_hpo_term(phen, user=None):
hpo_term_array = []
for ident in phen.identifiers:
if ident["identifier_type"].lower() in ["hp label", "hp term", "hpo label", "hpo term", "human phenotype ontology label", "human phenotype ontology term"]:
if ident["identifier"] not in hpo_id_array:
hpo_id_array.append(ident["identifier"])
if hpo_term_array:
return hpo_term_array
for ident in phen.identifiers:
if ident["identifier_type"].lower() in ["hp code", "hp id", "hp identifier", "hpo code", "hpo id", "hpo identifier", "human phenotype ontology code", "human phenotype ontology id", "human phenotype ontology identifier", "hp", "hpo", "human phenotype ontology"]:
if user:
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/content/current/source/HPO/" + ident["identifier"]
umls_tgt = User.umls_tgt(user)
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"ticket": tick, "pageNumber": page_num}
r = requests.get(base+ext, params=query)
r.encoding = 'utf-8'
try:
items = json.loads(r.text)
json_data = items["result"]
if "name" in json_data:
if json_data["name"] not in hpo_term_array:
hpo_term = json_data["name"]
gnomics.objects.phenotype.Phenotype.add_identifier(phen, identifier = hpo_term, identifier_type = "HPO Term", source = "UMLS", taxon = "H**o sapiens")
hpo_term_array.append(hpo_term)
else:
break
except:
break
break
else:
proc_id = ident["identifier"]
if ":" in proc_id:
proc_id = proc_id.replace(":", "_")
url = "https://www.ebi.ac.uk/ols/api/ontologies"
ext = "/hp/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252F" + proc_id
r = requests.get(url+ext, headers={"Content-Type": "application/json"})
if not r.ok:
print("Something went wrong.")
else:
new_decoded = r.json()
if new_decoded["label"] not in hpo_term_array:
gnomics.objects.phenotype.Phenotype.add_identifier(phen, identifier = new_decoded["label"], identifier_type = "HPO Term", source = "OLS", taxon = "H**o sapiens")
hpo_term_array.append(new_decoded["label"])
return hpo_term_array
def get_meddra_id(phen, user=None):
meddra_array = []
for ident in phen.identifiers:
if ident["identifier_type"].lower() in ["mdr", "mdr code", "mdr id", "mdr identifier", "meddra", "meddra code", "meddra id", "meddra identifier"]:
if ident["identifier"] not in meddra_array:
hpo_id_array.append(ident["identifier"])
ids_completed = []
for ident in phen.identifiers:
if ident["identifier_type"].lower() in ["meddra term", "meddra label", "mdr label", "mdr term"]:
if user is not None:
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/search/current?sabs=MDR&searchType=exact&returnIdType=code"
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"string": ident["identifier"], "ticket": tick, "pageNumber": page_num}
r = requests.get(base+ext, params=query)
r.encoding = 'utf-8'
try:
items = json.loads(r.text)
json_data = items["result"]
empty = False
for rep in json_data["results"]:
if rep["ui"] not in meddra_array and rep["ui"] != "NONE":
gnomics.objects.phenotype.Phenotype.add_identifier(phen, identifier = rep["ui"], identifier_type = "MedDRA ID", source = "UMLS")
meddra_array.append(rep["ui"])
if json_data["results"][0]["ui"] == "NONE":
empty = True
break
if not json_data:
break
if empty:
break
except:
break
elif ident["identifier_type"].lower() in ["hp code", "hp id", "hp identifier", "hpo code", "hpo id", "hpo identifier", "human phenotype ontology code", "human phenotype ontology id", "human phenotype ontology identifier", "hp", "hpo", "human phenotype ontology"]:
if ident["identifier"] not in ids_completed:
ids_completed.append(ident["identifier"])
hpo_id = ident["identifier"]
if ":" in hpo_id:
hpo_id = hpo_id.replace(":", "_")
url = "https://www.ebi.ac.uk/ols/api/ontologies"
ext = "/hp/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252F" + hpo_id
r = requests.get(url+ext, headers={"Content-Type": "application/json"})
if not r.ok:
print("Something went wrong.")
else:
decoded = r.json()
if meddra_array:
return meddra_array
for ident in phen.identifiers:
print("NOT FUNCTIONAL")
return ""
def get_hpo_id(phen, user=None):
hpo_id_array = []
for ident in phen.identifiers:
if ident["identifier_type"].lower() in ["hp code", "hp id", "hp identifier", "hpo code", "hpo id", "hpo identifier", "human phenotype ontology code", "human phenotype ontology id", "human phenotype ontology identifier", "hp", "hpo", "human phenotype ontology"]:
if ident["identifier"] not in hpo_id_array:
hpo_id_array.append(ident["identifier"])
if hpo_id_array:
return hpo_id_array
mesh_is_here = False
mesh_array = []
for ident in phen.identifiers:
if ident["identifier_type"].lower() in ["mesh", "mesh uid", "mesh unique id", "mesh unique identifier", "msh", "msh uid", "msh unique id", "msh unique identifier"]:
mesh_is_here = True
if ident["identifier"] not in mesh_array:
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/crosswalk/current/source/MSH/" + ident["identifier"] + "?targetSource=HPO"
umls_tgt = User.umls_tgt(user)
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"ticket": tick, "pageNumber": page_num}
r = requests.get(base+ext, params=query)
r.encoding = 'utf-8'
try:
items = json.loads(r.text)
json_data = items["result"]
for er in json_data:
if er["ui"] not in hpo_id_array and er["ui"] != "NONE":
hpo_id = er["ui"]
gnomics.objects.phenotype.Phenotype.add_identifier(phen, identifier = hpo_id, identifier_type = "HPO ID", source = "UMLS", taxon = "H**o sapiens")
hpo_id_array.append(hpo_id)
if not json_data:
break
except:
break
break
if hpo_id_array:
return hpo_id_array
if mesh_is_here:
return []
for ident in phen.identifiers:
if ident["identifier_type"].lower() in ["mdr", "mdr code", "mdr id", "mdr identifier", "meddra", "meddra code", "meddra id", "meddra identifier"]:
mesh_uid = gnomics.objects.phenotype.Phenotype.mesh_uid(phen, user)
if mesh_uid:
return get_hpo_id(phen, user)
else:
return []
for ident in phen.identifiers:
if ident["identifier_type"].lower() in ["meddra term", "meddra label", "mdr label", "mdr term"]:
gnomics.objects.phenotype.Phenotype.meddra_id(phen, user)
return get_hpo_id(phen, user)
def get_aod(anat, user=None, source="umls"):
aod_array = []
for iden in gnomics.objects.auxiliary_files.identifier.filter_identifiers(anat.identifiers, ["alcohol and other drug", "alcohol and other drug id", "alcohol and other drug identifier", "aod", "aod id", "aod identifier"]):
if iden["identifier"] not in aod_array:
aod_array.append(iden["identifier"])
if aod_array:
return aod_array
ids_completed = []
for iden in gnomics.objects.auxiliary_files.identifier.filter_identifiers(anat.identifiers, ["neu id", "neu identifier", "neuronames brain hierarchy id", "neuronames brain hierarchy identifier", "neu"]):
if iden["identifier"] not in ids_completed and user is not None:
ids_completed.append(iden["identifier"])
if source.lower() in ["umls", "all"]:
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/crosswalk/current/source/NEU/" + str(iden["identifier"])
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"ticket": tick, "pageNumber": page_num}
r = requests.get(base+ext, params=query)
r.encoding = 'utf-8'
items = json.loads(r.text)
json_data = items["result"]
for rep in json_data:
if rep["ui"] != "NONE":
# AOD ID.
if rep["rootSource"] == "AOD" and rep["ui"] not in aod_array:
aod_array.append(rep["ui"])
gnomics.objects.anatomical_structure.AnatomicalStructure.add_identifier(anat, identifier=rep["ui"], identifier_type="AOD ID", language=None, source="UMLS Metathesaurus")
if not json_data:
break
for iden in gnomics.objects.auxiliary_files.identifier.filter_identifiers(anat.identifiers, ["uwda", "uwda id", "uwda identifier"]):
if iden["identifier"] not in ids_completed and user is not None:
ids_completed.append(iden["identifier"])
if source.lower() in ["umls", "all"]:
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/crosswalk/current/source/UWDA/" + str(iden["identifier"])
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"ticket": tick, "pageNumber": page_num}
r = requests.get(base+ext, params=query)
r.encoding = 'utf-8'
items = json.loads(r.text)
json_data = items["result"]
for rep in json_data:
if rep["ui"] != "NONE":
# AOD ID.
if rep["rootSource"] == "AOD" and rep["ui"] not in aod_array:
aod_array.append(rep["ui"])
gnomics.objects.anatomical_structure.AnatomicalStructure.add_identifier(anat, identifier=rep["ui"], identifier_type="AOD ID", language=None, source="UMLS Metathesaurus")
if not json_data:
break
return aod_array
def get_mesh_uid(phen, user=None):
mesh_array = []
for ident in phen.identifiers:
if ident["identifier_type"].lower() in [
"mesh", "mesh uid", "mesh unique id", "mesh unique identifier",
"msh", "msh uid", "msh unique id", "msh unique identifier"
]:
if ident["identifier"] not in mesh_array:
mesh_array.append(ident["identifier"])
if mesh_array:
return mesh_array
meddra_array = []
ids_completed = []
for ident in phen.identifiers:
if ident["identifier_type"].lower() in [
"mdr", "mdr code", "mdr id", "mdr identifier", "meddra",
"meddra code", "meddra id", "meddra identifier"
]:
if user is not None:
if ident["identifier"] not in meddra_array:
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/crosswalk/current/source/MDR/" + str(
ident["identifier"]) + "?targetSource=MSH"
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {
"string": ident["identifier"],
"ticket": tick,
"pageNumber": page_num
}
r = requests.get(base + ext, params=query)
r.encoding = 'utf-8'
try:
items = json.loads(r.text)
json_data = items["result"]
empty = False
for rep in json_data:
if rep["ui"] not in mesh_array and rep[
"ui"] != "NONE":
gnomics.objects.phenotype.Phenotype.add_identifier(
phen,
identifier=rep["ui"],
identifier_type="MeSH ID",
source="UMLS")
mesh_array.append(rep["ui"])
if "ui" not in rep and not rep["result"]:
empty = True
break
if not json_data:
break
if empty:
break
except:
break
break
meddra_array.append(ident["identifier"])
elif ident["identifier_type"].lower() in [
"hp code", "hp id", "hp identifier", "hpo code", "hpo id",
"hpo identifier", "human phenotype ontology code",
"human phenotype ontology id",
"human phenotype ontology identifier", "hp", "hpo",
"human phenotype ontology"
]:
if ident["identifier"] not in ids_completed:
ids_completed.append(ident["identifier"])
hpo_id = ident["identifier"]
if ":" in hpo_id:
hpo_id = hpo_id.replace(":", "_")
url = "https://www.ebi.ac.uk/ols/api/ontologies"
ext = "/hp/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252F" + hpo_id
r = requests.get(url + ext,
headers={"Content-Type": "application/json"})
if not r.ok:
print("Something went wrong.")
else:
decoded = r.json()
for xref in decoded["annotation"][
"database_cross_reference"]:
if "MSH:" in xref:
mesh_uid = xref.split("MSH:")[1]
mesh_array.append(mesh_uid)
gnomics.objects.phenotype.Phenotype.add_identifier(
phen,
identifier=mesh_uid,
identifier_type="MeSH UID",
source="OLS")
return mesh_array
def search(query, user=None, search_type="exact", return_id_type="sourceUi"):
if search_type == "exact" and user is not None:
proc_array = []
proc_obj_array = []
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/search/current?string=" + query + "&inputType=sourceUi&searchType=words&returnIdType=" + return_id_type
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"string": query, "ticket": tick, "pageNumber": page_num}
r = requests.get(base + ext, params=query)
r.encoding = 'utf-8'
#print(r.text)
items = json.loads(r.text)
json_data = items["result"]
for rep in json_data["results"]:
if rep["ui"] not in proc_array and rep["ui"] != "NONE":
# Current Procedural Terminology.
if rep["rootSource"] == "CPT":
temp_proc = gnomics.objects.procedure.Procedure(
identifier=rep["ui"],
identifier_type="CPT ID",
language=None,
source="UMLS Metathesaurus",
name=rep["name"])
proc_obj_array.append(temp_proc)
# Current Procedural Terminology (Spanish).
elif rep["rootSource"] == "CPTSP":
temp_proc = gnomics.objects.procedure.Procedure(
identifier=rep["ui"],
identifier_type="CPTSP ID",
language=None,
source="UMLS Metathesaurus",
name=rep["name"])
proc_obj_array.append(temp_proc)
# Healthcare Common Procedure Coding System (HCPCS).
elif rep["rootSource"] == "HCPCS":
temp_proc = gnomics.objects.procedure.Procedure(
identifier=rep["ui"],
identifier_type="HCPCS ID",
language=None,
source="UMLS Metathesaurus",
name=rep["name"])
proc_obj_array.append(temp_proc)
# CPT in Healthcare Common Procedure Coding System (CPT in HCPCS).
elif rep["rootSource"] == "HCPT":
temp_proc = gnomics.objects.procedure.Procedure(
identifier=rep["ui"],
identifier_type="HCPT ID",
language=None,
source="UMLS Metathesaurus",
name=rep["name"])
proc_obj_array.append(temp_proc)
# ICD-10-PCS.
elif rep["rootSource"] == "ICD-10-PCS":
temp_proc = gnomics.objects.procedure.Procedure(
identifier=rep["ui"],
identifier_type="ICD-10-PCS Code",
language=None,
source="UMLS Metathesaurus",
name=rep["name"])
proc_obj_array.append(temp_proc)
# LOINC (English).
elif rep["rootSource"] == "LNC":
temp_proc = gnomics.objects.procedure.Procedure(
identifier=rep["ui"],
identifier_type="LOINC Code",
source="UMLS Metathesaurus",
name=rep["name"],
language="en")
proc_obj_array.append(temp_proc)
# LOINC (Austrian German).
elif rep["rootSource"] == "LNC-DE-AT":
temp_proc = gnomics.objects.procedure.Procedure(
identifier=rep["ui"],
identifier_type="LOINC Code",
source="UMLS Metathesaurus",
name=rep["name"],
language="de-AT")
proc_obj_array.append(temp_proc)
# LOINC (Swiss German).
elif rep["rootSource"] == "LNC-DE-CH":
temp_proc = gnomics.objects.procedure.Procedure(
identifier=rep["ui"],
identifier_type="LOINC Code",
source="UMLS Metathesaurus",
name=rep["name"],
language="gsw")
proc_obj_array.append(temp_proc)
# LOINC (German).
elif rep["rootSource"] == "LNC-DE-DE":
temp_proc = gnomics.objects.procedure.Procedure(
identifier=rep["ui"],
identifier_type="LOINC Code",
source="UMLS Metathesaurus",
name=rep["name"],
language="de")
proc_obj_array.append(temp_proc)
# LOINC (Greek).
elif rep["rootSource"] == "LNC-EL-GR":
temp_proc = gnomics.objects.procedure.Procedure(
identifier=rep["ui"],
identifier_type="LOINC Code",
source="UMLS Metathesaurus",
name=rep["name"],
language="el")
proc_obj_array.append(temp_proc)
# LOINC (Argentinian Spanish).
elif rep["rootSource"] == "LNC-ES-AR":
temp_proc = gnomics.objects.procedure.Procedure(
identifier=rep["ui"],
identifier_type="LOINC Code",
source="UMLS Metathesaurus",
name=rep["name"],
language="es-AR")
proc_obj_array.append(temp_proc)
# LOINC (Swiss Spanish).
elif rep["rootSource"] == "LNC-ES-CH":
temp_proc = gnomics.objects.procedure.Procedure(
identifier=rep["ui"],
identifier_type="LOINC Code",
source="UMLS Metathesaurus",
name=rep["name"],
language="es-CH")
proc_obj_array.append(temp_proc)
# LOINC (Spanish).
elif rep["rootSource"] == "LNC-ES-ES":
temp_proc = gnomics.objects.procedure.Procedure(
identifier=rep["ui"],
identifier_type="LOINC Code",
source="UMLS Metathesaurus",
name=rep["name"],
language="es")
proc_obj_array.append(temp_proc)
# LOINC (Estonian).
elif rep["rootSource"] == "LNC-ET-EE":
temp_proc = gnomics.objects.procedure.Procedure(
identifier=rep["ui"],
identifier_type="LOINC Code",
source="UMLS Metathesaurus",
name=rep["name"],
language="et")
proc_obj_array.append(temp_proc)
# LOINC (Belgian French).
elif rep["rootSource"] == "LNC-FR-BE":
temp_proc = gnomics.objects.procedure.Procedure(
identifier=rep["ui"],
identifier_type="LOINC Code",
source="UMLS Metathesaurus",
name=rep["name"],
language="fr-BE")
proc_obj_array.append(temp_proc)
# LOINC (Canadian French).
elif rep["rootSource"] == "LNC-FR-CA":
temp_proc = gnomics.objects.procedure.Procedure(
identifier=rep["ui"],
identifier_type="LOINC Code",
source="UMLS Metathesaurus",
name=rep["name"],
language="fr-CA")
proc_obj_array.append(temp_proc)
# LOINC (Swiss French).
elif rep["rootSource"] == "LNC-FR-CH":
temp_proc = gnomics.objects.procedure.Procedure(
identifier=rep["ui"],
identifier_type="LOINC Code",
source="UMLS Metathesaurus",
name=rep["name"],
language="fr-CH")
proc_obj_array.append(temp_proc)
# LOINC (French).
elif rep["rootSource"] == "LNC-FR-FR":
temp_proc = gnomics.objects.procedure.Procedure(
identifier=rep["ui"],
identifier_type="LOINC Code",
source="UMLS Metathesaurus",
name=rep["name"],
language="fr")
proc_obj_array.append(temp_proc)
# LOINC (Swiss Italian).
elif rep["rootSource"] == "LNC-IT-CH":
temp_proc = gnomics.objects.procedure.Procedure(
identifier=rep["ui"],
identifier_type="LOINC Code",
source="UMLS Metathesaurus",
name=rep["name"],
language="it-CH")
proc_obj_array.append(temp_proc)
# LOINC (Italian).
elif rep["rootSource"] == "LNC-IT-IT":
temp_proc = gnomics.objects.procedure.Procedure(
identifier=rep["ui"],
identifier_type="LOINC Code",
source="UMLS Metathesaurus",
name=rep["name"],
language="it")
proc_obj_array.append(temp_proc)
# LOINC (Korean).
elif rep["rootSource"] == "LNC-KO-KR":
temp_proc = gnomics.objects.procedure.Procedure(
identifier=rep["ui"],
identifier_type="LOINC Code",
source="UMLS Metathesaurus",
name=rep["name"],
language="ko")
proc_obj_array.append(temp_proc)
# LOINC (Dutch).
elif rep["rootSource"] == "LNC-NL-NL":
temp_proc = gnomics.objects.procedure.Procedure(
identifier=rep["ui"],
identifier_type="LOINC Code",
source="UMLS Metathesaurus",
name=rep["name"],
language="nl")
proc_obj_array.append(temp_proc)
# LOINC (Brazilian Portuguese).
elif rep["rootSource"] == "LNC-PT-BR":
temp_proc = gnomics.objects.procedure.Procedure(
identifier=rep["ui"],
identifier_type="LOINC Code",
source="UMLS Metathesaurus",
name=rep["name"],
language="pt-BR")
proc_obj_array.append(temp_proc)
# LOINC (Russian).
elif rep["rootSource"] == "LNC-RU-RU":
temp_proc = gnomics.objects.procedure.Procedure(
identifier=rep["ui"],
identifier_type="LOINC Code",
source="UMLS Metathesaurus",
name=rep["name"],
language="ru")
proc_obj_array.append(temp_proc)
# LOINC (Turkish).
elif rep["rootSource"] == "LNC-TR-TR":
temp_proc = gnomics.objects.procedure.Procedure(
identifier=rep["ui"],
identifier_type="LOINC Code",
source="UMLS Metathesaurus",
name=rep["name"],
language="tr")
proc_obj_array.append(temp_proc)
# LOINC (Chinese).
elif rep["rootSource"] == "LNC-ZH-CN":
temp_proc = gnomics.objects.procedure.Procedure(
identifier=rep["ui"],
identifier_type="LOINC Code",
source="UMLS Metathesaurus",
name=rep["name"],
language="zh")
proc_obj_array.append(temp_proc)
if json_data["results"][0]["ui"] == "NONE":
break
return proc_obj_array
elif search_type == "approximate" and user is not None:
proc_array = []
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/search/current?string=" + query + "&searchType=approximate&returnIdType=" + return_id_type
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"string": query, "ticket": tick, "pageNumber": page_num}
r = requests.get(base + ext, params=query)
r.encoding = 'utf-8'
print(r.text)
items = json.loads(r.text)
json_data = items["result"]
for rep in json_data["results"]:
if rep["ui"] not in proc_array and rep["ui"] != "NONE":
proc_array.append(rep["ui"])
if json_data["results"][0]["ui"] == "NONE":
break
return proc_array
def get_mesh_uid(phen, user=None):
mesh_array = []
for ident in phen.identifiers:
if ident["identifier_type"].lower() in ["mesh", "mesh uid", "mesh unique id", "mesh unique identifier", "msh", "msh uid", "msh unique id", "msh unique identifier"]:
if ident["identifier"] not in mesh_array:
mesh_array.append(ident["identifier"])
if mesh_array:
return mesh_array
meddra_array = []
ids_completed = []
for ident in phen.identifiers:
if ident["identifier_type"].lower() in ["mdr", "mdr code", "mdr id", "mdr identifier", "meddra", "meddra code", "meddra id", "meddra identifier"]:
if user is not None:
if ident["identifier"] not in meddra_array:
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/crosswalk/current/source/MDR/" + str(ident["identifier"]) + "?targetSource=MSH"
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"string": ident["identifier"], "ticket": tick, "pageNumber": page_num}
r = requests.get(base+ext, params=query)
r.encoding = 'utf-8'
try:
items = json.loads(r.text)
json_data = items["result"]
empty = False
for rep in json_data:
if rep["ui"] not in mesh_array and rep["ui"] != "NONE":
gnomics.objects.phenotype.Phenotype.add_identifier(phen, identifier = rep["ui"], identifier_type = "MeSH ID", source = "UMLS")
mesh_array.append(rep["ui"])
if "ui" not in rep and not rep["result"]:
empty = True
break
if not json_data:
break
if empty:
break
except:
break
break
meddra_array.append(ident["identifier"])
elif ident["identifier_type"].lower() in ["hp code", "hp id", "hp identifier", "hpo code", "hpo id", "hpo identifier", "human phenotype ontology code", "human phenotype ontology id", "human phenotype ontology identifier", "hp", "hpo", "human phenotype ontology"]:
if ident["identifier"] not in ids_completed:
ids_completed.append(ident["identifier"])
hpo_id = ident["identifier"]
if ":" in hpo_id:
hpo_id = hpo_id.replace(":", "_")
url = "https://www.ebi.ac.uk/ols/api/ontologies"
ext = "/hp/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252F" + hpo_id
r = requests.get(url+ext, headers={"Content-Type": "application/json"})
if not r.ok:
print("Something went wrong.")
else:
decoded = r.json()
for xref in decoded["annotation"]["database_cross_reference"]:
if "MSH:" in xref:
mesh_uid = xref.split("MSH:")[1]
mesh_array.append(mesh_uid)
gnomics.objects.phenotype.Phenotype.add_identifier(phen, identifier = mesh_uid, identifier_type = "MeSH UID", source = "OLS")
return mesh_array
def get_hpo_id(phen, user=None):
hpo_id_array = []
for ident in phen.identifiers:
if ident["identifier_type"].lower() in [
"hp code", "hp id", "hp identifier", "hpo code", "hpo id",
"hpo identifier", "human phenotype ontology code",
"human phenotype ontology id",
"human phenotype ontology identifier", "hp", "hpo",
"human phenotype ontology"
]:
if ident["identifier"] not in hpo_id_array:
hpo_id_array.append(ident["identifier"])
if hpo_id_array:
return hpo_id_array
mesh_is_here = False
mesh_array = []
for ident in phen.identifiers:
if ident["identifier_type"].lower() in [
"mesh", "mesh uid", "mesh unique id", "mesh unique identifier",
"msh", "msh uid", "msh unique id", "msh unique identifier"
]:
mesh_is_here = True
if ident["identifier"] not in mesh_array:
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/crosswalk/current/source/MSH/" + ident[
"identifier"] + "?targetSource=HPO"
umls_tgt = User.umls_tgt(user)
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"ticket": tick, "pageNumber": page_num}
r = requests.get(base + ext, params=query)
r.encoding = 'utf-8'
try:
items = json.loads(r.text)
json_data = items["result"]
for er in json_data:
if er["ui"] not in hpo_id_array and er[
"ui"] != "NONE":
hpo_id = er["ui"]
gnomics.objects.phenotype.Phenotype.add_identifier(
phen,
identifier=hpo_id,
identifier_type="HPO ID",
source="UMLS",
taxon="H**o sapiens")
hpo_id_array.append(hpo_id)
if not json_data:
break
except:
break
break
if hpo_id_array:
return hpo_id_array
if mesh_is_here:
return []
for ident in phen.identifiers:
if ident["identifier_type"].lower() in [
"mdr", "mdr code", "mdr id", "mdr identifier", "meddra",
"meddra code", "meddra id", "meddra identifier"
]:
mesh_uid = gnomics.objects.phenotype.Phenotype.mesh_uid(phen, user)
if mesh_uid:
return get_hpo_id(phen, user)
else:
return []
for ident in phen.identifiers:
if ident["identifier_type"].lower() in [
"meddra term", "meddra label", "mdr label", "mdr term"
]:
gnomics.objects.phenotype.Phenotype.meddra_id(phen, user)
return get_hpo_id(phen, user)
def get_psy(anat, user=None, source="umls"):
anat_array = []
for iden in anat.identifiers:
if iden["identifier_type"].lower() in [
"neu id", "neu identifier", "neu"
]:
if source.lower() in ["umls", "all"]:
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/crosswalk/current/source/NEU/" + iden["identifier"]
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"ticket": tick, "pageNumber": page_num}
r = requests.get(base + ext, params=query)
r.encoding = 'utf-8'
items = json.loads(r.text)
json_data = items["result"]
for rep in json_data:
if rep["ui"] not in anat_array and rep["ui"] != "NONE":
# PSY ID.
if rep["rootSource"] == "PSY":
anat_array.append(rep["ui"])
gnomics.objects.anatomical_structure.AnatomicalStructure.add_identifier(
anat,
identifier=rep["ui"],
identifier_type="PSY ID",
language=None,
source="UMLS Metathesaurus",
name=rep["name"])
if not json_data:
break
elif iden["identifier_type"].lower() in [
"uwda id", "uwda identifier", "uwda"
]:
if source.lower() in ["umls", "all"]:
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/crosswalk/current/source/UWDA/" + iden["identifier"]
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"ticket": tick, "pageNumber": page_num}
r = requests.get(base + ext, params=query)
r.encoding = 'utf-8'
items = json.loads(r.text)
json_data = items["result"]
for rep in json_data:
if rep["ui"] not in anat_array and rep["ui"] != "NONE":
# PSY ID.
if rep["rootSource"] == "PSY":
anat_array.append(rep["ui"])
gnomics.objects.anatomical_structure.AnatomicalStructure.add_identifier(
anat,
identifier=rep["ui"],
identifier_type="PSY ID",
language=None,
source="UMLS Metathesaurus",
name=rep["name"])
if not json_data:
break
elif iden["identifier_type"].lower() in [
"rcd id", "rcd identifier", "rcd"
]:
if source.lower() in ["umls", "all"]:
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/crosswalk/current/source/RCD/" + iden["identifier"]
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"ticket": tick, "pageNumber": page_num}
r = requests.get(base + ext, params=query)
r.encoding = 'utf-8'
items = json.loads(r.text)
json_data = items["result"]
for rep in json_data:
if rep["ui"] not in anat_array and rep["ui"] != "NONE":
# PSY ID.
if rep["rootSource"] == "PSY":
anat_array.append(rep["ui"])
gnomics.objects.anatomical_structure.AnatomicalStructure.add_identifier(
anat,
identifier=rep["ui"],
identifier_type="PSY ID",
language=None,
source="UMLS Metathesaurus",
name=rep["name"])
if not json_data:
break
elif iden["identifier_type"].lower() in [
"aod id", "aod identifier", "aod"
]:
if source.lower() in ["umls", "all"]:
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/crosswalk/current/source/AOD/" + iden["identifier"]
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"ticket": tick, "pageNumber": page_num}
r = requests.get(base + ext, params=query)
r.encoding = 'utf-8'
items = json.loads(r.text)
json_data = items["result"]
for rep in json_data:
if rep["ui"] not in anat_array and rep["ui"] != "NONE":
# PSY ID.
if rep["rootSource"] == "PSY":
anat_array.append(rep["ui"])
gnomics.objects.anatomical_structure.AnatomicalStructure.add_identifier(
anat,
identifier=rep["ui"],
identifier_type="PSY ID",
language=None,
source="UMLS Metathesaurus",
name=rep["name"])
if not json_data:
break
return anat_array
def umls_crosswalk(user,
from_source,
to_source,
source_id,
other="id",
verbose=False):
found_array = []
if user is None:
print(
"A valid user object with a valid UMLS API key is required for this function."
)
return found_array
elif user.umls_api_key is None:
print(
"A valid UMLS API key associated with the user object is required for this function."
)
return found_array
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/crosswalk/current/source/" + from_source.upper() + "/" + source_id
verbose = True
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"ticket": tick, "pageNumber": page_num}
try:
r = requests.get(
base + ext,
params=query,
headers={
"Content-Type":
"application/json",
"User-Agent":
"Mozilla/5.0 (Windows NT 6.0; WOW64; rv:24.0) Gecko/20100101 Firefox/24.0"
})
r.encoding = 'utf-8'
try:
items = json.loads(r.text)
json_data = items["result"]
empty = False
for rep in json_data:
if other == "id":
if rep["ui"] not in found_array and rep["ui"] != "NONE":
if rep["rootSource"] == to_source.upper():
found_array.append(rep["ui"])
elif other == "name":
if (rep["name"] not in found_array and rep["name"] !=
"NONE") and (rep["ui"] not in found_array
and rep["ui"] != "NONE"):
if rep["rootSource"] == to_source.upper():
found_array.append((rep["ui"], rep["name"]))
else:
print(
"This value for 'other' is not currently supported."
)
if "results" in json_data:
if json_data["results"][0]["ui"] == "NONE":
empty = True
break
if not json_data:
break
elif empty:
break
except ValueError as e:
if verbose:
print(
"A value error occurred while attempting to load resulting JSON."
)
print("ERROR: %s" % str(e))
break
except:
if verbose:
print("Some other unknown error occurred.")
break
else:
continue
except ConnectionError as e:
if verbose:
print("A connection error occurred while attempting request.")
print("ERROR: %s" % str(e))
break
except requests.exceptions.ConnectionError as e:
if verbose:
print("A connection error occurred while attempting request.")
print("ERROR: %s" % str(e))
break
except HTTPException as e:
if verbose:
print(
"An HTTP exception error occurred while attempting request."
)
print("ERROR: %s" % str(e))
break
except ProtocolError as e:
if verbose:
print("A protocol error occurred while attempting request.")
print("ERROR: %s" % str(e))
break
except urllib3.exceptions.ProtocolError as e:
if verbose:
print("A protocol error occurred while attempting request.")
print("ERROR: %s" % str(e))
break
except SysCallError as e:
if verbose:
print("A system call error occurred while attempting request.")
print("ERROR: %s" % str(e))
break
except OpenSSL.SSL.SysCallError as e:
if verbose:
print("A system call error occurred while attempting request.")
print("ERROR: %s" % str(e))
break
except ssl.SSLError as e:
if verbose:
print("A system call error occurred while attempting request.")
print("ERROR: %s" % str(e))
break
except SSLError as e:
if verbose:
print("A SSL error occurred while attempting request.")
print("ERROR: %s" % str(e))
break
except requests.exceptions.SSLError as e:
if verbose:
print("A SSL error occurred while attempting request.")
print("ERROR: %s" % str(e))
break
except BadStatusLine as e:
if verbose:
print(
"A bad status line error occurred while attempting request."
)
print("ERROR: %s" % str(e))
break
except httplib.BadStatusLine as e:
if verbose:
print(
"A bad status line error occurred while attempting request."
)
print("ERROR: %s" % str(e))
break
except http.client.BadStatusLine as e:
if verbose:
print("A protocol error occurred while attempting request.")
print("ERROR: %s" % str(e))
break
except MaxRetryError as e:
if verbose:
print("A max retry error occurred while attempting request.")
print("ERROR: %s" % str(e))
break
except urllib3.exceptions.MaxRetryError as e:
if verbose:
print("A max retry error occurred while attempting request.")
print("ERROR: %s" % str(e))
break
except:
print("Some other HTTP/URL error encountered.")
break
else:
break
return found_array
def umls_crosswalk(user, from_source, to_source, source_id, other="id", verbose=False):
found_array = []
if user is None:
print("A valid user object with a valid UMLS API key is required for this function.")
return found_array
elif user.umls_api_key is None:
print("A valid UMLS API key associated with the user object is required for this function.")
return found_array
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/crosswalk/current/source/" + from_source.upper() + "/" + source_id
verbose = True
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"ticket": tick, "pageNumber": page_num}
try:
r = requests.get(base+ext, params=query, headers = {"Content-Type": "application/json", "User-Agent": "Mozilla/5.0 (Windows NT 6.0; WOW64; rv:24.0) Gecko/20100101 Firefox/24.0"})
r.encoding = 'utf-8'
try:
items = json.loads(r.text)
json_data = items["result"]
empty = False
for rep in json_data:
if other == "id":
if rep["ui"] not in found_array and rep["ui"] != "NONE":
if rep["rootSource"] == to_source.upper():
found_array.append(rep["ui"])
elif other == "name":
if (rep["name"] not in found_array and rep["name"] != "NONE") and (rep["ui"] not in found_array and rep["ui"] != "NONE"):
if rep["rootSource"] == to_source.upper():
found_array.append((rep["ui"], rep["name"]))
else:
print("This value for 'other' is not currently supported.")
if "results" in json_data:
if json_data["results"][0]["ui"] == "NONE":
empty = True
break
if not json_data:
break
elif empty:
break
except ValueError as e:
if verbose:
print("A value error occurred while attempting to load resulting JSON.")
print("ERROR: %s" % str(e))
break
except:
if verbose:
print("Some other unknown error occurred.")
break
else:
continue
except ConnectionError as e:
if verbose:
print("A connection error occurred while attempting request.")
print("ERROR: %s" % str(e))
break
except requests.exceptions.ConnectionError as e:
if verbose:
print("A connection error occurred while attempting request.")
print("ERROR: %s" % str(e))
break
except HTTPException as e:
if verbose:
print("An HTTP exception error occurred while attempting request.")
print("ERROR: %s" % str(e))
break
except ProtocolError as e:
if verbose:
print("A protocol error occurred while attempting request.")
print("ERROR: %s" % str(e))
break
except urllib3.exceptions.ProtocolError as e:
if verbose:
print("A protocol error occurred while attempting request.")
print("ERROR: %s" % str(e))
break
except SysCallError as e:
if verbose:
print("A system call error occurred while attempting request.")
print("ERROR: %s" % str(e))
break
except OpenSSL.SSL.SysCallError as e:
if verbose:
print("A system call error occurred while attempting request.")
print("ERROR: %s" % str(e))
break
except ssl.SSLError as e:
if verbose:
print("A system call error occurred while attempting request.")
print("ERROR: %s" % str(e))
break
except SSLError as e:
if verbose:
print("A SSL error occurred while attempting request.")
print("ERROR: %s" % str(e))
break
except requests.exceptions.SSLError as e:
if verbose:
print("A SSL error occurred while attempting request.")
print("ERROR: %s" % str(e))
break
except BadStatusLine as e:
if verbose:
print("A bad status line error occurred while attempting request.")
print("ERROR: %s" % str(e))
break
except httplib.BadStatusLine as e:
if verbose:
print("A bad status line error occurred while attempting request.")
print("ERROR: %s" % str(e))
break
except http.client.BadStatusLine as e:
if verbose:
print("A protocol error occurred while attempting request.")
print("ERROR: %s" % str(e))
break
except MaxRetryError as e:
if verbose:
print("A max retry error occurred while attempting request.")
print("ERROR: %s" % str(e))
break
except urllib3.exceptions.MaxRetryError as e:
if verbose:
print("A max retry error occurred while attempting request.")
print("ERROR: %s" % str(e))
break
except:
print("Some other HTTP/URL error encountered.")
break
else:
break
return found_array
def get_psy(anat, user=None, source="umls"):
anat_array = []
for iden in anat.identifiers:
if iden["identifier_type"].lower() in ["neu id", "neu identifier", "neu"]:
if source.lower() in ["umls", "all"]:
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/crosswalk/current/source/NEU/" + iden["identifier"]
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"ticket": tick, "pageNumber": page_num}
r = requests.get(base+ext, params=query)
r.encoding = 'utf-8'
items = json.loads(r.text)
json_data = items["result"]
for rep in json_data:
if rep["ui"] not in anat_array and rep["ui"] != "NONE":
# PSY ID.
if rep["rootSource"] == "PSY":
anat_array.append(rep["ui"])
gnomics.objects.anatomical_structure.AnatomicalStructure.add_identifier(anat, identifier=rep["ui"], identifier_type="PSY ID", language=None, source="UMLS Metathesaurus", name=rep["name"])
if not json_data:
break
elif iden["identifier_type"].lower() in ["uwda id", "uwda identifier", "uwda"]:
if source.lower() in ["umls", "all"]:
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/crosswalk/current/source/UWDA/" + iden["identifier"]
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"ticket": tick, "pageNumber": page_num}
r = requests.get(base+ext, params=query)
r.encoding = 'utf-8'
items = json.loads(r.text)
json_data = items["result"]
for rep in json_data:
if rep["ui"] not in anat_array and rep["ui"] != "NONE":
# PSY ID.
if rep["rootSource"] == "PSY":
anat_array.append(rep["ui"])
gnomics.objects.anatomical_structure.AnatomicalStructure.add_identifier(anat, identifier=rep["ui"], identifier_type="PSY ID", language=None, source="UMLS Metathesaurus", name=rep["name"])
if not json_data:
break
elif iden["identifier_type"].lower() in ["rcd id", "rcd identifier", "rcd"]:
if source.lower() in ["umls", "all"]:
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/crosswalk/current/source/RCD/" + iden["identifier"]
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"ticket": tick, "pageNumber": page_num}
r = requests.get(base+ext, params=query)
r.encoding = 'utf-8'
items = json.loads(r.text)
json_data = items["result"]
for rep in json_data:
if rep["ui"] not in anat_array and rep["ui"] != "NONE":
# PSY ID.
if rep["rootSource"] == "PSY":
anat_array.append(rep["ui"])
gnomics.objects.anatomical_structure.AnatomicalStructure.add_identifier(anat, identifier=rep["ui"], identifier_type="PSY ID", language=None, source="UMLS Metathesaurus", name=rep["name"])
if not json_data:
break
elif iden["identifier_type"].lower() in ["aod id", "aod identifier", "aod"]:
if source.lower() in ["umls", "all"]:
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/crosswalk/current/source/AOD/" + iden["identifier"]
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"ticket": tick, "pageNumber": page_num}
r = requests.get(base+ext, params=query)
r.encoding = 'utf-8'
items = json.loads(r.text)
json_data = items["result"]
for rep in json_data:
if rep["ui"] not in anat_array and rep["ui"] != "NONE":
# PSY ID.
if rep["rootSource"] == "PSY":
anat_array.append(rep["ui"])
gnomics.objects.anatomical_structure.AnatomicalStructure.add_identifier(anat, identifier=rep["ui"], identifier_type="PSY ID", language=None, source="UMLS Metathesaurus", name=rep["name"])
if not json_data:
break
return anat_array
def get_meddra_id(phen, user=None):
meddra_array = []
for ident in phen.identifiers:
if ident["identifier_type"].lower() in [
"mdr", "mdr code", "mdr id", "mdr identifier", "meddra",
"meddra code", "meddra id", "meddra identifier"
]:
if ident["identifier"] not in meddra_array:
hpo_id_array.append(ident["identifier"])
ids_completed = []
for ident in phen.identifiers:
if ident["identifier_type"].lower() in [
"meddra term", "meddra label", "mdr label", "mdr term"
]:
if user is not None:
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/search/current?sabs=MDR&searchType=exact&returnIdType=code"
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {
"string": ident["identifier"],
"ticket": tick,
"pageNumber": page_num
}
r = requests.get(base + ext, params=query)
r.encoding = 'utf-8'
try:
items = json.loads(r.text)
json_data = items["result"]
empty = False
for rep in json_data["results"]:
if rep["ui"] not in meddra_array and rep[
"ui"] != "NONE":
gnomics.objects.phenotype.Phenotype.add_identifier(
phen,
identifier=rep["ui"],
identifier_type="MedDRA ID",
source="UMLS")
meddra_array.append(rep["ui"])
if json_data["results"][0]["ui"] == "NONE":
empty = True
break
if not json_data:
break
if empty:
break
except:
break
elif ident["identifier_type"].lower() in [
"hp code", "hp id", "hp identifier", "hpo code", "hpo id",
"hpo identifier", "human phenotype ontology code",
"human phenotype ontology id",
"human phenotype ontology identifier", "hp", "hpo",
"human phenotype ontology"
]:
if ident["identifier"] not in ids_completed:
ids_completed.append(ident["identifier"])
hpo_id = ident["identifier"]
if ":" in hpo_id:
hpo_id = hpo_id.replace(":", "_")
url = "https://www.ebi.ac.uk/ols/api/ontologies"
ext = "/hp/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252F" + hpo_id
r = requests.get(url + ext,
headers={"Content-Type": "application/json"})
if not r.ok:
print("Something went wrong.")
else:
decoded = r.json()
if meddra_array:
return meddra_array
for ident in phen.identifiers:
print("NOT FUNCTIONAL")
return ""
def get_aod(anat, user=None, source="umls"):
aod_array = []
for iden in gnomics.objects.auxiliary_files.identifier.filter_identifiers(
anat.identifiers, [
"alcohol and other drug", "alcohol and other drug id",
"alcohol and other drug identifier", "aod", "aod id",
"aod identifier"
]):
if iden["identifier"] not in aod_array:
aod_array.append(iden["identifier"])
if aod_array:
return aod_array
ids_completed = []
for iden in gnomics.objects.auxiliary_files.identifier.filter_identifiers(
anat.identifiers, [
"neu id", "neu identifier", "neuronames brain hierarchy id",
"neuronames brain hierarchy identifier", "neu"
]):
if iden["identifier"] not in ids_completed and user is not None:
ids_completed.append(iden["identifier"])
if source.lower() in ["umls", "all"]:
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/crosswalk/current/source/NEU/" + str(
iden["identifier"])
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"ticket": tick, "pageNumber": page_num}
r = requests.get(base + ext, params=query)
r.encoding = 'utf-8'
items = json.loads(r.text)
json_data = items["result"]
for rep in json_data:
if rep["ui"] != "NONE":
# AOD ID.
if rep["rootSource"] == "AOD" and rep[
"ui"] not in aod_array:
aod_array.append(rep["ui"])
gnomics.objects.anatomical_structure.AnatomicalStructure.add_identifier(
anat,
identifier=rep["ui"],
identifier_type="AOD ID",
language=None,
source="UMLS Metathesaurus")
if not json_data:
break
for iden in gnomics.objects.auxiliary_files.identifier.filter_identifiers(
anat.identifiers, ["uwda", "uwda id", "uwda identifier"]):
if iden["identifier"] not in ids_completed and user is not None:
ids_completed.append(iden["identifier"])
if source.lower() in ["umls", "all"]:
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/crosswalk/current/source/UWDA/" + str(
iden["identifier"])
while True:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"ticket": tick, "pageNumber": page_num}
r = requests.get(base + ext, params=query)
r.encoding = 'utf-8'
items = json.loads(r.text)
json_data = items["result"]
for rep in json_data:
if rep["ui"] != "NONE":
# AOD ID.
if rep["rootSource"] == "AOD" and rep[
"ui"] not in aod_array:
aod_array.append(rep["ui"])
gnomics.objects.anatomical_structure.AnatomicalStructure.add_identifier(
anat,
identifier=rep["ui"],
identifier_type="AOD ID",
language=None,
source="UMLS Metathesaurus")
if not json_data:
break
return aod_array
def get_phenotypes(adverse_event, user=None):
phen_array = []
ids_completed = []
for iden in gnomics.objects.auxiliary_files.identifier.filter_identifiers(adverse_event.identifiers, ["meddra term", "mdr label", "mdr name", "mdr term", "meddra label", "meddra name"]):
if iden["identifier"] not in ids_completed and user is not None:
ids_completed.append(iden["identifier"])
if user.ncbo_api_key is not None:
# Map MedDRA term to MedDRA ID.
meddra_id_array = gnomics.objects.adverse_event.AdverseEvent.meddra_id(adverse_event, user)
hpo_id_array = []
for iden in meddra_id_array:
base = "http://data.bioontology.org/ontologies/"
ext = "MEDDRA/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F" + str(iden) + "/mappings/?apikey=" + user.ncbo_api_key
r = requests.get(base+ext, headers={"Content-Type": "application/json"})
if not r.ok:
continue
else:
decoded = json.loads(r.text)
for result in decoded:
for subresult in result["classes"]:
if "http://purl.obolibrary.org/obo/HP_" in subresult["@id"]:
hpo_id = subresult["@id"].split("/obo/")[1]
if hpo_id not in hpo_id_array:
hpo_id_array.append(hpo_id)
temp_phen = gnomics.objects.phenotype.Phenotype(identifier = hpo_id, identifier_type = "HPO ID", source = "NCBO BioPortal", taxon = "H**o sapiens")
phen_array.append(temp_phen)
if not hpo_id_array:
mesh_uid_array = []
mesh_uids = gnomics.objects.adverse_event.AdverseEvent.mesh_uid(adverse_event, user)
mesh_uid_array.extend(mesh_uids)
for iden in mesh_uid_array:
umls_tgt = User.umls_tgt(user)
page_num = 0
base = "https://uts-ws.nlm.nih.gov/rest"
ext = "/crosswalk/current/source/MSH/" + iden + "?targetSource=HPO"
try:
tick = User.umls_st(umls_tgt)
page_num += 1
query = {"ticket": tick, "pageNumber": page_num}
r = requests.get(base+ext, params=query)
r.encoding = 'utf-8'
if not r.ok:
print("No mapping from MeSH to HPO found.")
else:
items = json.loads(r.text)
json_data = items["result"]
for er in json_data:
if er["ui"] not in hpo_id_array and er["ui"] != "NONE":
hpo_id = er["ui"]
hpo_id_array.append(hpo_id)
temp_phen = gnomics.objects.phenotype.Phenotype(identifier = hpo_id, identifier_type = "HPO ID", source = "UMLS", taxon = "H**o sapiens")
phen_array.append(temp_phen)
if not json_data:
continue
except:
continue
else:
print("A valid NCBO API key is necessary to access the NCBO Bioontology API. Please provide a valid user object with such a key.")
else:
print("A valid user object with an NCBO API key is necessary to access the NCBO Bioontology API. Please provide such an object.")
return phen_array
