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PMC:7265874 / 1705-4600 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T6 491-494 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T7 1123-1128 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T8 1154-1159 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T9 1451-1454 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T10 2292-2295 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T11 2502-2508 Body_part denotes kidney http://purl.org/sig/ont/fma/fma7203
T12 2831-2837 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T3 1123-1128 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T4 1154-1159 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T5 2502-2508 Body_part denotes kidney http://purl.obolibrary.org/obo/UBERON_0002113
T6 2831-2837 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T17 43-51 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T18 453-462 Disease denotes pemphigus http://purl.obolibrary.org/obo/MONDO_0006594
T19 796-804 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T20 805-814 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T21 906-914 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T22 962-970 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T23 1228-1235 Disease denotes Obesity http://purl.obolibrary.org/obo/MONDO_0011122
T24 1282-1284 Disease denotes DM http://purl.obolibrary.org/obo/MONDO_0005015|http://purl.obolibrary.org/obo/MONDO_0016367
T26 1319-1321 Disease denotes DM http://purl.obolibrary.org/obo/MONDO_0005015|http://purl.obolibrary.org/obo/MONDO_0016367
T28 1323-1330 Disease denotes obesity http://purl.obolibrary.org/obo/MONDO_0011122
T29 1383-1385 Disease denotes DM http://purl.obolibrary.org/obo/MONDO_0005015|http://purl.obolibrary.org/obo/MONDO_0016367
T31 1387-1390 Disease denotes CKD http://purl.obolibrary.org/obo/MONDO_0005300
T32 1397-1416 Disease denotes pemphigus foliaceus http://purl.obolibrary.org/obo/MONDO_0019324
T33 1397-1406 Disease denotes pemphigus http://purl.obolibrary.org/obo/MONDO_0006594
T34 1505-1508 Disease denotes AML http://purl.obolibrary.org/obo/MONDO_0018874
T35 1789-1796 Disease denotes Obesity http://purl.obolibrary.org/obo/MONDO_0011122
T36 1914-1916 Disease denotes DM http://purl.obolibrary.org/obo/MONDO_0005015|http://purl.obolibrary.org/obo/MONDO_0016367
T38 2016-2018 Disease denotes DM http://purl.obolibrary.org/obo/MONDO_0005015|http://purl.obolibrary.org/obo/MONDO_0016367
T40 2020-2027 Disease denotes obesity http://purl.obolibrary.org/obo/MONDO_0011122
T41 2151-2153 Disease denotes DM http://purl.obolibrary.org/obo/MONDO_0005015|http://purl.obolibrary.org/obo/MONDO_0016367
T43 2155-2158 Disease denotes CKD http://purl.obolibrary.org/obo/MONDO_0005300
T44 2165-2184 Disease denotes pemphigus foliaceus http://purl.obolibrary.org/obo/MONDO_0019324
T45 2165-2174 Disease denotes pemphigus http://purl.obolibrary.org/obo/MONDO_0006594
T46 2402-2405 Disease denotes AML http://purl.obolibrary.org/obo/MONDO_0018874
T47 2490-2493 Disease denotes CKD http://purl.obolibrary.org/obo/MONDO_0005300
T48 2494-2516 Disease denotes chronic kidney disease http://purl.obolibrary.org/obo/MONDO_0005300
T49 2502-2516 Disease denotes kidney disease http://purl.obolibrary.org/obo/MONDO_0001343|http://purl.obolibrary.org/obo/MONDO_0005240
T51 2518-2521 Disease denotes AML http://purl.obolibrary.org/obo/MONDO_0018874
T52 2570-2583 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T53 2656-2668 Disease denotes hypertension http://purl.obolibrary.org/obo/MONDO_0005044
T54 2670-2672 Disease denotes DM http://purl.obolibrary.org/obo/MONDO_0005015|http://purl.obolibrary.org/obo/MONDO_0016367
T56 2673-2690 Disease denotes diabetes mellitus http://purl.obolibrary.org/obo/MONDO_0005015
T57 2782-2794 Disease denotes hypertension http://purl.obolibrary.org/obo/MONDO_0005044

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T16 40-42 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T17 182-184 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T18 505-508 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T19 1182-1186 http://purl.obolibrary.org/obo/CLO_0007489 denotes M 86
T20 1205-1206 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T21 1209-1210 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T22 1419-1423 http://purl.obolibrary.org/obo/CLO_0054060 denotes 10 2
T23 1539-1540 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T24 1543-1544 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T25 1703-1707 http://purl.obolibrary.org/obo/CLO_0007489 denotes M 86
T26 1718-1719 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T27 1754-1755 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T28 1808-1809 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T29 1917-1918 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T30 2044-2045 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T31 2185-2186 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T32 2392-2394 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T33 2418-2419 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T34 2457-2458 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T35 2502-2508 http://purl.obolibrary.org/obo/UBERON_0002113 denotes kidney
T36 2502-2508 http://www.ebi.ac.uk/efo/EFO_0000927 denotes kidney
T37 2502-2508 http://www.ebi.ac.uk/efo/EFO_0000929 denotes kidney
T38 2587-2588 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T39 2647-2655 http://purl.obolibrary.org/obo/UBERON_0001637 denotes arterial
T40 2647-2655 http://www.ebi.ac.uk/efo/EFO_0000814 denotes arterial
T41 2773-2781 http://purl.obolibrary.org/obo/UBERON_0001637 denotes arterial
T42 2773-2781 http://www.ebi.ac.uk/efo/EFO_0000814 denotes arterial

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T10 205-208 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T12 424-438 Chemical denotes corticosteroid http://purl.obolibrary.org/obo/CHEBI_50858
T13 576-586 Chemical denotes lamivudine http://purl.obolibrary.org/obo/CHEBI_63577
T14 587-596 Chemical denotes tenofovir http://purl.obolibrary.org/obo/CHEBI_134504|http://purl.obolibrary.org/obo/CHEBI_63625|http://purl.obolibrary.org/obo/CHEBI_63716
T17 597-607 Chemical denotes nevirapine http://purl.obolibrary.org/obo/CHEBI_63613
T18 701-704 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T20 848-851 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T22 860-862 Chemical denotes ID http://purl.obolibrary.org/obo/CHEBI_141439
T23 1047-1050 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T25 1064-1067 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T26 1068-1081 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T27 1093-1096 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T28 1097-1110 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T29 1129-1142 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T30 1160-1173 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T31 1282-1284 Chemical denotes DM http://purl.obolibrary.org/obo/CHEBI_141426
T32 1319-1321 Chemical denotes DM http://purl.obolibrary.org/obo/CHEBI_141426
T33 1383-1385 Chemical denotes DM http://purl.obolibrary.org/obo/CHEBI_141426
T34 1510-1513 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T36 1553-1555 Chemical denotes ID http://purl.obolibrary.org/obo/CHEBI_141439
T37 1643-1646 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T39 1729-1732 Chemical denotes ETA http://purl.obolibrary.org/obo/CHEBI_16000|http://purl.obolibrary.org/obo/CHEBI_53460|http://purl.obolibrary.org/obo/CHEBI_71488
T42 1822-1825 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T43 1868-1881 Chemical denotes isavuconazole http://purl.obolibrary.org/obo/CHEBI_85979
T44 1891-1893 Chemical denotes MV http://purl.obolibrary.org/obo/CHEBI_73616
T45 1914-1916 Chemical denotes DM http://purl.obolibrary.org/obo/CHEBI_141426
T46 1931-1934 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T47 2016-2018 Chemical denotes DM http://purl.obolibrary.org/obo/CHEBI_141426
T48 2058-2061 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T49 2128-2130 Chemical denotes MV http://purl.obolibrary.org/obo/CHEBI_73616
T50 2151-2153 Chemical denotes DM http://purl.obolibrary.org/obo/CHEBI_141426
T51 2199-2202 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T52 2269-2271 Chemical denotes MV http://purl.obolibrary.org/obo/CHEBI_73616
T53 2364-2377 Chemical denotes isavuconazole http://purl.obolibrary.org/obo/CHEBI_85979
T54 2407-2410 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T56 2432-2435 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T57 2547-2550 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T59 2670-2672 Chemical denotes DM http://purl.obolibrary.org/obo/CHEBI_141426
T60 2692-2695 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T61 2720-2723 Chemical denotes ETA http://purl.obolibrary.org/obo/CHEBI_16000|http://purl.obolibrary.org/obo/CHEBI_53460|http://purl.obolibrary.org/obo/CHEBI_71488
T64 2747-2749 Chemical denotes MV http://purl.obolibrary.org/obo/CHEBI_73616

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T1 1068-1081 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T2 1097-1110 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T3 1129-1142 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T4 1160-1173 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T10 205-208 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103
T11 647-670 Phenotype denotes acute myeloid leukaemia http://purl.obolibrary.org/obo/HP_0004808
T12 701-704 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103
T13 805-814 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T14 848-851 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103
T15 1047-1050 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103
T16 1228-1235 Phenotype denotes Obesity http://purl.obolibrary.org/obo/HP_0001513
T17 1323-1330 Phenotype denotes obesity http://purl.obolibrary.org/obo/HP_0001513
T18 1505-1508 Phenotype denotes AML http://purl.obolibrary.org/obo/HP_0004808
T19 1510-1513 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103
T20 1643-1646 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103
T21 1789-1796 Phenotype denotes Obesity http://purl.obolibrary.org/obo/HP_0001513
T22 2020-2027 Phenotype denotes obesity http://purl.obolibrary.org/obo/HP_0001513
T23 2402-2405 Phenotype denotes AML http://purl.obolibrary.org/obo/HP_0004808
T24 2407-2410 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103
T25 2494-2516 Phenotype denotes chronic kidney disease http://purl.obolibrary.org/obo/HP_0012622
T26 2518-2521 Phenotype denotes AML http://purl.obolibrary.org/obo/HP_0004808
T27 2522-2545 Phenotype denotes acute myeloid leukaemia http://purl.obolibrary.org/obo/HP_0004808
T28 2547-2550 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103
T29 2551-2583 Phenotype denotes invasive pulmonary aspergillosis http://purl.obolibrary.org/obo/HP_0020103
T30 2656-2668 Phenotype denotes hypertension http://purl.obolibrary.org/obo/HP_0000822
T31 2673-2690 Phenotype denotes diabetes mellitus http://purl.obolibrary.org/obo/HP_0000819
T32 2782-2794 Phenotype denotes hypertension http://purl.obolibrary.org/obo/HP_0000822

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T13 0-145 Sentence denotes Between March 12th and April 25th 2020, 34 COVID-19 patients were admitted to our ICU, of whom 20 (59%) required invasive mechanical ventilation.
T14 146-219 Sentence denotes Seven of these ventilated patients (35%) were suspected of IPA (Table 1).
T15 220-294 Sentence denotes Median age in our patient cohort was 66 (interquartile range 56–77) years.
T16 295-350 Sentence denotes Underlying comorbidities were primarily cardiovascular.
T17 351-394 Sentence denotes Only three patients were immunocompromised.
T18 395-725 Sentence denotes One patient received chronic corticosteroid treatment for pemphigus foliaceous, one patient was HIV-positive (CD4 count > 250; viral load < 20 copies, treated with antiretrovirals [lamivudine/tenofovir/nevirapine]) and one patient had been treated for acute myeloid leukaemia 8 years ago and had developed IPA during chemotherapy.
T19 726-815 Sentence denotes All patients were intubated and mechanically ventilated due to severe COVID-19 pneumonia.
T20 816-851 Sentence denotes Table 1 Patients with suspected IPA
T21 852-1179 Sentence denotes Patient ID Sex (M/F) Age Medical history Time between COVID-19 symptoms and ICU admission (days) Time between COVID-19 symptoms and intubation (days) Time between intubation and first finding of IPA (days) First BAL galactomannan index Peak BAL galactomannan index First serum galactomannan index Peak serum galactomannan index
T22 1180-1220 Sentence denotes 1 M 86 Hyperchol 7 7 9 N/A N/A 0.10 0.10
T23 1221-1274 Sentence denotes 2 M 38 Obesity, hyperchol 9 9 6 2.40 > 2.80 0.30 0.30
T24 1275-1311 Sentence denotes 3 M 62 DM 7 7 16 0.72 2.00 0.20 0.20
T25 1312-1375 Sentence denotes 4 M 73 DM, obesity, AHT, hyperchol 9 10 5 2.65 > 2.80 0.10 0.10
T26 1376-1443 Sentence denotes 5 M 77 DM, CKD, AHT, pemphigus foliaceus 9 10 2 2.79 2.79 0.10 0.10
T27 1444-1497 Sentence denotes 6 M 55 HIV, AHT, hyperchol 8 9 13 0.69 0.69 0.18 0.80
T28 1498-1544 Sentence denotes 7 M 75 AML, IPA (2012) 3 3 8 2.63 2.63 N/A N/A
T29 1545-1700 Sentence denotes Patient ID Sex (M/F) Age Medical history First positive culture CT scan Histological examinationa IPA diagnosis AspICU algorithm Antifungal therapy Outcome
T30 1701-1781 Sentence denotes 1 M 86 Hyperchol A. flavus (ETA) No scan available N/A – – None Died, ICU day 10
T31 1782-1906 Sentence denotes 2 M 38 Obesity, hyperchol A. fumigatus (BAL) + Positive Proven Absolute Voriconazole, isavuconazole Alive on MV, ICU day 28b
T32 1907-2008 Sentence denotes 3 M 62 DM A. fumigatus (BAL) No scan available Positive Proven Absolute Voriconazole Died, ICU day 20
T33 2009-2143 Sentence denotes 4 M 73 DM, obesity, AHT, hyperchol A. fumigatus (BAL) No scan available Positive Proven Absolute Voriconazole Alive on MV, ICU day 24b
T34 2144-2284 Sentence denotes 5 M 77 DM, CKD, AHT, pemphigus foliaceus A. fumigatus (BAL) No scan available Positive Proven Absolute Voriconazole Alive on MV, ICU day 21b
T35 2285-2394 Sentence denotes 6 M 55 HIV, AHT, hyperchol Negative No scan available Negative – Voriconazole, isavuconazole Died, ICU day 27
T36 2395-2489 Sentence denotes 7 M 75 AML, IPA (2012) A. fumigatus (BAL) No scan available N/A – Voriconazole Died, ICU day 8
T37 2490-2584 Sentence denotes CKD chronic kidney disease, AML acute myeloid leukaemia, IPA invasive pulmonary aspergillosis.
T38 2585-2794 Sentence denotes N/A no sample available, Hyperchol hypercholesterolaemia, AHT arterial hypertension, DM diabetes mellitus, BAL bronchoalveolar lavage, ETA endotracheal aspirate, MV mechanical ventilation arterial hypertension
T39 2795-2871 Sentence denotes aAnatomopathological examination of tissue samples obtained via bronchoscopy
T40 2872-2895 Sentence denotes bAt the time of writing

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
55 1545-1552 Species denotes Patient Tax:9606
56 1718-1727 Species denotes A. flavus Tax:5059
57 1808-1820 Species denotes A. fumigatus Tax:746128
58 1917-1929 Species denotes A. fumigatus Tax:746128
59 2044-2056 Species denotes A. fumigatus Tax:746128
60 2185-2197 Species denotes A. fumigatus Tax:746128
61 2418-2430 Species denotes A. fumigatus Tax:746128
62 1765-1769 Disease denotes Died MESH:D003643
63 1914-1916 Disease denotes DM MESH:D009223
64 1992-1996 Disease denotes Died MESH:D003643
65 2016-2018 Disease denotes DM MESH:D009223
66 2020-2027 Disease denotes obesity MESH:D009765
67 2151-2153 Disease denotes DM MESH:D009223
68 2292-2295 Disease denotes HIV MESH:D015658
69 2378-2382 Disease denotes Died MESH:D003643
70 2402-2405 Disease denotes AML MESH:D015470
71 2474-2478 Disease denotes Died MESH:D003643
73 824-832 Species denotes Patients Tax:9606
80 2490-2516 Disease denotes CKD chronic kidney disease MESH:D051436
81 2518-2545 Disease denotes AML acute myeloid leukaemia MESH:D015470
82 2551-2583 Disease denotes invasive pulmonary aspergillosis MESH:D055744
83 2610-2668 Disease denotes Hyperchol hypercholesterolaemia, AHT arterial hypertension MESH:D000081029
84 2670-2690 Disease denotes DM diabetes mellitus MESH:D003920
85 2782-2794 Disease denotes hypertension MESH:D006973
102 505-508 Gene denotes CD4 Gene:920
103 52-60 Species denotes patients Tax:9606
104 172-180 Species denotes patients Tax:9606
105 238-245 Species denotes patient Tax:9606
106 362-370 Species denotes patients Tax:9606
107 399-406 Species denotes patient Tax:9606
108 479-486 Species denotes patient Tax:9606
109 618-625 Species denotes patient Tax:9606
110 730-738 Species denotes patients Tax:9606
111 576-586 Chemical denotes lamivudine MESH:D019259
112 587-596 Chemical denotes tenofovir MESH:D000068698
113 597-607 Chemical denotes nevirapine MESH:D019829
114 43-51 Disease denotes COVID-19 MESH:C000657245
115 491-494 Disease denotes HIV MESH:D015658
116 647-670 Disease denotes acute myeloid leukaemia MESH:D015470
117 796-814 Disease denotes COVID-19 pneumonia MESH:C000657245
211 906-914 Disease denotes COVID-19 MESH:C000657245