In [41]:
from wikidataintegrator import wdi_core, wdi_login
from wikidataintegrator.ref_handlers import update_retrieved_if_new_multiple_refs
import pandas as pd
import numpy as np
import requests
In [7]:
df = pd.read_csv('https://search.clinicalgenome.org/kb/gene-validity.csv', skiprows=6, header=None)
df
Out[7]:
0
1
2
3
4
5
6
7
0
A2ML1
HGNC:23336
Noonan syndrome with multiple lentigines
MONDO_0007893
SOP5
No Reported Evidence
https://search.clinicalgenome.org/kb/gene-vali...
2018-06-07T14:37:47.175Z
1
A2ML1
HGNC:23336
cardiofaciocutaneous syndrome
MONDO_0015280
SOP5
No Reported Evidence
https://search.clinicalgenome.org/kb/gene-vali...
2018-06-07T14:31:03.696Z
2
A2ML1
HGNC:23336
Costello syndrome
MONDO_0009026
SOP5
No Reported Evidence
https://search.clinicalgenome.org/kb/gene-vali...
2018-06-07T14:34:05.324Z
3
A2ML1
HGNC:23336
Noonan syndrome
MONDO_0018997
SOP5
Disputed
https://search.clinicalgenome.org/kb/gene-vali...
2018-06-07T14:23:53.157Z
4
A2ML1
HGNC:23336
Noonan syndrome-like disorder with loose anage...
MONDO_0011899
SOP5
No Reported Evidence
https://search.clinicalgenome.org/kb/gene-vali...
2018-06-07T14:40:11.599Z
5
AARS
HGNC:20
undetermined early-onset epileptic encephalopathy
MONDO_0018614
SOP6
Limited
https://search.clinicalgenome.org/kb/gene-vali...
2018-11-20T17:00:00.000Z
6
ABCC9
HGNC:60
hypertrichotic osteochondrodysplasia Cantu type
MONDO_0009406
SOP4
Definitive
https://search.clinicalgenome.org/kb/gene-vali...
2017-09-27T00:00:00
7
ABCD1
HGNC:61
X-linked cerebral adrenoleukodystrophy
MONDO_0010247
SOP4
Definitive
https://search.clinicalgenome.org/kb/gene-vali...
2018-02-07T14:00:00
8
ABHD12
HGNC:15868
PHARC syndrome
MONDO_0012984
SOP5
Definitive
https://search.clinicalgenome.org/kb/gene-vali...
2018-06-28T16:45:15.791Z
9
ACAD8
HGNC:87
isobutyryl-CoA dehydrogenase deficiency
MONDO_0012648
SOP6
Definitive
https://search.clinicalgenome.org/kb/gene-vali...
2019-04-26T16:00:00.000Z
10
ACAD9
HGNC:21497
acyl-CoA dehydrogenase 9 deficiency
MONDO_0012624
SOP6
Definitive
https://search.clinicalgenome.org/kb/gene-vali...
2018-03-27T16:00:00.000Z
11
ACADL
HGNC:88
long chain acyl-CoA dehydrogenase deficiency
MONDO_0020531
SOP6
Disputed
https://search.clinicalgenome.org/kb/gene-vali...
2018-09-25T16:00:00.000Z
12
ACADM
HGNC:89
medium chain acyl-CoA dehydrogenase deficiency
MONDO_0008721
SOP6
Definitive
https://search.clinicalgenome.org/kb/gene-vali...
2018-01-23T17:00:00.000Z
13
ACADS
HGNC:90
short chain acyl-CoA dehydrogenase deficiency
MONDO_0008722
SOP6
Definitive
https://search.clinicalgenome.org/kb/gene-vali...
2018-01-23T17:00:00.000Z
14
ACADSB
HGNC:91
2-methylbutyryl-CoA dehydrogenase deficiency
MONDO_0012392
SOP6
Definitive
https://search.clinicalgenome.org/kb/gene-vali...
2019-03-22T16:00:00.000Z
15
ACADVL
HGNC:92
very long chain acyl-CoA dehydrogenase deficiency
MONDO_0008723
SOP6
Definitive
https://search.clinicalgenome.org/kb/gene-vali...
2018-02-20T17:00:00.000Z
16
ACAT1
HGNC:93
beta-ketothiolase deficiency
MONDO_0008760
SOP6
Definitive
https://search.clinicalgenome.org/kb/gene-vali...
2018-05-22T16:00:00.000Z
17
ACSL4
HGNC:3571
non-syndromic X-linked intellectual disability
MONDO_0019181
SOP4
Moderate
https://search.clinicalgenome.org/kb/gene-vali...
2017-10-20T00:00:00
18
ACTA1
HGNC:129
hypertrophic cardiomyopathy
MONDO_0005045
SOP4
No Reported Evidence
https://search.clinicalgenome.org/kb/gene-vali...
false
19
ACTA2
HGNC:130
familial thoracic aortic aneurysm and aortic d...
MONDO_0019625
SOP4
Definitive
https://search.clinicalgenome.org/kb/gene-vali...
2016-09-27T00:00:00
20
ACTC1
HGNC:143
hypertrophic cardiomyopathy
MONDO_0005045
SOP4
Definitive
https://search.clinicalgenome.org/kb/gene-vali...
2017-10-23T14:00:00
21
ACTG1
HGNC:144
nonsyndromic genetic deafness
MONDO_0019497
SOP6
Definitive
https://search.clinicalgenome.org/kb/gene-vali...
2019-01-07T17:00:00.000Z
22
ACTG1
HGNC:144
Baraitser-winter syndrome 2
MONDO_0013812
SOP6
Definitive
https://search.clinicalgenome.org/kb/gene-vali...
2019-01-07T17:00:00.000Z
23
ACTN2
HGNC:164
intrinsic cardiomyopathy
MONDO_0000591
SOP5
Moderate
https://search.clinicalgenome.org/kb/gene-vali...
2018-08-06T13:12:55.615Z
24
ACVRL1
HGNC:175
telangiectasia, hereditary hemorrhagic, type 2
MONDO_0010880
SOP6
Definitive
https://search.clinicalgenome.org/kb/gene-vali...
2019-08-28T16:00:00.000Z
25
ADCY1
HGNC:232
autosomal recessive nonsyndromic deafness
MONDO_0019588
SOP4
Limited
https://search.clinicalgenome.org/kb/gene-vali...
2017-05-10T00:00:00
26
ADGRV1
HGNC:17416
Usher syndrome type 2C
MONDO_0011558
SOP4
Definitive
https://search.clinicalgenome.org/kb/gene-vali...
2017-02-15T00:00:00
27
ADGRV1
HGNC:17416
nonsyndromic genetic deafness
MONDO_0019497
SOP6
Disputed
https://search.clinicalgenome.org/kb/gene-vali...
2019-03-19T16:00:00.000Z
28
AFF2
HGNC:3776
FRAXE intellectual disability
MONDO_0010659
SOP4
Definitive
https://search.clinicalgenome.org/kb/gene-vali...
2017-10-20T00:00:00
29
AGTR2
HGNC:338
non-syndromic X-linked intellectual disability
MONDO_0019181
SOP4
Disputed
https://search.clinicalgenome.org/kb/gene-vali...
2016-11-16T00:00:00
...
...
...
...
...
...
...
...
...
767
TUBB4B
HGNC:20771
Leber congenital amaurosis with early-onset de...
MONDO_0060650
SOP6
Moderate
https://search.clinicalgenome.org/kb/gene-vali...
2018-06-26T16:00:00.000Z
768
UBE2A
HGNC:12472
syndromic X-linked intellectual disability Nas...
MONDO_0010461
SOP5
Definitive
https://search.clinicalgenome.org/kb/gene-vali...
2018-07-13T13:49:34.109Z
769
UBE3A
HGNC:12496
Angelman syndrome
MONDO_0007113
SOP5
Definitive
https://search.clinicalgenome.org/kb/gene-vali...
2018-05-02T13:23:44.716Z
770
UPF3B
HGNC:20439
complex neurodevelopmental disorder
MONDO_0100038
SOP6
Definitive
https://search.clinicalgenome.org/kb/gene-vali...
2019-07-03T20:14:44.825Z
771
USH1C
HGNC:12597
Usher syndrome type 1
MONDO_0010168
SOP4
Definitive
https://search.clinicalgenome.org/kb/gene-vali...
2017-02-15T00:00:00
772
USH1C
HGNC:12597
nonsyndromic genetic deafness
MONDO_0019497
SOP6
Limited
https://search.clinicalgenome.org/kb/gene-vali...
2018-06-11T04:00:00.000Z
773
USH1G
HGNC:16356
Usher syndrome type 1
MONDO_0010168
SOP4
Definitive
https://search.clinicalgenome.org/kb/gene-vali...
2017-02-15T00:00:00
774
USH1G
HGNC:16356
nonsyndromic genetic deafness
MONDO_0019497
SOP6
Disputed
https://search.clinicalgenome.org/kb/gene-vali...
2019-05-21T16:00:00.000Z
775
USH2A
HGNC:12601
Usher syndrome type 2
MONDO_0016484
SOP4
Definitive
https://search.clinicalgenome.org/kb/gene-vali...
2017-02-15T00:00:00
776
VCL
HGNC:12665
hypertrophic cardiomyopathy
MONDO_0005045
SOP4
Limited
https://search.clinicalgenome.org/kb/gene-vali...
2017-06-01T00:00:00
777
VHL
HGNC:12687
hereditary pheochromocytoma-paraganglioma
MONDO_0017366
SOP4
Definitive
https://search.clinicalgenome.org/kb/gene-vali...
2017-06-16T00:00:00
778
VPS13B
HGNC:2183
Cohen syndrome
MONDO_0008999
SOP6
Definitive
https://search.clinicalgenome.org/kb/gene-vali...
2018-11-13T15:34:57.342Z
779
VPS8
HGNC:29122
arthrogryposis multiplex congenita
MONDO_0015168
SOP4
Limited
https://search.clinicalgenome.org/kb/gene-vali...
2016-11-24T00:00:00
780
WAS
HGNC:12731
Wiskott-Aldrich syndrome
MONDO_0010518
SOP6
Definitive
https://search.clinicalgenome.org/kb/gene-vali...
2018-10-12T20:54:25.459Z
781
WBP2
HGNC:12738
autosomal recessive nonsyndromic deafness
MONDO_0019588
SOP6
Limited
https://search.clinicalgenome.org/kb/gene-vali...
2018-12-09T17:00:00.000Z
782
WDR45
HGNC:28912
complex neurodevelopmental disorder
MONDO_0100038
SOP6
Definitive
https://search.clinicalgenome.org/kb/gene-vali...
2019-06-18T18:00:00.000Z
783
WFS1
HGNC:12762
Wolfram syndrome
MONDO_0018105
SOP5
Definitive
https://search.clinicalgenome.org/kb/gene-vali...
2018-09-11T18:54:09.174Z
784
WFS1
HGNC:12762
Wolfram-like syndrome
MONDO_0013673
SOP6
Definitive
https://search.clinicalgenome.org/kb/gene-vali...
2018-04-17T04:00:00.000Z
785
WHRN
HGNC:16361
Usher syndrome type 2D
MONDO_0012662
SOP4
Definitive
https://search.clinicalgenome.org/kb/gene-vali...
2017-05-10T00:00:00
786
WHRN
HGNC:16361
nonsyndromic genetic deafness
MONDO_0019497
SOP6
Moderate
https://search.clinicalgenome.org/kb/gene-vali...
2018-12-26T17:00:00.000Z
787
WRAP53
HGNC:25522
dyskeratosis congenita
MONDO_0015780
SOP4
Moderate
https://search.clinicalgenome.org/kb/gene-vali...
2017-01-25T00:00:00
788
WRN
HGNC:12791
Werner syndrome
MONDO_0010196
SOP6
Definitive
https://search.clinicalgenome.org/kb/gene-vali...
2018-10-09T17:00:00.000Z
789
XPA
HGNC:12814
xeroderma pigmentosum group A
MONDO_0010210
SOP6
Definitive
https://search.clinicalgenome.org/kb/gene-vali...
2018-11-02T21:36:51.734Z
790
XPC
HGNC:12816
xeroderma pigmentosum group C
MONDO_0010211
SOP6
Definitive
https://search.clinicalgenome.org/kb/gene-vali...
2018-11-02T21:42:21.860Z
791
XRCC2
HGNC:12829
hereditary breast carcinoma
MONDO_0016419
SOP4
Limited
https://search.clinicalgenome.org/kb/gene-vali...
2017-05-10T00:00:00
792
XRCC2
HGNC:12829
familial ovarian cancer
MONDO_0016248
SOP4
No Reported Evidence
https://search.clinicalgenome.org/kb/gene-vali...
2017-04-26T00:00:00
793
XRCC4
HGNC:12831
hereditary nonpolyposis colon cancer
MONDO_0018630
SOP4
Limited
https://search.clinicalgenome.org/kb/gene-vali...
2017-05-08T00:00:00
794
ZEB2
HGNC:14881
Mowat-Wilson syndrome
MONDO_0009341
SOP5
Definitive
https://search.clinicalgenome.org/kb/gene-vali...
2018-05-24T12:34:43.951Z
795
ZNF292
HGNC:18410
complex neurodevelopmental disorder
MONDO_0100038
SOP6
Limited
https://search.clinicalgenome.org/kb/gene-vali...
2019-01-15T17:00:00.000Z
796
ZNF81
HGNC:13156
non-syndromic X-linked intellectual disability
MONDO_0019181
SOP5
Disputed
https://search.clinicalgenome.org/kb/gene-vali...
2018-06-28T18:56:10.060Z
797 rows × 8 columns
In [35]:
print("Logging in...")
#if "WDUSER" in os.environ and "WDPASS" in os.environ:
# WDUSER = os.environ['WDUSER']
# WDPASS = os.environ['WDPASS']
#else:
# raise ValueError("WDUSER and WDPASS must be specified in local.py or as environment variables")
login = wdi_login.WDLogin("<username>", "<password>")
Logging in...
https://www.wikidata.org/w/api.php
Successfully logged in as Andrawaag
In [6]:
# Retrieve the QID for the
HGNC = "A2ML1"
sparqlQuery = "SELECT * WHERE {?gene wdt:P353 \""+HGNC+"\"}"
result = wdi_core.WDItemEngine.execute_sparql_query(sparqlQuery)
HGNC_qid = result["results"]["bindings"][0]["gene"]["value"].replace("http://www.wikidata.org/entity/", "")
HGNC_qid
Out[6]:
'Q18051234'
In [43]:
MONDO = "MONDO_0009026".replace("_", ":")
sparqlQuery = "SELECT * WHERE {?disease wdt:P5270 \""+MONDO+"\"}"
result = wdi_core.WDItemEngine.execute_sparql_query(sparqlQuery)
MONDO_qid = result["results"]["bindings"][0]["disease"]["value"].replace("http://www.wikidata.org/entity/", "")
MONDO_qid
Out[43]:
'Q1136492'
In [44]:
from datetime import datetime
import copy
def create_reference():
refStatedIn = wdi_core.WDItemID(value="Q64403342", prop_nr="P248", is_reference=True)
timeStringNow = datetime.now().strftime("+%Y-%m-%dT00:00:00Z")
refRetrieved = wdi_core.WDTime(timeStringNow, prop_nr="P813", is_reference=True)
refURL = wdi_core.WDUrl(value="https://search.clinicalgenome.org/kb/gene-validity/d910a9d8-516e-443d-acba-8d61f7574792--2018-06-07T14:23:53", prop_nr="P854", is_reference=True)
return [refStatedIn, refRetrieved, refURL]
In [38]:
reference = create_reference()
statement = [wdi_core.WDItemID(value=MONDO_qid, prop_nr="P2293", references=[copy.deepcopy(reference)])]
In [45]:
#wikidata_item = wdi_core.WDItemEngine(wd_item_id=HGNC_qid,data=statement, append_value=["P2293"])
wikidata_item = wdi_core.WDItemEngine(wd_item_id=HGNC_qid)
wikidata_item.get_wd_json_representation()
Out[45]:
{'labels': {'en': {'language': 'en', 'value': 'A2ML1'},
'fr': {'language': 'fr', 'value': 'A2ML1'},
'nl': {'language': 'nl', 'value': 'A2ML1'},
'srn': {'language': 'srn', 'value': 'A2ML1'},
'de': {'language': 'de', 'value': 'A2ML1'},
'it': {'language': 'it', 'value': 'A2ML1'},
'pt': {'language': 'pt', 'value': 'A2ML1'},
'es': {'language': 'es', 'value': 'A2ML1'},
'sv': {'language': 'sv', 'value': 'A2ML1'},
'uk': {'language': 'uk', 'value': 'A2ML1'},
'ar': {'language': 'ar', 'value': 'A2ML1'}},
'descriptions': {'en': {'language': 'en',
'value': 'protein-coding gene in the species Homo sapiens'},
'fr': {'language': 'fr', 'value': "gène de l'espèce Homo sapiens"},
'nl': {'language': 'nl', 'value': 'gen van de soort Homo sapiens'},
'it': {'language': 'it', 'value': 'gene umano'},
'de': {'language': 'de', 'value': 'Gen der Spezies Homo sapiens'},
'pt': {'language': 'pt', 'value': 'gene da espécie Homo sapiens'},
'es': {'language': 'es', 'value': 'gen de la especie Homo sapiens'},
'srn': {'language': 'srn', 'value': 'gen fu a sortu Homo sapiens'},
'sv': {'language': 'sv', 'value': 'Genen från arten Homo sapiens'},
'ar': {'language': 'ar', 'value': 'جين من أنواع جينات الإنسان العاقل'},
'uk': {'language': 'uk', 'value': 'білок-кодуючий ген Homo Sapiens'},
'sq': {'language': 'sq', 'value': 'gjen i llojit Homo sapiens'},
'zh': {'language': 'zh', 'value': '位於12號人類染色體的基因'}},
'claims': {'P351': [{'mainsnak': {'snaktype': 'value',
'property': 'P351',
'datavalue': {'value': '144568', 'type': 'string'},
'datatype': 'external-id'},
'type': 'statement',
'rank': 'normal',
'qualifiers': {},
'qualifiers-order': [],
'references': [{'snaks': {'P248': [{'snaktype': 'value',
'property': 'P248',
'datavalue': {'value': {'entity-type': 'item',
'numeric-id': 20641742,
'id': 'Q20641742'},
'type': 'wikibase-entityid'},
'datatype': 'wikibase-item'}],
'P813': [{'snaktype': 'value',
'property': 'P813',
'datavalue': {'value': {'time': '+2019-05-10T00:00:00Z',
'timezone': 0,
'before': 0,
'after': 0,
'precision': 11,
'calendarmodel': 'http://www.wikidata.org/entity/Q1985727'},
'type': 'time'},
'datatype': 'time'}],
'P351': [{'snaktype': 'value',
'property': 'P351',
'datavalue': {'value': '144568', 'type': 'string'},
'datatype': 'external-id'}]},
'snaks-order': ['P248', 'P813', 'P351'],
'hash': '38e991b816d8cfb0ddc7caa2626210ed8e351485'}],
'id': 'Q18051234$FA31B124-5397-4AF8-BCB1-CD8A46D0B716'}],
'P279': [{'mainsnak': {'snaktype': 'value',
'property': 'P279',
'datavalue': {'value': {'entity-type': 'item',
'numeric-id': 20747295,
'id': 'Q20747295'},
'type': 'wikibase-entityid'},
'datatype': 'wikibase-item'},
'type': 'statement',
'rank': 'normal',
'qualifiers': {},
'qualifiers-order': [],
'references': [{'snaks': {'P248': [{'snaktype': 'value',
'property': 'P248',
'datavalue': {'value': {'entity-type': 'item',
'numeric-id': 27975061,
'id': 'Q27975061'},
'type': 'wikibase-entityid'},
'datatype': 'wikibase-item'}],
'P594': [{'snaktype': 'value',
'property': 'P594',
'datavalue': {'value': 'ENSG00000166535', 'type': 'string'},
'datatype': 'external-id'}]},
'snaks-order': ['P248', 'P594'],
'hash': '0835e0f7d54bd504f23350c0a097e602803ccb16'}],
'id': 'Q18051234$529335C1-8B65-4517-BB2F-242E958F55B7'}],
'P594': [{'mainsnak': {'snaktype': 'value',
'property': 'P594',
'datavalue': {'value': 'ENSG00000166535', 'type': 'string'},
'datatype': 'external-id'},
'type': 'statement',
'rank': 'normal',
'qualifiers': {},
'qualifiers-order': [],
'references': [{'snaks': {'P248': [{'snaktype': 'value',
'property': 'P248',
'datavalue': {'value': {'entity-type': 'item',
'numeric-id': 67600000,
'id': 'Q67600000'},
'type': 'wikibase-entityid'},
'datatype': 'wikibase-item'}],
'P594': [{'snaktype': 'value',
'property': 'P594',
'datavalue': {'value': 'ENSG00000166535', 'type': 'string'},
'datatype': 'external-id'}]},
'snaks-order': ['P248', 'P594'],
'hash': 'd5c836483a65c7efa10aebc4f1b1ee79c6a4b579'}],
'id': 'Q18051234$CCE936D8-8D5C-48A1-8591-44345E132527'}],
'P704': [{'mainsnak': {'snaktype': 'value',
'property': 'P704',
'datavalue': {'value': 'ENST00000545850', 'type': 'string'},
'datatype': 'external-id'},
'type': 'statement',
'rank': 'normal',
'qualifiers': {},
'qualifiers-order': [],
'references': [{'snaks': {'P248': [{'snaktype': 'value',
'property': 'P248',
'datavalue': {'value': {'entity-type': 'item',
'numeric-id': 67600000,
'id': 'Q67600000'},
'type': 'wikibase-entityid'},
'datatype': 'wikibase-item'}],
'P594': [{'snaktype': 'value',
'property': 'P594',
'datavalue': {'value': 'ENSG00000166535', 'type': 'string'},
'datatype': 'external-id'}]},
'snaks-order': ['P248', 'P594'],
'hash': 'd5c836483a65c7efa10aebc4f1b1ee79c6a4b579'}],
'id': 'Q18051234$96179B7E-7B00-44CD-BC3C-CAEF18A36D46'},
{'mainsnak': {'snaktype': 'value',
'property': 'P704',
'datavalue': {'value': 'ENST00000299698', 'type': 'string'},
'datatype': 'external-id'},
'type': 'statement',
'rank': 'normal',
'qualifiers': {},
'qualifiers-order': [],
'references': [{'snaks': {'P248': [{'snaktype': 'value',
'property': 'P248',
'datavalue': {'value': {'entity-type': 'item',
'numeric-id': 67600000,
'id': 'Q67600000'},
'type': 'wikibase-entityid'},
'datatype': 'wikibase-item'}],
'P594': [{'snaktype': 'value',
'property': 'P594',
'datavalue': {'value': 'ENSG00000166535', 'type': 'string'},
'datatype': 'external-id'}]},
'snaks-order': ['P248', 'P594'],
'hash': 'd5c836483a65c7efa10aebc4f1b1ee79c6a4b579'}],
'id': 'Q18051234$88C67E97-2549-4FAD-AD3D-C140077CE647'},
{'mainsnak': {'snaktype': 'value',
'property': 'P704',
'datavalue': {'value': 'ENST00000536789', 'type': 'string'},
'datatype': 'external-id'},
'type': 'statement',
'rank': 'normal',
'qualifiers': {},
'qualifiers-order': [],
'references': [{'snaks': {'P248': [{'snaktype': 'value',
'property': 'P248',
'datavalue': {'value': {'entity-type': 'item',
'numeric-id': 67600000,
'id': 'Q67600000'},
'type': 'wikibase-entityid'},
'datatype': 'wikibase-item'}],
'P594': [{'snaktype': 'value',
'property': 'P594',
'datavalue': {'value': 'ENSG00000166535', 'type': 'string'},
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'datavalue': {'value': 'https://search.clinicalgenome.org/kb/gene-validity/fc3c41d8-8497-489b-a350-c9e30016bc6a--2018-06-07T14:31:03',
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'aliases': {'en': [{'language': 'en', 'value': 'CPAMD9'},
{'language': 'en', 'value': 'alpha-2-macroglobulin like 1'},
{'language': 'en', 'value': 'p170'},
{'language': 'en', 'value': 'OMS'}],
'ar': [{'language': 'ar', 'value': 'A٢ML١'}]},
'sitelinks': {}}
In [36]:
# wikidata_item.write(login)
Out[36]:
'Q18051234'
In [ ]:
Content source: SuLab/WikidataIntegrator
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