def setUpClass(cls):
ht = Hint()
cxcr4 = ht.query("CXCR4")["Gene"][0]
fc = FindConnection(input_obj=cxcr4,
output_obj="ChemicalSubstance",
intermediate_nodes=None)
fc.connect(verbose=True)
cls.response = fc.to_reasoner_std()
def setUp(self):
ht = Hint()
cxcr4 = ht.query('CXCR4')['Gene'][0]
fc = FindConnection(input_obj=cxcr4,
output_obj='ChemicalSubstance',
intermediate_nodes=None)
fc.connect(verbose=True)
self.response = fc.to_reasoner_std()
def test_one_filt(self):
ht = Hint()
input = ht.query('hyperphenylalaninemia')['Disease'][0]
filt = [{}, {'name': 'NodeDegree', 'count': 25}]
fc = FindConnection(input_obj=input,
output_obj='ChemicalSubstance',
intermediate_nodes=['Gene'],
filters=filt)
fc.connect()
self.assertEqual(27, len(fc.fc.G.nodes))
def test_no_filter(self):
ht = Hint()
input = ht.query('hyperphenylalaninemia')['Disease'][0]
filt = []
fc = FindConnection(input_obj=input,
output_obj='ChemicalSubstance',
intermediate_nodes=['Gene'],
filters=filt)
fc.connect()
for node, y in fc.fc.G.nodes(data=True):
self.assertTrue('filteredBy' not in y.keys())
class TestHint(unittest.TestCase):
def setUp(self):
self.ht = Hint()
def test_gene_entrez_id_as_input(self):
"""test the output of Hint query when providing gene entrez id as input"""
res = self.ht.query('1017')
self.assertIsNotNone(res)
self.assertIsNotNone(res.get('Gene'))
self.assertIsNotNone(res.get('Gene')[0])
bioentity = res.get('Gene')[0]
self.assertEqual(bioentity['entrez'], '1017')
self.assertEqual(bioentity['type'], 'Gene')
self.assertEqual(bioentity['primary']['identifier'], 'entrez')
self.assertEqual(bioentity['primary']['value'], '1017')
self.assertEqual(bioentity['symbol'], 'CDK2')
def test_gene_symbol_as_input(self):
"""test the output of Hint query when providing gene symbol as input"""
res = self.ht.query('CDK2')
self.assertIsNotNone(res)
self.assertIsNotNone(res.get('Gene'))
self.assertIsNotNone(res.get('Gene')[0])
bioentity = res.get('Gene')[0]
self.assertEqual(bioentity['entrez'], '1017')
self.assertEqual(bioentity['type'], 'Gene')
self.assertEqual(bioentity['primary']['identifier'], 'entrez')
self.assertEqual(bioentity['primary']['value'], '1017')
self.assertEqual(bioentity['symbol'], 'CDK2')
def test_gene_umls_id_as_input(self):
"""test the output of Hint query when providing gene umls id as input"""
res = self.ht.query('C1332823')
self.assertIsNotNone(res)
self.assertIsNotNone(res.get('Gene'))
self.assertIsNotNone(res.get('Gene')[0])
bioentity = res.get('Gene')[0]
self.assertEqual(bioentity['entrez'], '7852')
self.assertEqual(bioentity['type'], 'Gene')
self.assertEqual(bioentity['primary']['identifier'], 'entrez')
self.assertEqual(bioentity['primary']['value'], '7852')
self.assertEqual(bioentity['symbol'], 'CXCR4')
def test_two_filt(self):
ht = Hint()
input = ht.query('hyperphenylalaninemia')['Disease'][0]
filt = [{
'name': 'NodeDegree',
'count': 20
}, {
'name': 'EdgeLabel',
'label': 'related_to'
}]
fc = FindConnection(input_obj=input,
output_obj='ChemicalSubstance',
intermediate_nodes=['Gene'],
filters=filt)
fc.connect()
self.assertEqual(52, len(fc.fc.G.nodes))
for node, y in fc.fc.G.nodes(data=True):
if node != 'mild hyperphenylalaninemia':
if y['type'] == 'Gene':
self.assertEqual('NodeDegree', y['filteredBy'])
elif y['type'] == 'ChemicalSubstance':
self.assertEqual('EdgeLabel', y['filteredBy'])
class TestHint(unittest.TestCase):
def setUp(self):
self.ht = Hint()
def mygene_test(self, res):
self.assertIsNotNone(res)
self.assertIsNotNone(res.get('Gene'))
self.assertIsNotNone(res.get('Gene')[0])
bioentity = res.get('Gene')[0]
self.assertEqual(bioentity['NCBIGene'], '1017')
self.assertEqual(bioentity['type'], 'Gene')
self.assertEqual(bioentity['primary']['identifier'], 'NCBIGene')
self.assertEqual(bioentity['primary']['value'], '1017')
self.assertEqual(bioentity['SYMBOL'], 'CDK2')
def myvariant_test(self, res):
self.assertIsNotNone(res)
self.assertIsNotNone(res.get('SequenceVariant'))
self.assertIsNotNone(res.get('SequenceVariant')[0])
bioentity = res.get('SequenceVariant')[0]
self.assertEqual(bioentity['DBSNP'], 'rs12190874')
self.assertEqual(bioentity['type'], 'SequenceVariant')
self.assertEqual(bioentity['primary']['identifier'], 'DBSNP')
self.assertEqual(bioentity['primary']['value'], 'rs12190874')
def test_gene_NCBIGene_id_as_input(self):
"""Test the output of Hint query when providing gene NCBIGene id as input."""
res = self.ht.query('1017')
self.mygene_test(res)
def test_gene_SYMBOL_as_input(self):
"""Test the output of Hint query when providing gene SYMBOL as input."""
res = self.ht.query('CDK2')
self.mygene_test(res)
def test_gene_UMLS_id_as_input(self):
"""Test the output of Hint query when providing gene UMLS id as input."""
res = self.ht.query('C1332823')
self.assertIsNotNone(res)
self.assertIsNotNone(res.get('Gene'))
self.assertIsNotNone(res.get('Gene')[0])
bioentity = res.get('Gene')[0]
self.assertEqual(bioentity['UMLS'], 'C1332823')
self.assertEqual(bioentity['type'], 'Gene')
self.assertEqual(bioentity['primary']['identifier'], 'NCBIGene')
self.assertEqual(bioentity['primary']['value'], '7852')
self.assertEqual(bioentity['SYMBOL'], 'CXCR4')
def test_gene_hgnc_id_as_input(self):
"""Test the output of Hint query when providing gene hgnc id as input."""
res = self.ht.query('1771')
self.mygene_test(res)
def test_gene_uniprot_id_as_input(self):
"""Test the output of Hint query when providing gene uniprot id as input."""
res = self.ht.query('P24941')
self.mygene_test(res)
def test_variant_rsid_as_input(self):
"""Test the output of Hint query when providing variant dbsnp id as input."""
res = self.ht.query('rs12190874')
self.myvariant_test(res)
def test_variant_hgvs_as_input(self):
"""Test the output of Hint query when providing variant hgvs id as input."""
res = self.ht.query('chr6:g.42454850G>A')
self.myvariant_test(res)
def test_chemical(self):
"""Test the output of Hint query when providing chemical drugbank ID as input."""
res = self.ht.query("DB01926")
bioentity = res.get('ChemicalSubstance')[0]
self.assertIsNotNone(res)
self.assertEqual(bioentity['name'], 'Carboxymycobactin S')
def step_impl(context, name):
ht = Hint()
disease_hint = ht.query(name)
context.disease = disease_hint['DiseaseOrPhenotypicFeature'][0]
class TestHint(unittest.TestCase):
def setUp(self):
self.ht = Hint()
def mygene_test(self, res):
self.assertIsNotNone(res)
self.assertIsNotNone(res.get("Gene"))
self.assertIsNotNone(res.get("Gene")[0])
bioentity = res.get("Gene")[0]
self.assertEqual(bioentity["NCBIGene"], "1017")
self.assertEqual(bioentity["type"], "Gene")
self.assertEqual(bioentity["primary"]["identifier"], "NCBIGene")
self.assertEqual(bioentity["primary"]["value"], "1017")
self.assertEqual(bioentity["SYMBOL"], "CDK2")
def myvariant_test(self, res):
self.assertIsNotNone(res)
self.assertIsNotNone(res.get("SequenceVariant"))
self.assertIsNotNone(res.get("SequenceVariant")[0])
bioentity = res.get("SequenceVariant")[0]
self.assertEqual(bioentity["DBSNP"], "rs12190874")
self.assertEqual(bioentity["type"], "SequenceVariant")
self.assertEqual(bioentity["primary"]["identifier"], "DBSNP")
self.assertEqual(bioentity["primary"]["value"], "rs12190874")
def test_gene_NCBIGene_id_as_input(self):
"""Test the output of Hint query when providing gene NCBIGene id as input."""
res = self.ht.query("1017")
self.mygene_test(res)
def test_gene_SYMBOL_as_input(self):
"""Test the output of Hint query when providing gene SYMBOL as input."""
res = self.ht.query("CDK2")
self.mygene_test(res)
def test_gene_UMLS_id_as_input(self):
"""Test the output of Hint query when providing gene UMLS id as input."""
res = self.ht.query("C1332823")
self.assertIsNotNone(res)
self.assertIsNotNone(res.get("Gene"))
self.assertIsNotNone(res.get("Gene")[0])
bioentity = res.get("Gene")[0]
self.assertEqual(bioentity["UMLS"], "C1332823")
self.assertEqual(bioentity["type"], "Gene")
self.assertEqual(bioentity["primary"]["identifier"], "NCBIGene")
self.assertEqual(bioentity["primary"]["value"], "7852")
self.assertEqual(bioentity["SYMBOL"], "CXCR4")
def test_gene_hgnc_id_as_input(self):
"""Test the output of Hint query when providing gene hgnc id as input."""
res = self.ht.query("1771")
self.assertIsNotNone(res)
self.assertIsNotNone(res.get("Gene"))
self.assertIsNotNone(res.get("Gene")[0])
bioentity = [
item for item in res.get("Gene") if item.get("HGNC") == "1771"
][0]
self.assertEqual(bioentity["type"], "Gene")
self.assertEqual(bioentity["primary"]["identifier"], "NCBIGene")
self.assertEqual(bioentity["primary"]["value"], "1017")
def test_gene_uniprot_id_as_input(self):
"""Test the output of Hint query when providing gene uniprot id as input."""
res = self.ht.query("P24941")
self.mygene_test(res)
def test_variant_rsid_as_input(self):
"""Test the output of Hint query when providing variant dbsnp id as input."""
res = self.ht.query("rs12190874")
self.myvariant_test(res)
def test_chemical(self):
"""Test the output of Hint query when providing chemical drugbank ID as input."""
res = self.ht.query("DB01926")
bioentity = res.get("ChemicalSubstance")[0]
self.assertIsNotNone(res)
self.assertEqual(bioentity["name"], "Carboxymycobactin S")
def test_chemical_with_cas_id(self):
"""Test the output of Hint query when providing chemical CAS ID as input."""
res = self.ht.query("1744-22-5")
bioentity = res.get("ChemicalSubstance")[0]
self.assertIsNotNone(res)
self.assertEqual(bioentity["CHEMBL.COMPOUND"], "CHEMBL744")
def test_chemical_with_iupac_id(self):
"""Test the output of Hint query when providing chemical IUPAC ID as input."""
res = self.ht.query(
"[6-(trifluoromethoxy)-1,3-benzothiazol-2-yl]amine")
bioentity = res.get("ChemicalSubstance")[0]
self.assertIsNotNone(res)
self.assertEqual(bioentity["IUPAC"],
"[6-(trifluoromethoxy)-1,3-benzothiazol-2-yl]amine")
def test_chemical_with_formula(self):
"""Test the output of Hint query when providing chemical formula as input."""
res = self.ht.query("H2O")
bioentity = res.get("ChemicalSubstance")[0]
self.assertIsNotNone(res)
self.assertEqual(bioentity["formula"], "H2O")
def test_chemical_with_abbreviations(self):
"""Test the output of Hint query when providing chemical abbreviations as input."""
res = self.ht.query("AZT")
names = [item.get("name") for item in res.get("ChemicalSubstance")]
self.assertIsNotNone(res)
self.assertIn("zidovudine", names)
def test_chemical_with_international_brand_names(self):
"""Test the output of Hint query when providing drug international brand name as input."""
res = self.ht.query("Dulane")
names = [item.get("name") for item in res.get("ChemicalSubstance")]
self.assertIsNotNone(res)
self.assertIn("DULOXETINE", names)
def test_mf_with_lowercase_go_term(self):
"""Test the output of Hint query when providing lower case go term as input."""
res = self.ht.query("go:0001790")
bioentity = res.get("MolecularActivity")[0]
self.assertIsNotNone(res)
self.assertEqual(bioentity["GO"], "GO:0001790")
def test_bp_with_lowercase_go_term(self):
"""Test the output of Hint query when providing lower case go term as input."""
res = self.ht.query("go:0002354")
bioentity = res.get("BiologicalProcess")[0]
self.assertIsNotNone(res)
self.assertEqual(bioentity["GO"], "GO:0002354")
def test_cc_with_lowercase_go_term(self):
"""Test the output of Hint query when providing lower case go term as input."""
res = self.ht.query("go:1903503")
bioentity = res.get("CellularComponent")[0]
self.assertIsNotNone(res)
self.assertEqual(bioentity["GO"], "GO:1903503")
def test_anatomy_with_uberon_id(self):
"""Test the output of Hint query when providing UBERON ID as input."""
res = self.ht.query("UBERON:0035924")
bioentity = res.get("AnatomicalEntity")[0]
self.assertIsNotNone(res)
self.assertEqual(bioentity["UBERON"], "UBERON:0035924")
def test_resolving_by_synonyms(self):
"""Test the output of Hint query when providing disease synonyms"""
res = self.ht.query("GIST")
bioentity = res.get("Disease")
ids = [item.get("MONDO") for item in bioentity]
self.assertIsNotNone(res)
self.assertIn("MONDO:0011719", ids)
from biothings_explorer.hint import Hint
import json
from .base import BaseHandler
ht = Hint()
class HintHandler(BaseHandler):
def get(self):
_input = self.get_query_argument('q', None)
print('input is {}'.format(_input))
if _input:
result = ht.query(_input)
self.set_status(200)
self.write(json.dumps(result))
self.finish()
else:
self.set_status(400)
self.write(json.dumps({'No input is found'}))
def getDrugHints(drug):
hint = Hint()
ht = hint.query(drug)
return {ImmutableHint(ht): drug}
def getGeneHints(gene):
hint = Hint()
ht = hint.query(gene)
return {ImmutableHint(ht): gene}
def getCancerHints(cancer):
hint = Hint()
ht = hint.query(cancer)
return {ImmutableHint(ht): cancer}
def step_impl(context, disease, chemical):
ht = Hint()
context.disease = ht.query(disease)['DiseaseOrPhenotypicFeature'][0]
context.chemical = ht.query(chemical)['ChemicalSubstance'][0]
class TestHint(unittest.TestCase):
def setUp(self):
self.ht = Hint()
def test_gene_entrez_id_as_input(self):
"""Test the output of Hint query when providing gene entrez id as input."""
res = self.ht.query('1017')
self.assertIsNotNone(res)
self.assertIsNotNone(res.get('Gene'))
self.assertIsNotNone(res.get('Gene')[0])
bioentity = res.get('Gene')[0]
self.assertEqual(bioentity['entrez'], '1017')
self.assertEqual(bioentity['type'], 'Gene')
self.assertEqual(bioentity['primary']['identifier'], 'entrez')
self.assertEqual(bioentity['primary']['value'], '1017')
self.assertEqual(bioentity['symbol'], 'CDK2')
def test_gene_symbol_as_input(self):
"""Test the output of Hint query when providing gene symbol as input."""
res = self.ht.query('CDK2')
self.assertIsNotNone(res)
self.assertIsNotNone(res.get('Gene'))
self.assertIsNotNone(res.get('Gene')[0])
bioentity = res.get('Gene')[0]
self.assertEqual(bioentity['entrez'], '1017')
self.assertEqual(bioentity['type'], 'Gene')
self.assertEqual(bioentity['primary']['identifier'], 'entrez')
self.assertEqual(bioentity['primary']['value'], '1017')
self.assertEqual(bioentity['symbol'], 'CDK2')
def test_gene_umls_id_as_input(self):
"""Test the output of Hint query when providing gene umls id as input."""
res = self.ht.query('C1332823')
self.assertIsNotNone(res)
self.assertIsNotNone(res.get('Gene'))
self.assertIsNotNone(res.get('Gene')[0])
bioentity = res.get('Gene')[0]
self.assertEqual(bioentity['umls'], 'C1332823')
self.assertEqual(bioentity['type'], 'Gene')
self.assertEqual(bioentity['primary']['identifier'], 'entrez')
self.assertEqual(bioentity['primary']['value'], '7852')
self.assertEqual(bioentity['symbol'], 'CXCR4')
def test_gene_hgnc_id_as_input(self):
"""Test the output of Hint query when providing gene hgnc id as input."""
res = self.ht.query('1771')
self.assertIsNotNone(res)
self.assertIsNotNone(res.get('Gene'))
self.assertIsNotNone(res.get('Gene')[0])
bioentity = res.get('Gene')[0]
self.assertEqual(bioentity['hgnc'], '1771')
self.assertEqual(bioentity['type'], 'Gene')
self.assertEqual(bioentity['primary']['identifier'], 'entrez')
self.assertEqual(bioentity['primary']['value'], '1017')
self.assertEqual(bioentity['symbol'], 'CDK2')
def test_gene_uniprot_id_as_input(self):
"""Test the output of Hint query when providing gene uniprot id as input."""
res = self.ht.query('P24941')
self.assertIsNotNone(res)
self.assertIsNotNone(res.get('Gene'))
self.assertIsNotNone(res.get('Gene')[0])
bioentity = res.get('Gene')[0]
self.assertEqual(bioentity['uniprot'], 'P24941')
self.assertEqual(bioentity['type'], 'Gene')
self.assertEqual(bioentity['primary']['identifier'], 'entrez')
self.assertEqual(bioentity['primary']['value'], '1017')
self.assertEqual(bioentity['symbol'], 'CDK2')
def test_variant_rsid_as_input(self):
"""Test the output of Hint query when providing variant dbsnp id as input."""
res = self.ht.query('rs12190874')
self.assertIsNotNone(res)
self.assertIsNotNone(res.get('SequenceVariant'))
self.assertIsNotNone(res.get('SequenceVariant')[0])
bioentity = res.get('SequenceVariant')[0]
self.assertEqual(bioentity['dbsnp'], 'rs12190874')
self.assertEqual(bioentity['type'], 'SequenceVariant')
self.assertEqual(bioentity['primary']['identifier'], 'dbsnp')
self.assertEqual(bioentity['primary']['value'], 'rs12190874')
self.assertEqual(bioentity['hgvs'], 'chr6:g.42454850G>A')
def test_variant_hgvs_as_input(self):
"""Test the output of Hint query when providing variant hgvs id as input."""
res = self.ht.query('chr6:g.42454850G>A')
self.assertIsNotNone(res)
self.assertIsNotNone(res.get('SequenceVariant'))
self.assertIsNotNone(res.get('SequenceVariant')[0])
bioentity = res.get('SequenceVariant')[0]
self.assertEqual(bioentity['hgvs'], 'chr6:g.42454850G>A')
self.assertEqual(bioentity['type'], 'SequenceVariant')
self.assertEqual(bioentity['primary']['identifier'], 'dbsnp')
self.assertEqual(bioentity['primary']['value'], 'rs12190874')
from biothings_explorer.hint import Hint
from biothings_explorer.user_query_dispatcher import FindConnection
ht = Hint()
ace2 = ht.query("ACE2")['Gene'][0]
# print(ace2)
fc = FindConnection(input_obj=ace2,
output_obj='DiseaseOrPhenotypicFeature',
intermediate_nodes='ChemicalSubstance')
fc.connect(verbose=True)
# save graphml file to test.graphml
output = fc.to_graphml("test.graphml")
import numpy as np
import pickle
import os
from biothings_explorer.hint import Hint
from biothings_explorer.user_query_dispatcher import FindConnection
from chp.core.query import Query
from chp.core.reasoner_std import ReasonerStdHandler
query_path = '/home/cyakaboski/src/python/projects/bkb-pathway-provider/tests/reasonerStdTests/sample_query.pk'
if os.path.exists(query_path):
with open(query_path, 'rb') as f_:
reasoner_std = pickle.load(f_)
else:
ht = Hint()
breast_cancer = ht.query('breast cancer')['Disease'][0]
tamoxifin = ht.query('tamoxifen')['ChemicalSubstance'][0]
fc = FindConnection(input_obj=breast_cancer,
output_obj=tamoxifin,
intermediate_nodes='Gene')
fc.connect(verbose=True)
reasoner_std = fc.to_reasoner_std()
#-- Add target node and edge to Query Graph
reasoner_std['query_graph']['nodes'].append({
'id': 't1',
'type': 'PhenotypicFeature',
from biothings_explorer.hint import Hint
ht = Hint()
# produce a python dictionary containing covid related information
covid_hint = ht.query('covid-19')
# they keys to access the dictionary - most are empty except for the Disease tab
print(covid_hint.keys())
# covid disease information
print(covid_hint['Disease'])
# iterate the items under the disease tab
for h_t in covid_hint['Disease']:
print(h_t)
# Each h_t is in of itself a dictionary object that can be indexed with its own set of keys.
# What might be confusing is what 'MONDO' is. This is what is called a curie identifier.
# Curie identifiers are unique names within some dataase or ontology. In this case MONDO is
# an ontology. For example the unique curie identifier that map to the ontology names are:
for h_t in covid_hint['Disease']:
print("Printing Mondo:")
print(h_t['MONDO'] + "\n")
print("Printing name")
print(h_t['name'])
# import modules from biothings_explorer
from biothings_explorer.hint import Hint
from biothings_explorer.user_query_dispatcher import FindConnection
ht = Hint()
# Find all potential representations of TBI
tbi_hint = ht.query("traumatic brain injury")
print(tbi_hint)
print()
# Select the correct representation of TBI
tbi = tbi_hint["Disease"][0]
print(tbi)
print()
# Find all potential representations of unipolar depression
depression_hint = ht.query("unipolar depression")
print(depression_hint)
print()
# Select the correct representation of depression
depression = depression_hint["Disease"][0]
print(depression)
print()
# help(FindConnection.__init__)
fc = FindConnection(input_obj=depression,
output_obj=tbi,
intermediate_nodes="BiologicalEntity")
# BTE finding connection
fc.connect(verbose=True)
print()
def setUp(self):
self.ht = Hint()
def step_impl(context, symbol):
ht = Hint()
gene_hint = ht.query(symbol)
context.gene = gene_hint['Gene'][0]