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PMC:7346000 / 14873-19686 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T46 203-209 Body_part denotes throat http://purl.org/sig/ont/fma/fma228738
T47 1456-1479 Body_part denotes upper respiratory tract http://purl.org/sig/ont/fma/fma45661
T48 3290-3295 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T49 3569-3592 Body_part denotes upper respiratory tract http://purl.org/sig/ont/fma/fma45661
T50 4471-4476 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T13 203-209 Body_part denotes throat http://purl.obolibrary.org/obo/UBERON_0000341
T14 1456-1479 Body_part denotes upper respiratory tract http://purl.obolibrary.org/obo/UBERON_0001557
T15 1462-1479 Body_part denotes respiratory tract http://purl.obolibrary.org/obo/UBERON_0000065
T16 3290-3295 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T17 3569-3592 Body_part denotes upper respiratory tract http://purl.obolibrary.org/obo/UBERON_0001557
T18 3575-3592 Body_part denotes respiratory tract http://purl.obolibrary.org/obo/UBERON_0000065
T19 4471-4476 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id tao:has_standard_notation
455 107-115 Species denotes patients Tax:9606
456 190-198 Species denotes patients Tax:9606
457 382-390 Species denotes patients Tax:9606
458 412-420 Species denotes patients Tax:9606
459 584-592 Species denotes patients Tax:9606
460 689-697 Species denotes patients Tax:9606
461 1298-1306 Species denotes patients Tax:9606
462 69-80 Species denotes Aspergillus Tax:746128
463 248-259 Species denotes Aspergillus Tax:746128
464 1424-1435 Species denotes Aspergillus Tax:746128
465 1483-1494 Species denotes Aspergillus Tax:746128
466 1116-1129 Chemical denotes galactomannan MESH:C012990
467 81-91 Disease denotes infections MESH:D007239
468 98-106 Disease denotes COVID-19 MESH:C000657245
469 173-181 Disease denotes COVID-19 MESH:C000657245
470 286-311 Disease denotes Aspergillus co-infections MESH:D060085
471 396-404 Disease denotes COVID-19 MESH:C000657245
472 680-688 Disease denotes COVID-19 MESH:C000657245
473 716-733 Disease denotes fungal infections MESH:D009181
474 817-827 Disease denotes infections MESH:D007239
475 1020-1043 Disease denotes pulmonary aspergillosis MESH:D055732
476 1312-1320 Disease denotes COVID-19 MESH:C000657245
477 1495-1504 Disease denotes infection MESH:D007239
518 2505-2513 Species denotes patients Tax:9606
519 2601-2609 Species denotes patients Tax:9606
520 2736-2744 Species denotes children Tax:9606
521 3125-3132 Species denotes patient Tax:9606
522 3207-3219 Species denotes A. fumigatus Tax:746128
523 3686-3694 Species denotes patients Tax:9606
524 3727-3739 Species denotes A. fumigatus Tax:746128
525 3933-3945 Species denotes A. fumigatus Tax:746128
526 4153-4165 Species denotes A. fumigatus Tax:746128
527 4578-4585 Species denotes patient Tax:9606
528 4645-4657 Species denotes A. fumigatus Tax:746128
529 4792-4801 Species denotes A. flavus Tax:5059
530 2712-2721 Species denotes influenza Tax:11309
531 3525-3536 Species denotes Aspergillus Tax:746128
532 4692-4703 Species denotes Aspergillus Tax:746128
533 3296-3309 Chemical denotes galactomannan MESH:C012990
534 3605-3610 Chemical denotes azole MESH:D001393
535 3709-3714 Chemical denotes azole MESH:D001393
536 3894-3899 Chemical denotes azole MESH:D001393
537 3917-3922 Chemical denotes Azole MESH:D001393
538 4033-4038 Chemical denotes azole MESH:D001393
539 4137-4142 Chemical denotes azole MESH:D001393
540 4175-4187 Chemical denotes itraconazole MESH:D017964
541 4189-4201 Chemical denotes voriconazole MESH:D065819
542 4207-4219 Chemical denotes posaconazole MESH:C101425
543 4458-4470 Chemical denotes voriconazole MESH:D065819
544 4551-4563 Chemical denotes voriconazole MESH:D065819
545 4567-4572 Chemical denotes l-AmB
546 1652-1660 Disease denotes COVID-19 MESH:C000657245
547 1672-1676 Disease denotes ARDS MESH:D012128
548 2150-2159 Disease denotes mortality MESH:D003643
549 2253-2262 Disease denotes mortality MESH:D003643
550 2592-2600 Disease denotes COVID-19 MESH:C000657245
551 2625-2629 Disease denotes ARDS MESH:D012128
552 2684-2688 Disease denotes ARDS MESH:D012128
553 2698-2706 Disease denotes infected MESH:D007239
554 2930-2939 Disease denotes mortality MESH:D003643
555 3654-3663 Disease denotes mortality MESH:D003643
556 3695-3703 Disease denotes infected MESH:D007239
557 4303-4307 Mutation denotes L98H p.L98H

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T161 3-7 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T162 81-91 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T163 98-106 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T164 173-181 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T165 301-311 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T166 396-404 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T167 680-688 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T168 716-733 Disease denotes fungal infections http://purl.obolibrary.org/obo/MONDO_0002041
T169 810-827 Disease denotes fungal infections http://purl.obolibrary.org/obo/MONDO_0002041
T170 992-996 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T171 1030-1043 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T172 1312-1320 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T173 1495-1504 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T174 1641-1645 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T175 1652-1660 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T176 1672-1676 Disease denotes ARDS http://purl.obolibrary.org/obo/MONDO_0006502
T177 1742-1746 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T178 1866-1870 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T179 2063-2067 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T180 2592-2600 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T181 2625-2629 Disease denotes ARDS http://purl.obolibrary.org/obo/MONDO_0006502
T182 2684-2688 Disease denotes ARDS http://purl.obolibrary.org/obo/MONDO_0006502
T183 2712-2721 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T184 2821-2825 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T185 3337-3341 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T186 4108-4112 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T123 228-234 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T124 625-627 http://purl.obolibrary.org/obo/CLO_0054055 denotes 71
T125 669-671 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T126 702-704 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48
T127 1130-1137 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T128 1202-1203 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T129 1436-1448 http://purl.obolibrary.org/obo/UBERON_0001155 denotes colonization
T130 1694-1696 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T131 1770-1771 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T132 2060-2062 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T133 2103-2104 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T134 2174-2176 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T135 2177-2179 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T136 2200-2206 http://purl.obolibrary.org/obo/UBERON_0003100 denotes female
T137 2208-2211 http://purl.obolibrary.org/obo/CLO_0001382 denotes 4/8
T138 2230-2234 http://purl.obolibrary.org/obo/UBERON_0003101 denotes male
T139 2230-2234 http://www.ebi.ac.uk/efo/EFO_0000970 denotes male
T140 2236-2238 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T141 2239-2241 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T142 2975-2976 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T143 3150-3151 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T144 3207-3208 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T145 3310-3314 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T146 3394-3395 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T147 3645-3646 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T148 3727-3728 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T149 3813-3820 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T150 3933-3934 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T151 4106-4107 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T152 4153-4154 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T153 4230-4235 http://purl.obolibrary.org/obo/CLO_0001002 denotes 16, 2
T154 4275-4276 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T155 4567-4572 http://purl.obolibrary.org/obo/NCBITaxon_9940 denotes l-AmB
T156 4645-4646 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T157 4792-4793 http://purl.obolibrary.org/obo/CLO_0001020 denotes A

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T88 443-446 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T90 512-515 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T92 551-554 Chemical denotes MSG http://purl.obolibrary.org/obo/CHEBI_64220|http://purl.obolibrary.org/obo/CHEBI_64243
T94 1116-1129 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T95 1150-1154 Chemical denotes gold http://purl.obolibrary.org/obo/CHEBI_29287|http://purl.obolibrary.org/obo/CHEBI_30050
T97 1291-1294 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T99 2230-2234 Chemical denotes male http://purl.obolibrary.org/obo/CHEBI_30780
T100 3296-3309 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T101 3453-3463 Chemical denotes antifungal http://purl.obolibrary.org/obo/CHEBI_35718
T102 3605-3610 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T103 3709-3714 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T104 3787-3797 Chemical denotes antifungal http://purl.obolibrary.org/obo/CHEBI_35718
T105 3840-3850 Chemical denotes antifungal http://purl.obolibrary.org/obo/CHEBI_35718
T106 3894-3899 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T107 4033-4038 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T108 4137-4142 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T109 4175-4187 Chemical denotes itraconazole http://purl.obolibrary.org/obo/CHEBI_6076
T110 4189-4201 Chemical denotes voriconazole http://purl.obolibrary.org/obo/CHEBI_10023
T111 4207-4219 Chemical denotes posaconazole http://purl.obolibrary.org/obo/CHEBI_64355
T112 4385-4388 Chemical denotes MIC http://purl.obolibrary.org/obo/CHEBI_59059
T113 4458-4470 Chemical denotes voriconazole http://purl.obolibrary.org/obo/CHEBI_10023
T114 4551-4563 Chemical denotes voriconazole http://purl.obolibrary.org/obo/CHEBI_10023

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T2 1116-1129 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T3 3296-3309 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T44 443-446 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103
T45 512-515 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103
T46 1291-1294 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T76 0-2 Sentence denotes 4.
T77 3-18 Sentence denotes CAPA Prevalence
T78 19-116 Sentence denotes Several studies from China reported high rates of Aspergillus infections among COVID-19 patients.
T79 117-316 Sentence denotes In one study from the Jiangsu province in China, 60/257 COVID-19 (23.3%) patients had throat swab samples that tested positive for Aspergillus spp. and were reported as Aspergillus co-infections [8].
T80 317-629 Sentence denotes In another Chinese study from the Zhejiang province 8 of the 104 patients with COVID-19 (7.7%) patients were reported to have IPA although questions remain regarding criteria used for diagnosing IPA in this study (authors state EORTC/MSG criteria were used but all 8 patients seemingly lacked host factors) [71].
T81 630-765 Sentence denotes Another study from China reported that 27% of the COVID-19 patients (13/48) developed fungal infections but lacked further details [7].
T82 766-876 Sentence denotes In other reports from China, lower rates of fungal infections were reported ranging between 3.2–5% [54,55,72].
T83 877-997 Sentence denotes None of those studies have used specific definitions and standardized diagnostic algorithms to identify and define CAPA.
T84 998-1198 Sentence denotes In fact, diagnosis of pulmonary aspergillosis is challenging with culture exhibiting limited sensitivity [73,74], and galactomannan testing—the current gold standard—is rarely available in China [75].
T85 1199-1505 Sentence denotes As a result, some of these reported rates are likely an underestimate of the real burden of IPA in patients with COVID-19 requiring ICU admission, while other rates may be an overestimation due to potentially misinterpreting Aspergillus colonization in the upper respiratory tract as Aspergillus infection.
T86 1506-1722 Sentence denotes More recently, several studies and case-series from Europe (France, Germany, Belgium, and the Netherlands) have reported high rates of CAPA among COVID-19 cases with ARDS, ranging from 20–35% (Table 1) [47,50,51,52].
T87 1723-1840 Sentence denotes The development of CAPA was fairly rapid, with a median of 6 days and range of 3–28 days after ICU admission [47,52].
T88 1841-2053 Sentence denotes Moreover, two additional CAPA cases have been reported from Germany [61] and single cases have also been reported from the Netherlands [62], Austria [60], Italy [59], Australia [63], and France [57,58] (Table 1).
T89 2054-2137 Sentence denotes Among 35 CAPA cases reported to date, there were a total of 5 proven cases [52,59].
T90 2138-2248 Sentence denotes The overall mortality rate was 63% (22/35), among whom 4 were female (4/8; 50%) and 14 were male (18/27; 67%).
T91 2249-2373 Sentence denotes The mortality in case series reported from France, Germany, Belgium and Netherlands ranged between 44.5–66.7% [47,50,51,52].
T92 2374-2563 Sentence denotes Of particular importance was the 100% fatality rate of those with underlying diseases reported from the Netherlands, while the two patients without underlying conditions both survived [47].
T93 2564-2789 Sentence denotes Noteworthy is the fact that COVID-19 patients presented with ARDS typically fall into the elderly category [6], whereas ARDS in those infected with influenza involves both children <5 years old and elderly >65 years old [76].
T94 2790-2946 Sentence denotes The difficulties in diagnosing CAPA, which are outlined in more detail in the next section of this review, may also contribute to increased mortality rates.
T95 2947-3146 Sentence denotes The most notable example is a study from France [57], where both culture and serology assays were negative for the initial respiratory samples and became only positive after the patient expired [57].
T96 3147-3336 Sentence denotes In a case from Italy, initial BALF culture was positive for A. fumigatus but the treatment was delayed for two days and only started after the serum galactomannan test became positive [59].
T97 3337-3390 Sentence denotes CAPA was later confirmed by autopsy examination [59].
T98 3391-3598 Sentence denotes As a result, authors encouraged prompt initiation of systemic antifungal therapy immediately after obtaining positive results even if Aspergillus is detected in samples from the upper respiratory tract [59].
T99 3599-3916 Sentence denotes Since azole resistance can be associated with a higher mortality rate when compared to patients infected with azole susceptible A. fumigatus isolates, it is of paramount importance to use antifungal susceptibility testing to inform targeted antifungal treatment, especially in regions with high azole resistance [77].
T100 3917-4132 Sentence denotes Azole-resistant A. fumigatus isolates were also persistently recovered from tracheal aspirates during the course of azole treatment in the most recent study from the Netherlands implicated a CAPA case for whom [62].
T101 4133-4371 Sentence denotes The azole-resistant A. fumigatus isolate (itraconazole, voriconazole, and posaconazole MICs were 16, 2, and 0.5 µg/mL, respectively) harbored a well-known mutation, TR34/L98H [62], presumed to have been acquired from the environment [77].
T102 4372-4635 Sentence denotes The in vitro MIC value of the isolate obtained at day 19 (2 mg/L) was higher than the voriconazole serum trough concentration measured on day 17 (1.43 mg/L) and despite switching voriconazole to l-AmB, the patient died due to deteriorating health conditions [62].
T103 4636-4813 Sentence denotes Overall, A. fumigatus appeared to be the most prevalent Aspergillus spp. isolated among respiratory samples with positive culture (26/29; 90%), followed by A. flavus (2/29; 7%).

2_test

Id Subject Object Predicate Lexical cue
32599813-32503617-60095119 625-627 32503617 denotes 71
32599813-32242738-60095120 869-871 32242738 denotes 55
32599813-32311650-60095121 872-874 32311650 denotes 72
32599813-31569472-60095122 1104-1106 31569472 denotes 73
32599813-29036605-60095123 1194-1196 29036605 denotes 75
32599813-32339350-60095124 1712-1714 32339350 denotes 50
32599813-32488446-60095125 1718-1720 32488446 denotes 52
32599813-32488446-60095126 1836-1838 32488446 denotes 52
32599813-32517166-60095127 1977-1979 32517166 denotes 62
32599813-32470620-60095128 2003-2005 32470620 denotes 59
32599813-32488446-60095129 2130-2132 32488446 denotes 52
32599813-32470620-60095130 2133-2135 32470620 denotes 59
32599813-32339350-60095131 2363-2365 32339350 denotes 50
32599813-32488446-60095132 2369-2371 32488446 denotes 52
32599813-31324202-60095133 2785-2787 31324202 denotes 76
32599813-32470620-60095134 3332-3334 32470620 denotes 59
32599813-32470620-60095135 3386-3388 32470620 denotes 59
32599813-32470620-60095136 3594-3596 32470620 denotes 59
32599813-30580035-60095137 3912-3914 30580035 denotes 77
32599813-32517166-60095138 4128-4130 32517166 denotes 62
32599813-32517166-60095139 4309-4311 32517166 denotes 62
32599813-30580035-60095140 4367-4369 30580035 denotes 77
32599813-32517166-60095141 4631-4633 32517166 denotes 62