def test():
parser = argparse.ArgumentParser(description='test similarity service')
parser.add_argument('-username', required=True, help='username')
parser.add_argument('-password', required=True, help='password')
args = parser.parse_args()
api = KnowledgeHubAPI()
api.set_service('DEV')
status = api.login(args.username, args.password)
print(status)
terms = api.SemanticService().lookup('Terbinafine', 'RxNorm')
print(json.dumps(terms, indent=4, sort_keys=True))
#if len(terms['terms']) > 0:
#concepts = api.SemanticService().normalize(terms['terms'][0], 'RxNorm')
#print(json.dumps(concepts, indent=4, sort_keys=True))
#if len(concepts['concepts']) == 1:
compounds = [
"Minoxidil","Estradiol","Anastrozole","Felodipine","Amphetamine",",Adenosine","Azathioprine","Levamisole",
#"Zolmitriptan","Lidocaine","Alprazolam","Ropivacaine","Foscarnet","Rimonabant","Remoxipride","Cyclophosphamide",
#"Aripiprazole","Bambuterol","Sulfamethoxazole","Rosiglitazone","Clozapine","Budesonide","Omeprazole","Raltitrexed",
#"Clonidine","Gefitinib","Ximelagatran","Diazepam","Olanzapine","Zafirlukast","Nifedipine","Indomethacin","Erlotinib",
#"Formoterol","Diclofenac","Metoprolol","Enprofylline","Bicalutamide","Chlordiazepoxide","Simvastatin","Ranitidine",
#"Ticagrelor","Sulfinpyrazone","Phenylbutazone","Benazepril","Isosorbide Mononitrate","Deferoxamine","Guanfacine",
#"Naftifine","Chlorthalidone","Guanethidine","Valproic Acid","Clozapine","Baclofen","Maprotiline","Thioridazine",
#"Aminoglutethimide","Bromocriptine","Phentolamine","Amantadine","Thiethylperazine","Pindolol","Lidocaine",
#"Linezolid","Prednisolone","Candoxatril","Diazepam","Orlistat","Carprofen","Cilazapril"
]
def main():
parser = argparse.ArgumentParser(
description=
'Process parameters for collecting findings from primitive adapter')
parser.add_argument('-username', required=True, help='username')
parser.add_argument('-password', required=True, help='password')
args = parser.parse_args()
api = KnowledgeHubAPI(server='TEST',
client_secret='39c644b3-1f23-4d94-a71f-e0fb43ebd760')
api.login(args.username, args.password)
compoundSmile = api.ChemistryService().getSMILESByName('omeprazole')
similar_compounds = api.SimilarityService().get(compoundSmile[0])
names = []
smiles = []
similarities = []
if similar_compounds is not None:
for similar_compound in similar_compounds:
names.append(similar_compound['name'])
smiles.append(similar_compound['smiles'])
similarities.append(similar_compound['distance'])
studies = filterStudies(api.eToxSys().getStudiesByCompoundNames(names))
print(f'Found {len(studies)} studies.')
for study in studies:
print(study)
api.SemanticService().getSocs(studies)
otherStudies = [
study for study in studies if study['FINDING']['__soc'] == 'Other'
]
print(f'#others:{len(otherStudies)}')
def main():
parser = argparse.ArgumentParser(
description=
'Process parameters for collecting findings from primitive adapter')
parser.add_argument('-username', required=True, help='username')
parser.add_argument('-password', required=True, help='password')
args = parser.parse_args()
api = KnowledgeHubAPI(server='DEV',
client_secret='3db5a6d7-4694-48a4-8a2e-e9c30d78f9ab')
api.login(args.username, args.password)
socs = {}
studies = api.eToxSys().getStudiesByCompoundNames(['omeprazole'])
#studies = api.eToxSys().getStudiesBySMILES(['COc1ccc2[nH]c([S+]([O-])Cc3ncc(C)c(OC)c3C)nc2c1'])
print(f'#studies:{len(studies)}')
#print(studies[0])
findings_per_specimen_organ = {}
for study in studies:
if study['FINDING']['finding'] != None and study['FINDING'][
'finding'] != 'No abnormalities detected' and len(
study['FINDING']['finding']) > 0:
specimenOrgans = api.SemanticService().getSocs(
study['FINDING']['specimenOrgan'])
for specimenOrgan in specimenOrgans:
if len(specimenOrgan) > 0:
finding = study['FINDING']['specimenOrgan']
if specimenOrgan not in findings_per_specimen_organ:
findings_per_specimen_organ[specimenOrgan] = []
if finding not in findings_per_specimen_organ[
specimenOrgan]:
findings_per_specimen_organ[specimenOrgan].append(
finding)
for specimen_organ in findings_per_specimen_organ:
print(
f'{specimen_organ}: {len(findings_per_specimen_organ[specimen_organ])}'
)
for finding in findings_per_specimen_organ[specimen_organ]:
print(' ' + finding)
def main():
api = KnowledgeHubAPI()
terms = api.SemanticService().lookup('inflamm', 'HPATH')
print(terms)
session_state = SessionState.get(compoundName="Omeprazole",
compoundSmile="",
similar_compounds="",
compoundIds=[],
compoundNames=[],
studies={},
df_sim=[])
api = KnowledgeHubAPI()
compoundSmile = ''
############1. Translate compound to SMILES using semantic services
compoundName = st.text_input("compound name: (e.g. Omeprazole)",
value=session_state.compoundName)
session_state.compoundName = compoundName
if st.button('Retrieve') and len(compoundName) > 0:
compound = api.SemanticService().normalize(compoundName,
['RxNorm', 'smiles'])
if 'concepts' in compound:
for concept in compound['concepts']:
if 'vocabularyId' in concept:
if concept['vocabularyId'] == 'smiles':
# global compoundSmile
compoundSmile = concept['conceptCode']
st.text(f'Found SMILES {compoundSmile} for {compoundName}')
session_state.compoundSmile = compoundSmile
session_state.similar_compounds = []
session_state.compoundIds = []
session_state.compoundNames = []
session_state.studies = {}
session_state.df_sim = []
########2. Retrieve similar compounds
from knowledgehub.api import KnowledgeHubAPI
api = KnowledgeHubAPI(server='DEV',
client_secret='3db5a6d7-4694-48a4-8a2e-e9c30d78f9ab')
api.login('tester', 'tester')
socs = api.SemanticService().getSocByCode('10000060')
print(socs)