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PMC:7340597 / 163-1645 JSONTXT

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LitCovid_Glycan-Motif-Structure

Id Subject Object Predicate Lexical cue
T1 640-653 https://glytoucan.org/Structures/Glycans/G93424OB denotes galactomannan

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 176-180 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T2 759-764 Body_part denotes Chest http://purl.org/sig/ont/fma/fma9576
T3 972-980 Body_part denotes alveolar http://purl.org/sig/ont/fma/fma264783

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 176-180 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T2 759-764 Body_part denotes Chest http://purl.obolibrary.org/obo/UBERON_0001443

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
10 51-59 Species denotes patients Tax:9606
11 42-50 Disease denotes COVID-19 MESH:C000657245
15 199-207 Species denotes patients Tax:9606
16 213-221 Disease denotes COVID-19 MESH:C000657245
17 230-234 Disease denotes ARDS MESH:D012128
32 380-388 Species denotes Patients Tax:9606
33 618-626 Species denotes patients Tax:9606
34 693-701 Species denotes patients Tax:9606
35 775-783 Species denotes patients Tax:9606
36 1024-1032 Species denotes patients Tax:9606
37 640-653 Chemical denotes galactomannan MESH:C012990
38 591-609 Disease denotes pulmonary embolism MESH:D011655
39 714-722 Disease denotes COVID-19 MESH:C000657245
40 734-757 Disease denotes pulmonary aspergillosis MESH:D055732
41 953-962 Disease denotes pneumonia MESH:D011014
42 972-987 Disease denotes alveolar damage MESH:D055370
43 989-997 Disease denotes fibrosis MESH:D005355
44 1047-1056 Disease denotes pneumonia MESH:D011014
45 1107-1129 Disease denotes invasive aspergillosis MESH:D055744
55 1215-1223 Species denotes patients Tax:9606
56 1367-1375 Species denotes patients Tax:9606
57 1194-1208 Disease denotes critically ill MESH:D016638
58 1209-1214 Disease denotes COVID MESH:C000657245
59 1300-1309 Disease denotes pneumonia MESH:D011014
60 1358-1366 Disease denotes COVID-19 MESH:C000657245
61 1390-1398 Disease denotes COVID-19 MESH:C000657245
62 1410-1433 Disease denotes pulmonary aspergillosis MESH:D055732
63 1459-1481 Disease denotes invasive aspergillosis MESH:D055744

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T4 42-50 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T5 213-221 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T6 230-234 Disease denotes ARDS http://purl.obolibrary.org/obo/MONDO_0006502
T7 591-609 Disease denotes pulmonary embolism http://purl.obolibrary.org/obo/MONDO_0005279
T8 714-722 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T9 744-757 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T10 942-962 Disease denotes organizing pneumonia http://purl.obolibrary.org/obo/MONDO_0015265|http://purl.obolibrary.org/obo/MONDO_0056821
T12 953-962 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T13 1036-1056 Disease denotes organizing pneumonia http://purl.obolibrary.org/obo/MONDO_0015265|http://purl.obolibrary.org/obo/MONDO_0056821
T15 1047-1056 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T16 1107-1129 Disease denotes invasive aspergillosis http://purl.obolibrary.org/obo/MONDO_0000240
T17 1116-1129 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T18 1289-1309 Disease denotes organizing pneumonia http://purl.obolibrary.org/obo/MONDO_0015265|http://purl.obolibrary.org/obo/MONDO_0056821
T20 1300-1309 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T21 1358-1366 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T22 1390-1398 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T23 1420-1433 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T24 1459-1481 Disease denotes invasive aspergillosis http://purl.obolibrary.org/obo/MONDO_0000240
T25 1468-1481 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T2 176-180 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T3 176-180 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T4 426-431 http://purl.obolibrary.org/obo/UBERON_0003101 denotes males
T5 426-431 http://www.ebi.ac.uk/efo/EFO_0000970 denotes males
T6 440-447 http://purl.obolibrary.org/obo/UBERON_0003100 denotes females
T7 519-521 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T8 533-534 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T9 759-764 http://www.ebi.ac.uk/efo/EFO_0000965 denotes Chest
T10 942-952 http://purl.obolibrary.org/obo/OBI_0000245 denotes organizing
T11 1036-1046 http://purl.obolibrary.org/obo/OBI_0000245 denotes organizing
T12 1289-1299 http://purl.obolibrary.org/obo/OBI_0000245 denotes organizing

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 640-653 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 591-609 Phenotype denotes pulmonary embolism http://purl.obolibrary.org/obo/HP_0002204
T2 953-962 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T3 964-987 Phenotype denotes diffuse alveolar damage http://purl.obolibrary.org/obo/HP_0033006
T4 1047-1056 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T5 1300-1309 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T1 640-653 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T4 0-7 Sentence denotes Purpose
T5 8-117 Sentence denotes Pathological data of critical ill COVID-19 patients is essential in the search for optimal treatment options.
T6 119-139 Sentence denotes Material and methods
T7 140-235 Sentence denotes We performed postmortem needle core lung biopsies in seven patients with COVID-19 related ARDS.
T8 236-349 Sentence denotes Clinical, radiological and microbiological characteristics are reported together with histopathological findings.
T9 351-379 Sentence denotes Measurement and main results
T10 380-462 Sentence denotes Patients age ranged from 58 to 83 years, five males and two females were included.
T11 463-562 Sentence denotes Time from hospital admission to death ranged from 12 to 36 days, with a mean of 20 ventilated days.
T12 563-758 Sentence denotes ICU stay was complicated by pulmonary embolism in five patients and positive galactomannan on bronchoalveolar lavage fluid in six patients, suggesting COVID-19 associated pulmonary aspergillosis.
T13 759-867 Sentence denotes Chest CT in all patients showed ground glass opacities, commonly progressing to nondependent consolidations.
T14 868-1057 Sentence denotes We observed four distinct histopathological patterns: acute fibrinous and organizing pneumonia, diffuse alveolar damage, fibrosis and, in four out of seven patients an organizing pneumonia.
T15 1058-1130 Sentence denotes None of the biopsy specimens showed any signs of invasive aspergillosis.
T16 1132-1143 Sentence denotes Conclusions
T17 1144-1310 Sentence denotes In this case series common late histopathology in critically ill COVID patients is not classic DAD but heterogeneous with predominant pattern of organizing pneumonia.
T18 1311-1482 Sentence denotes Postmortem biopsy investigations in critically COVID-19 patients with probable COVID-19 associated pulmonary aspergillosis obtained no evidence for invasive aspergillosis.

LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T2 42-50 SP_7 denotes COVID-19
T3 153-163 GO:0016265 denotes postmortem
T4 176-180 UBERON:0002048 denotes lung
T5 213-221 SP_7 denotes COVID-19
T6 495-500 GO:0016265 denotes death
T7 591-600 UBERON:0002048 denotes pulmonary
T8 640-653 CHEBI:27680;CHEBI:27680 denotes galactomannan
T9 657-672 UBERON:0002186;BV_4 denotes bronchoalveolar
T10 673-679 BV_4 denotes lavage
T11 680-685 BV_4;UBERON:0006314 denotes fluid
T12 714-722 SP_7 denotes COVID-19
T13 734-743 UBERON:0002048 denotes pulmonary
T14 972-980 UBERON:0003215 denotes alveolar
T15 1311-1321 GO:0016265 denotes Postmortem
T16 1358-1366 SP_7 denotes COVID-19
T17 1390-1398 SP_7 denotes COVID-19
T18 1410-1419 UBERON:0002048 denotes pulmonary
T43630 38-42 UBERON:0007221 denotes ill
T69896 81-91 UBERON:0001004 denotes earch for
T89860 229-235 UBERON:0000915 denotes ARDS.
T77448 272-282 UBERON:0001004 denotes ogical cha
T47338 407-415 SP_7 denotes to 83 y
T50253 511-515 UBERON:0002048 denotes m 12
T37393 832-846 GO:0007596 denotes ing to nondepe
T57275 919-925 UBERON:0001638 denotes s: acu
T97784 926-941 GO:0007596 denotes e fibrinous and
T2103 962-970 SP_7 denotes , diffus
T61739 1014-1023 UBERON:0002048 denotes of seven
T56562 1077-1085 SP_7 denotes specimen
T20701 1124-1133 SP_7 denotes losis. C
T44207 1232-1241 UBERON:0002048 denotes lassic DA
T36528 1242-1248 UBERON:0000479 denotes but h
T77817 1363-1371 SP_7 denotes -19 pati
T24460 1394-1402 UBERON:0003215 denotes D-19 ass