In [4]:
raw_corpus = []
with open('corpus/NCBItrainset_corpus.txt', 'r') as rf:
lines = rf.readlines()
for line in lines:
raw_corpus.append(line)
In [64]:
text_indices = []
blank_lines = []
for i in range(len(raw_corpus)):
if raw_corpus[i] in ['\n', '\r\n']:
blank_lines.append(i)
text_indices.append((i+1, i+2))
ann_indices = []
for i in range(len(raw_corpus)):
if (i, i+1) not in text_indices and (i-1, i) not in text_indices and i not in blank_lines:
ann_indices.append(i)
In [103]:
#titles = []
#abstracts = []
#text_corpus = {} # as dictionary
text_corpus = []
for indices in text_indices:
# titles.append(raw_corpus[indices[0]][11:])
# abstracts.append(raw_corpus[indices[1]][11:])
# find end of id string (second pipe)
title_noID = raw_corpus[indices[0]].split('|')[2].strip('\n')
abstract_noID = raw_corpus[indices[1]].split('|')[2].strip('\n')
# as dictionary
# text_corpus[raw_corpus[indices[0]].split('|')[0]] = [title_noID + ' ' + abstract_noID]
# as list
text_corpus.append(title_noID + ' ' + abstract_noID)
In [105]:
# each element in list corresponds to one title+abstract combo
print text_corpus[0]
A common human skin tumour is caused by activating mutations in beta-catenin. WNT signalling orchestrates a number of developmental programs. In response to this stimulus, cytoplasmic beta-catenin (encoded by CTNNB1) is stabilized, enabling downstream transcriptional activation by members of the LEF/TCF family. One of the target genes for beta-catenin/TCF encodes c-MYC, explaining why constitutive activation of the WNT pathway can lead to cancer, particularly in the colon. Most colon cancers arise from mutations in the gene encoding adenomatous polyposis coli (APC), a protein required for ubiquitin-mediated degradation of beta-catenin, but a small percentage of colon and some other cancers harbour beta-catenin-stabilizing mutations. Recently, we discovered that transgenic mice expressing an activated beta-catenin are predisposed to developing skin tumours resembling pilomatricomas. Given that the skin of these adult mice also exhibits signs of de novo hair-follicle morphogenesis, we wondered whether human pilomatricomas might originate from hair matrix cells and whether they might possess beta-catenin-stabilizing mutations. Here, we explore the cell origin and aetiology of this common human skin tumour. We found nuclear LEF-1 in the dividing tumour cells, providing biochemical evidence that pilomatricomas are derived from hair matrix cells. At least 75% of these tumours possess mutations affecting the amino-terminal segment, normally involved in phosphorylation-dependent, ubiquitin-mediated degradation of the protein. This percentage of CTNNB1 mutations is greater than in all other human tumours examined thus far, and directly implicates beta-catenin/LEF misregulation as the major cause of hair matrix cell tumorigenesis in humans..
In [123]:
# save corpus to separate files to be read into nltk
for indices in text_indices:
# find end of id string (second pipe)
ID = raw_corpus[indices[0]].split('|')[0]
title_noID = raw_corpus[indices[0]].split('|')[2].strip('\n')
abstract_noID = raw_corpus[indices[1]].split('|')[2].strip('\n')
save_file = 'corpus_nltk/' + ID + '.txt'
with open(save_file, 'w') as wf:
wf.write('\n')
wf.write(title_noID + ' ' + abstract_noID)
wf.write('\n')
In [76]:
annotations = {}
for index in ann_indices:
entry = raw_corpus[index].split('\t')
entry_id = entry[0]
start = entry[1]
end = entry[2]
ann_mention = entry[3]
ann_type = entry[4]
ann_concept = entry[5]
annotations[(entry_id, ann_mention)] = [start, end, ann_type, ann_concept]
In [106]:
annotations
Out[106]:
{('7663517', 'breast and/or ovarian cancer'): ['325',
'353',
'Modifier',
'D001943|D010051\n'],
('10533031', 'FRDA'): ['157', '161', 'Modifier', 'D005621\n'],
('8375105', 'Duchenne muscular dystrophy'): ['189',
'216',
'SpecificDisease',
'D020388\n'],
('6337374', 'malaria'): ['811', '818', 'SpecificDisease', 'D008288\n'],
('2862466', 'CAH'): ['709', '712', 'SpecificDisease', 'D006521\n'],
('1338904', 'FAP'): ['273', '276', 'Modifier', 'D011125\n'],
('10465113', 'EDM2'): ['1455', '1459', 'SpecificDisease', 'OMIM:600204\n'],
('1505217', 'lysosomal storage disorder'): ['208',
'234',
'DiseaseClass',
'D016464\n'],
('1978564', 'colorectal carcinomas'): ['1005',
'1026',
'SpecificDisease',
'D015179\n'],
('1301937', 'TSD'): ['673', '676', 'Modifier', 'D013661\n'],
('1303171', 'NDP'): ['888', '891', 'Modifier', 'C537849\n'],
('10403837', 'Hereditary progressive dystonia'): ['154',
'185',
'SpecificDisease',
'D020821\n'],
('8571953', 'breast and ovarian cancer'): ['688',
'713',
'CompositeMention',
'D061325\n'],
('7315872', 'tendinous xanthomas'): ['630',
'649',
'SpecificDisease',
'D014973\n'],
('1833974', 'Tay-Sachs disease'): ['817', '834', 'Modifier', 'D013661\n'],
('2241452', 'recurrent meningitis'): ['1112',
'1132',
'SpecificDisease',
'D008581+D012008\n'],
('3362213', 'autosomal recessive genetic disorder'): ['97',
'133',
'DiseaseClass',
'D030342\n'],
('3169738', 'Duchenne and Becker muscular dystrophy'): ['95',
'133',
'CompositeMention',
'D020388|C537666\n'],
('2894613', 'hemangioblastomas'): ['233',
'250',
'SpecificDisease',
'D018325\n'],
('2310692', 'inherited deficiency in the ninth complement component'): ['226',
'280',
'SpecificDisease',
'OMIM:613825\n'],
('10923035', 'BFIC'): ['1353', '1357', 'Modifier', 'D020936\n'],
('7599636', 'inherited disorders'): ['305',
'324',
'DiseaseClass',
'D030342\n'],
('10417280', 'Angelman syndrome'): ['189',
'206',
'SpecificDisease',
'D017204\n'],
('2303408', 'C5-deficient'): ['1577', '1589', 'Modifier', 'OMIM:609536\n'],
('8533762', 'G6PD deficiency'): ['991',
'1006',
'SpecificDisease',
'D005955\n'],
('10190331', 'Pendred syndrome'): ['533',
'549',
'SpecificDisease',
'C536648\n'],
('3012567', 'chromosomal abnormalities'): ['1253',
'1278',
'DiseaseClass',
'D002869\n'],
('3524231', 'DMD'): ['1052', '1055', 'Modifier', 'D020388\n'],
('7481765', 'BRCA1 abnormalities'): ['613',
'632',
'DiseaseClass',
'OMIM:604370\n'],
('10369876', 'neuronal damage'): ['488', '503', 'DiseaseClass', 'D009410\n'],
('8408659', 'CETP deficiency'): ['338',
'353',
'SpecificDisease',
'OMIM:143470\n'],
('2390095', 'CETP-deficient'): ['245', '259', 'Modifier', 'OMIM:143470\n'],
('7663517', 'hereditary breast and ovarian cancer'): ['114',
'150',
'Modifier',
'D061325\n'],
('8302543', 'choriocapillaris of the macula'): ['1049',
'1079',
'SpecificDisease',
'D008268\n'],
('10943845', 'breast cancer'): ['90', '103', 'SpecificDisease', 'D001943\n'],
('8533757', 'breast cancers'): ['1526',
'1540',
'SpecificDisease',
'D001943\n'],
('10470286', 'neurofibrosarcomas'): ['368',
'386',
'SpecificDisease',
'D018319\n'],
('10447258', 'infantile Refsum disease'): ['208',
'232',
'SpecificDisease',
'D052919\n'],
('10094559', 'Alkaptonuria'): ['64', '76', 'SpecificDisease', 'D000474\n'],
('10742101', 'partial or complete deficiency of Hmgic'): ['646',
'685',
'CompositeMention',
'OMIM:600698\n'],
('10441573', 'ovarian cancers'): ['1104',
'1119',
'SpecificDisease',
'D010051\n'],
('8530105', 'trichorhinophalangeal syndrome'): ['886',
'916',
'SpecificDisease',
'OMIM:190350\n'],
('3346018', 'DMD'): ['275', '278', 'Modifier', 'D020388\n'],
('8528198', 'Wiskott-Aldrich syndrome'): ['50',
'74',
'SpecificDisease',
'D014923\n'],
('10589394', 'cleft lip'): ['348', '357', 'SpecificDisease', 'D002971\n'],
('2852474', 'congenital adrenal hypoplasia'): ['1547',
'1576',
'SpecificDisease',
'D000312\n'],
('10554035', 'von Hippel-Lindau (VHL) disease'): ['118',
'149',
'SpecificDisease',
'D006623\n'],
('8116611', 'myotonic dystrophy'): ['94',
'112',
'SpecificDisease',
'D009223\n'],
('10737981', 'GM1-gangliosidosis'): ['532',
'550',
'SpecificDisease',
'D016537\n'],
('2886237', 'Progressive Tapeto-Choroidal Dystrophy'): ['263',
'301',
'SpecificDisease',
'C531652\n'],
('2450401', 'DMD'): ['408', '411', 'Modifier', 'D020388\n'],
('7611277', 'breast and prostate cancer'): ['960',
'986',
'CompositeMention',
'D001943|D011471\n'],
('7857677', 'Gaucher disease'): ['163',
'178',
'SpecificDisease',
'D005776\n'],
('10915770', 'PWS'): ['1694', '1697', 'SpecificDisease', 'D011218\n'],
('3862128', 'PKU'): ['1225', '1228', 'Modifier', 'D010661\n'],
('1301190', 'TSD'): ['1284', '1287', 'Modifier', 'D013661\n'],
('10598803', 'colorectal cancer'): ['526',
'543',
'SpecificDisease',
'D015179\n'],
('6103091', 'proteinuria'): ['328', '339', 'SpecificDisease', 'D011507\n'],
('1717985', 'Piebaldism'): ['739', '749', 'SpecificDisease', 'D016116\n'],
('10470088', 'attenuated polyposis'): ['440', '460', 'Modifier', 'C538265\n'],
('8589721', 'MCF-7 tumours'): ['770', '783', 'DiseaseClass', 'D009369\n'],
('7717396', 'ALD'): ['1349', '1352', 'SpecificDisease', 'D000326\n'],
('1358807', 'X-linked amelogenesis imperfecta'): ['227',
'259',
'SpecificDisease',
'C538243\n'],
('10382909', 'X-linked Emery-Dreifuss muscular dystrophy'): ['31',
'73',
'SpecificDisease',
'D020389\n'],
('8533762', 'malaria'): ['262', '269', 'SpecificDisease', 'D008288\n'],
('2544995', 'aniridia'): ['299', '307', 'SpecificDisease', 'D015783\n'],
('7543316', 'Myotonic dystrophy'): ['0',
'18',
'SpecificDisease',
'D009223\n'],
('10071185', 'clinical abnormalities'): ['1252',
'1274',
'DiseaseClass',
'D013568\n'],
('8301658', 'X linked recessive thrombocytopenia'): ['882',
'917',
'SpecificDisease',
'OMIM:313900\n'],
('7605382', 'CETP deficiency'): ['1566',
'1581',
'SpecificDisease',
'OMIM:143470\n'],
('2760209', 'Lesch-Nyhan'): ['31', '42', 'Modifier', 'D007926\n'],
('1301161', 'congenital blindness'): ['161',
'181',
'SpecificDisease',
'D057130\n'],
('10471457', 'hereditary hemochromatosis'): ['1950',
'1976',
'SpecificDisease',
'D006432\n'],
('10071185', 'mental retardation'): ['1029',
'1047',
'DiseaseClass',
'D008607\n'],
('10051005', 'hereditary non-polyposis cancer syndrome'): ['278',
'318',
'SpecificDisease',
'D003123\n'],
('2773936', 'inborn errors of myelin metabolism'): ['1444',
'1478',
'DiseaseClass',
'D020279\n'],
('10083733', 'APC'): ['1410', '1413', 'Modifier', 'D011125\n'],
('8317477', 'HD'): ['721', '723', 'Modifier', 'D006816\n'],
('10737980', 'X-linked adrenoleukodystrophy'): ['20',
'49',
'Modifier',
'D000326\n'],
('10607954', 'defect of the anterior midline scalp'): ['252',
'288',
'DiseaseClass',
'C538225\n'],
('3348216', 'hematologic malignancy'): ['62',
'84',
'DiseaseClass',
'D019337\n'],
('7523157',
'completely deficient in the seventh component of complement'): ['577', '636', 'SpecificDisease', 'OMIM:610102\n'],
('10556283', 'medulloblastomas'): ['1347',
'1363',
'SpecificDisease',
'D008527\n'],
('10426139', 'McLeod'): ['690', '696', 'Modifier', 'OMIM:300842\n'],
('3343337', 'inherited disorder'): ['1465',
'1483',
'DiseaseClass',
'D030342\n'],
('7573040', 'MJD'): ['844', '847', 'SpecificDisease', 'D017827\n'],
('6524872', 'adrenal cortical insufficiency'): ['199',
'229',
'DiseaseClass',
'D000309\n'],
('10528860', 'maternal heterodisomy'): ['1180',
'1201',
'DiseaseClass',
'D024182\n'],
('2352258', 'renal cell carcinoma'): ['1209',
'1229',
'SpecificDisease',
'D002292\n'],
('1307245', 'Norrie disease'): ['944', '958', 'SpecificDisease', 'C537849\n'],
('7607677', 'deficiency in N-acetylgalactosamine-6-sulfatase'): ['193',
'240',
'SpecificDisease',
'D009085\n'],
('8301658', 'thrombocytopenia'): ['88',
'104',
'SpecificDisease',
'D013921\n'],
('10330430', 'familial hypertrophic cardiomyopathy'): ['188',
'224',
'SpecificDisease',
'D024741\n'],
('7964884', 'cerebrotendinous xanthomatosis'): ['329',
'359',
'SpecificDisease',
'D019294\n'],
('1684088', 'metachromatic leukodystrophy'): ['179',
'207',
'SpecificDisease',
'D007966\n'],
('6103091', 'nephritis'): ['746', '755', 'SpecificDisease', 'D009393\n'],
('2995231', 'Becker muscular dystrophy'): ['236',
'261',
'SpecificDisease',
'C537666\n'],
('10817650', 'ataxia-telangiectasia'): ['103',
'124',
'Modifier',
'D001260\n'],
('2895982', 'Lowe syndrome'): ['821', '834', 'SpecificDisease', 'D009800\n'],
('10500204', 'absence of deep tendon reflexes'): ['293',
'324',
'DiseaseClass',
'D012021\n'],
('10465113', 'club foot'): ['749', '758', 'SpecificDisease', 'D003025\n'],
('7717396', 'X-ALD'): ['1527', '1532', 'Modifier', 'D000326\n'],
('10817650', 'A-T'): ['1573', '1576', 'Modifier', 'D001260\n'],
('7581380', 'dominant non-dystrophic myotonias'): ['61',
'94',
'DiseaseClass',
'C536245\n'],
('10571943', 'WT1 gene abnormality'): ['642',
'662',
'SpecificDisease',
'D009396\n'],
('7315872', 'CTX'): ['702', '705', 'SpecificDisease', 'D019294\n'],
('7599636', 'amelogenesis imperfecta'): ['245',
'268',
'DiseaseClass',
'D000567\n'],
('1468459', 'developmental delay'): ['623',
'642',
'DiseaseClass',
'D002658\n'],
('10788334', 'breast and ovarian cancer'): ['1097',
'1122',
'CompositeMention',
'D001943|D010051\n'],
('1361318', 'cutaneous vasculitis'): ['312',
'332',
'SpecificDisease',
'D018366\n'],
('8004674', 'McLeod syndrome'): ['903',
'918',
'SpecificDisease',
'OMIM:300842\n'],
('2703233', 'myotonic dystrophy'): ['527',
'545',
'SpecificDisease',
'D009223\n'],
('10861282', 'ankylosing spondylitis'): ['60',
'82',
'SpecificDisease',
'D013167\n'],
('10190331', 'EVA'): ['628', '631', 'SpecificDisease', 'OMIM:600791\n'],
('3591825', 'ALD'): ['721', '724', 'SpecificDisease', 'D000326\n'],
('2792129', 'recurrent meningitis'): ['158',
'178',
'SpecificDisease',
'D008581+D012008\n'],
('2912886', 'glucose 6 phosphate dehydrogenase (G6PD) deficiency'): ['52',
'103',
'SpecificDisease',
'D005955\n'],
('10205262', 'AKU'): ['653', '656', 'SpecificDisease', 'D000474\n'],
('10533031', 'diabetes mellitus'): ['948',
'965',
'SpecificDisease',
'D003920\n'],
('1248000', 'A-T'): ['1319', '1322', 'Modifier', 'D001260\n'],
('8198128', 'neurodegenerative disease'): ['167',
'192',
'DiseaseClass',
'D019636\n'],
('10556283', 'gliomas'): ['1125', '1132', 'SpecificDisease', 'D005910\n'],
('2209091', 'Friedreich ataxia'): ['120', '137', 'Modifier', 'D005621\n'],
('10194428', 'Hereditary hemochromatosis'): ['119',
'145',
'SpecificDisease',
'D006432\n'],
('1279971', 'piebald'): ['786', '793', 'Modifier', 'D016116\n'],
('10571950', 'recessive inherited disorder'): ['133',
'161',
'DiseaseClass',
'D030342\n'],
('3464560', 'Duchenne muscular dystrophy'): ['241',
'268',
'SpecificDisease',
'D020388\n'],
('10447259', 'WAS'): ['1488', '1491', 'SpecificDisease', 'D014923\n'],
('10484981', 'cancers'): ['300', '307', 'DiseaseClass', 'D009369\n'],
('10077614', 'DDS'): ['1037', '1040', 'SpecificDisease', 'D030321\n'],
('7857677', 'deficiency of beta-glucocerebrosidase'): ['200',
'237',
'SpecificDisease',
'D005776\n'],
('10612394', 'NBS'): ['371', '374', 'SpecificDisease', 'D049932\n'],
('7076260', 'G6PD deficient'): ['253', '267', 'Modifier', 'D005955\n'],
('10747931', 'adipose tissue inflammation'): ['721',
'748',
'SpecificDisease',
'D007249\n'],
('7759075', 'familial breast cancer'): ['73',
'95',
'SpecificDisease',
'D001943\n'],
('10369876', 'neurohypophyseal diabetes insipidus'): ['627',
'662',
'SpecificDisease',
'D020790\n'],
('2352258', 'Sporadic cerebellar haemangioblastoma'): ['1162',
'1199',
'SpecificDisease',
'D018325\n'],
('1056013', 'leukemia'): ['971', '979', 'DiseaseClass', 'D007938\n'],
('3422216', 'choroideremia'): ['601', '614', 'Modifier', 'D015794\n'],
('10766245', 'NBS'): ['1239', '1242', 'Modifier', 'D049932\n'],
('7769092', 'VLCAD deficiency'): ['1145',
'1161',
'SpecificDisease',
'C536353\n'],
('8198128', 'FRDA'): ['1255', '1259', 'Modifier', 'D005621\n'],
('8554067', 'breast and ovarian cancer'): ['280',
'305',
'Modifier',
'D061325\n'],
('7599636', 'AIH1'): ['610', '614', 'SpecificDisease', 'C538243\n'],
('10915776', 'retinoblastoma'): ['1376', '1390', 'Modifier', 'D012175\n'],
('1303277', 'maternal disomy for chromosome 15'): ['234',
'267',
'SpecificDisease',
'C538037\n'],
('8281142', 'breast tumour'): ['724', '737', 'Modifier', 'D001943\n'],
('10982189', 'APC tumor'): ['30', '39', 'Modifier', 'D011125\n'],
('10465113', 'Multiple epiphyseal dysplasia'): ['1323',
'1352',
'SpecificDisease',
'D010009\n'],
('3455778', 'PKU'): ['1322', '1325', 'SpecificDisease', 'D010661\n'],
('10593994', 'Papillon-Lefevre syndrome'): ['81',
'106',
'SpecificDisease',
'D010214\n'],
('1248000', 'ataxia-telangiectasia'): ['53',
'74',
'SpecificDisease',
'D001260\n'],
('1056013', 'chromosome instability'): ['145',
'167',
'DiseaseClass',
'D043171\n'],
('2303408', 'Deficiency of the murine fifth complement component (C5)'): ['0',
'56',
'SpecificDisease',
'OMIM:609536\n'],
('7991123', 'impaired function of adrenal cortex and testes'): ['355',
'401',
'CompositeMention',
'D000303\n'],
('10581027', 'PLS'): ['1386', '1389', 'Modifier', 'D010214\n'],
('7298854', 'CTX'): ['1399', '1402', 'SpecificDisease', 'D019294\n'],
('8252631', 'adenomatous polyposis coli'): ['181',
'207',
'SpecificDisease',
'D011125\n'],
('8375105', 'DMD'): ['551', '554', 'Modifier', 'D020388\n'],
('10417286', 'H'): ['351', '352', 'SpecificDisease', 'D000848\n'],
('2786201', 'type IIA vWD'): ['989', '1001', 'Modifier', 'D056728\n'],
('8563759', 'neuroepithelial abnormalities'): ['71',
'100',
'DiseaseClass',
'D018302\n'],
('10571950', 'developmental abnormalities of the cochlea'): ['179',
'221',
'DiseaseClass',
'D015834\n'],
('3014348', 'Duchenne muscular dystrophy'): ['88',
'115',
'SpecificDisease',
'D020388\n'],
('10196381', 'X-linked adrenoleukodystrophy'): ['296',
'325',
'SpecificDisease',
'D000326\n'],
('6783144', 'meningococcal meningitis'): ['271',
'295',
'SpecificDisease',
'D008585\n'],
('7611277', 'male breast cancer'): ['1516',
'1534',
'SpecificDisease',
'D018567\n'],
('2316519', 'Duchenne muscular dystrophy'): ['201',
'228',
'SpecificDisease',
'D020388\n'],
('7076260', 'Glucose-6-phosphate dehydrogenase deficiency'): ['0',
'44',
'SpecificDisease',
'D005955\n'],
('8441467', 'Central nervous system demyelination'): ['353',
'389',
'DiseaseClass',
'D003711\n'],
('7762560', 'DM'): ['1344', '1346', 'SpecificDisease', 'D009223\n'],
('8554067', 'breast-ovarian syndrome'): ['1154',
'1177',
'SpecificDisease',
'D061325\n'],
('8266996', 'Prader-Willi syndrome'): ['240',
'261',
'SpecificDisease',
'D011218\n'],
('10930571', 'X-linked agammaglobulinemia'): ['1291',
'1318',
'SpecificDisease',
'OMIM:300755\n'],
('10192399', 'syndromic deafness'): ['115',
'133',
'DiseaseClass',
'D003638\n'],
('1269174', 'corneal arcus'): ['237', '250', 'SpecificDisease', 'D001112\n'],
('777027', 'C5-deficient'): ['317', '329', 'Modifier', 'OMIM:609536\n'],
('10353787', 'Overgrowth of oral mucosa and facial skin'): ['0',
'41',
'CompositeMention',
'D006965\n'],
('10807385', 'BRCA-linked and sporadic ovarian cancer'): ['30',
'69',
'CompositeMention',
'OMIM:604370|OMIM:612555|OMIM:613399|D010051\n'],
('8530105', 'TRPS'): ['918', '922', 'SpecificDisease', 'OMIM:190350\n'],
('3480530', 'retinoblastoma'): ['824', '838', 'SpecificDisease', 'D012175\n'],
('10802668', 'cardiac arrhythmia'): ['185',
'203',
'DiseaseClass',
'D001145\n'],
('10814710', 'MPS IVA'): ['1880', '1887', 'SpecificDisease', 'OMIM:253000\n'],
('10077651', 'hereditary hemochromatosis'): ['58',
'84',
'SpecificDisease',
'D006432\n'],
('3524231', 'Duchenne muscular dystrophy'): ['236',
'263',
'SpecificDisease',
'D020388\n'],
('10737981', 'cardiomyopathy'): ['1124', '1138', 'DiseaseClass', 'D009202\n'],
('2404853', 'Becker muscular dystrophy'): ['399',
'424',
'SpecificDisease',
'C537666\n'],
('7586656', 'HPRT enzyme deficiency'): ['274',
'296',
'SpecificDisease',
'D007926\n'],
('7390473', 'G6PD deficiency'): ['189',
'204',
'SpecificDisease',
'D005955\n'],
('10484772', 'Norrie disease'): ['544',
'558',
'SpecificDisease',
'C537849\n'],
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'1256',
'DiseaseClass',
'D007567\n'],
('2894613', 'renal cell carcinomas'): ['331',
'352',
'SpecificDisease',
'D002292\n'],
('7815415', 'mentally retarded'): ['1211',
'1228',
'DiseaseClass',
'D008607\n'],
('3032521', 'retinoblastoma'): ['490', '504', 'Modifier', 'D012175\n'],
('7937795', 'serous cystadenocarcinoma'): ['354',
'379',
'SpecificDisease',
'D018284\n'],
('1316718', 'Wiskott-Aldrich syndrome'): ['207',
'231',
'SpecificDisease',
'D014923\n'],
('10571950', 'sensorineural hearing loss'): ['223',
'249',
'SpecificDisease',
'D006319\n'],
('10447259', 'Wiskott-Aldrich syndrome'): ['139',
'163',
'SpecificDisease',
'D014923\n'],
('4019732', 'cleft palate'): ['337', '349', 'SpecificDisease', 'D002972\n'],
('3362213', 'Tay-Sachs disease'): ['1046',
'1063',
'SpecificDisease',
'D013661\n'],
('3393536', 'G6PD deficiency'): ['1726',
'1741',
'SpecificDisease',
'D005955\n'],
('10369860', 'rearrangement disorders'): ['29',
'52',
'DiseaseClass',
'D002869\n'],
('8002973', 'ALD'): ['834', '837', 'Modifier', 'D000326\n'],
('10353787', 'leucoedema'): ['995', '1005', 'SpecificDisease', 'D007967\n'],
('10830915', 'FRDA'): ['359', '363', 'Modifier', 'D005621\n'],
('6859721', 'Chronic neisserial infection'): ['527',
'555',
'SpecificDisease',
'D016870\n'],
('10830910', 'VHL'): ['1263', '1266', 'Modifier', 'D006623\n'],
('10417286', 'CL/P'): ['454', '458', 'SpecificDisease', 'D002971|D002972\n'],
('10581027', 'Keratosis'): ['580', '589', 'SpecificDisease', 'D007642\n'],
('1323345', 'G6PD deficiency'): ['1125',
'1140',
'SpecificDisease',
'D005955\n'],
('10446987', 'DFSP'): ['1742', '1746', 'SpecificDisease', 'C538219\n'],
('2884570', 'molecular lesion'): ['888', '904', 'DiseaseClass', 'D030342\n'],
('3674116', 'Prader-Willi syndrome'): ['101',
'122',
'SpecificDisease',
'D011218\n'],
('2563633', 'PKU'): ['917', '920', 'Modifier', 'D010661\n'],
('10484772', 'intraretinal and subretinal lipid accumulation'): ['284',
'330',
'CompositeMention',
'D006949\n'],
('6087154', 'HPRT deficiencies'): ['248',
'265',
'DiseaseClass',
'OMIM:300323\n'],
('1346924', 'muscle weakness'): ['263', '278', 'DiseaseClass', 'D018908\n'],
('7874117', 'mid-face hypoplasia'): ['313',
'332',
'DiseaseClass',
'D019767\n'],
('10930361', 'FRDA'): ['625', '629', 'SpecificDisease', 'D005621\n'],
('523196', 'Lesch-Nyhan'): ['1635', '1646', 'Modifier', 'D007926\n'],
('8364574', 'congenital malformation of the eye'): ['42',
'76',
'DiseaseClass',
'D005124\n'],
('8259519', 'APC'): ['313', '316', 'SpecificDisease', 'D011125\n'],
('10716718', 'neuropathological abnormalities'): ['803',
'834',
'DiseaseClass',
'D009422\n'],
('495634', 'deficiency of the fifth component of complement'): ['179',
'226',
'SpecificDisease',
'OMIM:609536\n'],
('2390095',
'Total deficiency of plasma cholesteryl ester transfer protein'): ['0',
'61',
'SpecificDisease',
'OMIM:143470\n'],
('10064668', 'cancer'): ['1277', '1283', 'DiseaseClass', 'D009369\n'],
('10404839', 'pendred syndrome'): ['37', '53', 'Modifier', 'C536648\n'],
('7166314', 'congenital hemolytic anemia'): ['78',
'105',
'SpecificDisease',
'D000745\n'],
('8500791', 'hemophilia'): ['1582',
'1592',
'SpecificDisease',
'D006467|D002836\n'],
('7605382', 'coronary heart disease'): ['1487',
'1509',
'SpecificDisease',
'D003327\n'],
('1380672', 'oligodendrocyte degeneration'): ['1010',
'1038',
'SpecificDisease',
'D056784\n'],
('10077614', 'nonneoplastic'): ['318', '331', 'Modifier', 'D004194\n'],
('3198117', 'enzyme deficiency'): ['218', '235', 'DiseaseClass', 'D008661\n'],
('2760209',
'hypoxanthine phosphoribosyltransferase [HPRT] deficiency'): ['151', '207', 'SpecificDisease', 'D007926\n'],
('10528243', 'familial Mediterranean fever'): ['224',
'252',
'SpecificDisease',
'D010505\n'],
('8566952', 'adrenoleukodystrophy'): ['655',
'675',
'SpecificDisease',
'D000326\n'],
('1301937', 'hexosaminidase A deficiency'): ['19',
'46',
'SpecificDisease',
'D013661\n'],
('2491010', 'Duchenne muscular dystrophy'): ['174',
'201',
'SpecificDisease',
'D020388\n'],
('7759106', 'HD'): ['1230', '1232', 'Modifier', 'D006816\n'],
('1384323', 'deficient in Hex A'): ['234',
'252',
'SpecificDisease',
'D013661\n'],
('10818206', 'FMF'): ['1162', '1165', 'Modifier', 'D010505\n'],
('10930571', 'Aarskog-Scott Syndrome'): ['142',
'164',
'SpecificDisease',
'C535331\n'],
('10323740', 'Van der Woude syndrome'): ['82',
'104',
'SpecificDisease',
'C536528\n'],
('2852474', 'complex glycerol kinase deficiency'): ['149',
'183',
'SpecificDisease',
'C538138\n'],
('10364521', 'fragile X syndrome'): ['756',
'774',
'SpecificDisease',
'D005600\n'],
('10446987', 'dermatofibrosarcoma protuberans'): ['4',
'35',
'Modifier',
'C538219\n'],
('6604602', 'HEREDITARY MULTIFOCAL RELAPSING INFLAMMATION'): ['1321',
'1365',
'SpecificDisease',
'D007249+D030342\n'],
('10556285', 'MJD'): ['1653', '1656', 'SpecificDisease', 'D017827\n'],
('10447258', 'Zellweger syndrome'): ['1539',
'1557',
'SpecificDisease',
'D015211\n'],
('2220826', 'AT'): ['851', '853', 'Modifier', 'D001260\n'],
('10589394', 'hypodontia'): ['392', '402', 'SpecificDisease', 'D000848\n'],
('8279472', 'WND'): ['737', '740', 'SpecificDisease', 'D006527\n'],
('1302008', 'Wilms tumour'): ['371', '383', 'Modifier', 'D009396\n'],
('102474', 'sub-total deficiency of C6 and C7'): ['117',
'150',
'CompositeMention',
'OMIM:610102|OMIM:612446\n'],
('10192393', 'adenomatous polyposis coli'): ['539',
'565',
'SpecificDisease',
'D011125\n'],
('10767347', 'embryonic lethality'): ['897',
'916',
'SpecificDisease',
'D020964\n'],
('8084618', 'desmoplastic small round cell tumors'): ['406',
'442',
'DiseaseClass',
'D058405\n'],
('1483696', 'Tay-Sachs disease'): ['155',
'172',
'SpecificDisease',
'D013661\n'],
('10323252', 'cardiomyopathy'): ['339',
'353',
'SpecificDisease',
'D009202\n'],
('2773936', 'Pelizaeus-Merzbacher disease'): ['1746',
'1774',
'SpecificDisease',
'OMIM:312080\n'],
('7298854', 'genetic disease'): ['178', '193', 'DiseaseClass', 'D030342\n'],
('10051005', 'colorectal'): ['840', '850', 'Modifier', 'D015179\n'],
('10987655', 'episodic ataxia type 2'): ['274',
'296',
'SpecificDisease',
'C535506\n'],
('1338764', 'APC'): ['1222', '1225', 'Modifier', 'D011125\n'],
('2601691', 'RB tumors'): ['924', '933', 'SpecificDisease', 'D012175\n'],
('10556298', 'PWS'): ['1471', '1474', 'SpecificDisease', 'D011218\n'],
('10802667', 'abnormalities of skeletal muscle function'): ['1033',
'1074',
'DiseaseClass',
'D009139\n'],
('10426139', 'muscular atrophy'): ['206', '222', 'DiseaseClass', 'D009133\n'],
('7825586', 'breast cancer'): ['1154',
'1167',
'SpecificDisease',
'D001943\n'],
('7166314', 'G6PD deficiency'): ['347',
'362',
'SpecificDisease',
'D005955\n'],
('10842298', 'Hypotonia'): ['363', '372', 'DiseaseClass', 'D009123\n'],
('10484765', 'DMPK haploinsufficiency'): ['1630',
'1653',
'SpecificDisease',
'D058495\n'],
('2575483', 'aniridia'): ['681', '689', 'SpecificDisease', 'D015783\n'],
('10521293', 'psychiatric disorders'): ['1547',
'1568',
'DiseaseClass',
'D001523\n'],
('10556298', 'neurogenetic disorder'): ['151',
'172',
'DiseaseClass',
'D020271\n'],
('7857677', 'type GD II'): ['575', '585', 'SpecificDisease', 'D005776\n'],
('10213492', 'polyposis'): ['951', '960', 'SpecificDisease', 'D044483\n'],
('1562739',
'Glucose-6-PHOSPHATE dehydrogenase (G6PD; EC 1.1. 1. 49) deficiency'): ['99',
'165',
'SpecificDisease',
'D005955\n'],
('7761412', 'Lowe syndrome'): ['1715',
'1728',
'SpecificDisease',
'D009800\n'],
('2352258', 'VHL disease'): ['869', '880', 'SpecificDisease', 'D006623\n'],
('10915776', 'retinal dystrophy'): ['1779',
'1796',
'DiseaseClass',
'D058499\n'],
('3258663', 'severe von Willebrand disease'): ['1519',
'1548',
'SpecificDisease',
'D056729\n'],
('8528199', 'Wiskott-Aldrich syndrome'): ['183',
'207',
'SpecificDisease',
'D014923\n'],
('10874302', 'multifactorial diseases'): ['301',
'324',
'DiseaseClass',
'D004194\n'],
('1324223', 'Familial adenomatous polyposis'): ['116',
'146',
'SpecificDisease',
'D011125\n'],
('2390095', 'cholesteryl ester transfer protein (CETP) deficiency'): ['160',
'212',
'SpecificDisease',
'OMIM:143470\n'],
('1302032', 'fragile X syndrome'): ['572',
'590',
'SpecificDisease',
'D005600\n'],
('3417303', 'DM'): ['994', '996', 'Modifier', 'D009223\n'],
('8071955', 'DM'): ['1378', '1380', 'SpecificDisease', 'D009223\n'],
('2651669', 'Langer-Giedion syndrome'): ['270',
'293',
'SpecificDisease',
'D015826\n'],
('10406661', 'kniest dysplasia'): ['61',
'77',
'SpecificDisease',
'C537207\n'],
('10830910', 'Von Hippel-Lindau (VHL) disease'): ['96',
'127',
'SpecificDisease',
'D006623\n'],
('1302003', 'choroideremia'): ['60', '73', 'SpecificDisease', 'D015794\n'],
('10943845', 'cancer'): ['783', '789', 'DiseaseClass', 'D009369\n'],
('8566965', 'breast and ovarian cancer'): ['140',
'165',
'Modifier',
'D061325\n'],
('1338904', 'familial adenomatous polyposis'): ['241',
'271',
'Modifier',
'D011125\n'],
('10426139', 'McLeod syndrome'): ['152',
'167',
'SpecificDisease',
'OMIM:300842\n'],
('10051007', 'neurodegeneration'): ['1051',
'1068',
'DiseaseClass',
'D019636\n'],
('10465113', 'atelosteogenesis 2'): ['311',
'329',
'SpecificDisease',
'C535395\n'],
('7450778', 'glucose-6-phosphate dehydrogenase deficiency'): ['38',
'82',
'SpecificDisease',
'D005955\n'],
('10398436', 'adenomatous polyposis coli'): ['734',
'760',
'SpecificDisease',
'D011125\n'],
('7962532', 'cholesteryl ester transfer protein deficiency'): ['8',
'53',
'SpecificDisease',
'OMIM:143470\n'],
('10861298', 'goiter'): ['1330', '1336', 'DiseaseClass', 'D006042\n'],
('7479827', 'VLCAD deficiency'): ['1356',
'1372',
'SpecificDisease',
'C536353\n'],
('1376553', 'Pelizaeus-merzbacher disease'): ['241',
'269',
'SpecificDisease',
'OMIM:312080\n'],
('1973404', 'aspartylglucosaminuria'): ['11',
'33',
'SpecificDisease',
'D054880\n'],
('3572301', 'Wiskott-Aldrich syndrome'): ['58',
'82',
'SpecificDisease',
'D014923\n'],
('3563511', 'Lesch-Nyhan'): ['685', '696', 'Modifier', 'D007926\n'],
('492812', 'neisserial infections'): ['801',
'822',
'SpecificDisease',
'D016870\n'],
('161677', 'C2-deficient'): ['386', '398', 'Modifier', 'OMIM:217000\n'],
('10533031', 'impaired proprioception'): ['1224',
'1247',
'DiseaseClass',
'D020886\n'],
('2852474', 'Complex glycerol kinase deficiency'): ['0',
'34',
'SpecificDisease',
'C538138\n'],
('8302543', 'central scotoma'): ['967',
'982',
'SpecificDisease',
'D012607\n'],
('6650504', 'TSD'): ['967', '970', 'Modifier', 'D013661\n'],
('218453', 'ALD'): ['979', '982', 'SpecificDisease', 'D000326\n'],
('523196', 'dysarthric speech'): ['469',
'486',
'SpecificDisease',
'D004401\n'],
('10426999', 'familial breast and ovarian cancers'): ['137',
'172',
'CompositeMention',
'D061325\n'],
('8589721', 'breast cancer'): ['445', '458', 'Modifier', 'D001943\n'],
('10533031', 'cardiomyopathy'): ['932',
'946',
'SpecificDisease',
'D009202\n'],
('8128954', 'Myotonic dystrophy'): ['159',
'177',
'SpecificDisease',
'D009223\n'],
('2568588', 'tumour'): ['308', '314', 'DiseaseClass', 'D009369\n'],
('10071193', 'BFLS syndrome'): ['1452',
'1465',
'SpecificDisease',
'C536575\n'],
('10406661', 'myopia'): ['226', '232', 'DiseaseClass', 'D009216\n'],
('318684', 'skin rash'): ['1787', '1796', 'DiseaseClass', 'D005076\n'],
('7795653', 'invasive cancer'): ['454', '469', 'DiseaseClass', 'D009362\n'],
('495634', 'Deficiency of the fifth component of complement'): ['0',
'47',
'SpecificDisease',
'OMIM:609536\n'],
('1709636',
'deficiency of a hepatic enzyme, phenylalanine hydroxylase'): ['182', '239', 'SpecificDisease', 'OMIM:261600\n'],
('7696601', 'cerebral atrophy'): ['1164',
'1180',
'SpecificDisease',
'D001284\n'],
('10817650', 'autosomal recessive syndrome'): ['182',
'210',
'DiseaseClass',
'D030342\n'],
('10465113', 'DTDST disorders'): ['1189',
'1204',
'SpecificDisease',
'D030342\n'],
('1682919', 'centrocytic lymphomas'): ['1095',
'1116',
'DiseaseClass',
'D008223\n'],
('10094559', 'alkaptonuria'): ['38', '50', 'Modifier', 'D000474\n'],
('2355960', 'GM2 gangliosidosis, type 1'): ['177',
'203',
'SpecificDisease',
'D013661\n'],
('10618304', 'idiopathic ventricular fibrillation'): ['263',
'298',
'SpecificDisease',
'C537182\n'],
('8434621', 'familial Mediterranean fever'): ['174',
'202',
'SpecificDisease',
'D010505\n'],
...}
In [107]:
import nltk
In [111]:
# Find the directory where the corpus lives.
genesis_dir = nltk.data.find('corpora/genesis')
# Create our custom sentence tokenizer.
my_sent_tokenizer = nltk.RegexpTokenizer('[^.!?]+')
# Create the new corpus reader object.
my_genesis = nltk.corpus.PlaintextCorpusReader(genesis_dir, '.*\.txt', sent_tokenizer=my_sent_tokenizer)
# Use the new corpus reader object.
#print(my_genesis.sents('english-kjv.txt')[0]) # doctest: +NORMALIZE_WHITESPACE
In [118]:
print(my_genesis.sents('english-kjv.txt')[0])
[u'In', u'the', u'beginning', u'God', u'created', u'the', u'heaven', u'and', u'the', u'earth']
In [124]:
ncbi_dir = nltk.data.find('corpora/ncbi_corpus_nltk')
ncbi = nltk.corpus.PlaintextCorpusReader(ncbi_dir, '.*\.txt')
In [126]:
[u'Glucose', u'6', u'-', u'phosphate', u'dehydrogenase', u'variants', u':', u'Gd', u'(+)', u'Alexandra', u'associated', u'with', u'neonatal', u'jaundice', u'and', u'Gd', u'(-)', u'Camperdown', u'in', u'a', u'young', u'man', u'with', u'lamellar', u'cataracts', u'.']
In [ ]:
Content source: NUNLP/NCBI-Disease-Corpus
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