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PMC:7558333 / 14679-19833 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T36 809-820 Body_part denotes solid organ http://purl.org/sig/ont/fma/fma55670
T37 1691-1696 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T38 2455-2460 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T39 2884-2888 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T40 2985-2990 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T41 3393-3401 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T42 3595-3600 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T43 3608-3613 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T44 3746-3754 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T45 4663-4668 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T24 815-820 Body_part denotes organ http://purl.obolibrary.org/obo/UBERON_0000062
T25 1691-1696 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T26 2455-2460 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T27 2985-2990 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T28 3595-3600 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T29 3608-3613 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T30 4663-4668 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T75 53-69 Disease denotes fungal infection http://purl.obolibrary.org/obo/MONDO_0002041
T76 60-69 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T77 143-146 Disease denotes IFD http://purl.obolibrary.org/obo/MONDO_0009852
T78 249-257 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T79 318-326 Disease denotes Sars-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T80 333-342 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T81 343-353 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T82 399-402 Disease denotes IFD http://purl.obolibrary.org/obo/MONDO_0009852
T83 482-484 Disease denotes IA http://purl.obolibrary.org/obo/MONDO_0000240
T84 523-525 Disease denotes IA http://purl.obolibrary.org/obo/MONDO_0000240
T85 869-872 Disease denotes IFD http://purl.obolibrary.org/obo/MONDO_0009852
T86 885-887 Disease denotes IA http://purl.obolibrary.org/obo/MONDO_0000240
T87 1058-1071 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T88 1240-1257 Disease denotes FUNgal infections http://purl.obolibrary.org/obo/MONDO_0002041
T89 1354-1357 Disease denotes IFD http://purl.obolibrary.org/obo/MONDO_0009852
T90 1411-1419 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T91 1425-1434 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T92 1519-1527 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T93 1551-1555 Disease denotes ARDS http://purl.obolibrary.org/obo/MONDO_0006502
T94 1853-1861 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T95 1968-1977 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T96 2000-2002 Disease denotes IA http://purl.obolibrary.org/obo/MONDO_0000240
T97 2010-2018 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T98 2356-2358 Disease denotes IA http://purl.obolibrary.org/obo/MONDO_0000240
T99 3805-3825 Disease denotes respiratory diseases http://purl.obolibrary.org/obo/MONDO_0005087
T100 3881-3894 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T101 3907-3909 Disease denotes IA http://purl.obolibrary.org/obo/MONDO_0000240
T102 4014-4023 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T103 4048-4050 Disease denotes IA http://purl.obolibrary.org/obo/MONDO_0000240
T104 4061-4063 Disease denotes IA http://purl.obolibrary.org/obo/MONDO_0000240
T105 4075-4077 Disease denotes IA http://purl.obolibrary.org/obo/MONDO_0000240
T106 4097-4099 Disease denotes IA http://purl.obolibrary.org/obo/MONDO_0000240
T107 4845-4848 Disease denotes IFD http://purl.obolibrary.org/obo/MONDO_0009852
T108 4863-4865 Disease denotes IA http://purl.obolibrary.org/obo/MONDO_0000240
T109 4925-4937 Disease denotes Pneumocystis http://purl.obolibrary.org/obo/MONDO_0019121
T110 4961-4971 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T110 159-160 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T111 563-564 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T112 815-820 http://purl.obolibrary.org/obo/UBERON_0003103 denotes organ
T113 1028-1029 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T114 1320-1321 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T115 1454-1455 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T116 1691-1696 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T117 1951-1963 http://purl.obolibrary.org/obo/UBERON_0001155 denotes colonization
T118 1990-1991 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T119 2019-2022 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T120 2042-2043 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T121 2213-2214 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T122 2372-2373 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T123 2392-2393 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T124 2455-2460 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T125 2455-2460 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T126 2710-2711 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T127 2784-2786 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T128 2884-2888 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T129 2985-2990 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T130 2985-2990 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T131 3402-3409 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T132 3434-3446 http://purl.obolibrary.org/obo/UBERON_0001155 denotes colonization
T133 3486-3498 http://purl.obolibrary.org/obo/UBERON_0001155 denotes colonization
T134 3608-3613 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T135 3608-3613 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T136 3755-3762 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T137 3840-3841 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T138 4025-4037 http://purl.obolibrary.org/obo/UBERON_0001155 denotes colonization
T139 4121-4122 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T140 4604-4605 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T141 4713-4714 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T142 4729-4732 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T143 4772-4774 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T6 1674-1679 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T7 1691-1701 Phenotype denotes chest pain http://purl.obolibrary.org/obo/HP_0100749
T8 1711-1718 Phenotype denotes dyspnea http://purl.obolibrary.org/obo/HP_0002094
T9 1720-1730 Phenotype denotes hemoptysis http://purl.obolibrary.org/obo/HP_0002105
T10 1745-1770 Phenotype denotes respiratory insufficiency http://purl.obolibrary.org/obo/HP_0002093

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T15 2506-2508 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T16 2969-2971 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T17 3601-3603 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T18 3776-3778 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T113 0-2 Sentence denotes 4.
T114 3-13 Sentence denotes Discussion
T115 14-237 Sentence denotes In France, the global burden of severe fungal infection is estimated at approximately 1,000,000 (1.47%) cases each year [13] and IFD account for a higher risk of mortality in patients with co-morbidities from 9 to 40% [14].
T116 238-411 Sentence denotes During the COVID-19 pandemic, warning messages considering similarities between Sars-CoV-2 and influenza infections stressed the importance of vigilance towards IFD [15,16].
T117 412-505 Sentence denotes Local experiences are now published and show high numbers of putative IA [17,18,19,20,21,22].
T118 506-671 Sentence denotes The diagnosis of IA still remains challenging because of a wide diversity of underlying conditions and growing number of criteria, particularly biological tools [6].
T119 672-965 Sentence denotes In deeply immunosuppressed patients, such as neutropenic patients, patients under antineoplastic and prolonged corticosteroid therapy or solid organ transplantation, criteria for classification of IFD and notably IA have recently been revised incorporating Aspergillus molecular detection [2].
T120 966-1135 Sentence denotes In ICU, the AspICU algorithm published by Blot et al., [3] is a robust and helpful tool for aspergillosis classification but needs to be more evaluated and even updated.
T121 1136-1389 Sentence denotes In order to address limitations of the various classification definitions for ICU patients, the ongoing FUNgal infections Definitions in ICU patients (FUNDICU) project aims to develop a standard set of definitions for IFD in critically ill patients [5].
T122 1390-1510 Sentence denotes The breaking news of SARS-CoV-2 co-infection urges the need for a critical analysis of the criteria of AspICU algorithm.
T123 1511-1986 Sentence denotes Indeed, COVID-19 patients, particularly ARDS patients with mechanical ventilation, present with compatible clinical signs as depicted by the algorithm (refractory fever, pleuritic chest pain and rub, dyspnea, hemoptysis and worsening respiratory insufficiency, see [3] for full description) and CT-scan signs are hard to interpret because of COVID-19 CT-scan presentation, leading to absence or very poor discrimination between Aspergillus colonization and infection [19,23].
T124 1987-2195 Sentence denotes As a result, IA during COVID-19 has been reported with a possible overestimated high prevalence (until 30%), as favorable outcomes have been described in patients who did not receive any antifungal treatment.
T125 2196-2547 Sentence denotes In order to have a well-balanced patient management, limiting unnecessary and costly antifungal treatments while not neglecting the life-threatening feature of IA, we included A. fumigatus PCR as a monitoring tool for fungal detection in both respiratory and blood samples in addition to classical culture and GM approaches but with some restrictions.
T126 2548-2628 Sentence denotes As expected, PCR allowed detecting Aspergillus in much more respiratory samples.
T127 2629-2788 Sentence denotes We previously showed that PCR improved the detection of Aspergillus in BAL, with a particular added value in ICU patients compared to hematology patients [11].
T128 2789-2940 Sentence denotes Furthermore, PCR using in-house but also marketed kits is also capable of identifying specific gene mutations associated with azole resistance [11,24].
T129 2941-3070 Sentence denotes Besides, the sensitivity of GM detection in blood is less sensitive in ICU than for patients with hematological malignancies [5].
T130 3071-3211 Sentence denotes Here, the higher sensitivity of Aspergillus detection also incites us to adopt modified criteria for case definition to gain in specificity.
T131 3212-3673 Sentence denotes Two major changes were introduced to modify the granularity of the classification: (i) the first one is to combine Aspergillus detection in respiratory samples and anti-Aspergillus antibody testing, to distinguish chronic colonization (positive serology) from acute massive colonization (negative serology) and (ii) the second is to introduce of obvious biomarkers of angioinvasion (serum GM and blood PCR), similar to those of the EORTC/MSG classification [2].
T132 3674-3918 Sentence denotes Of note, the combination of positive culture, positive anti-Aspergillus antibody testing and positive GM in the context of chronic respiratory diseases characterized a transition step from chronic pulmonary aspergillosis to probable IA [25,26].
T133 3919-4240 Sentence denotes Using this refined classification, we were able to categorize our patients in five classes: no infection, colonization, putative IA, probable IA and proven IA (no case of proven IA in the cohort), with a better relevance than the initial AspICU classification, and better specificity than the AspICU + PCR classification.
T134 4241-4412 Sentence denotes The decision of antifungal treatment onset was taken according to this modified AspICU classification and the outcome observed gives confidence in this patient management.
T135 4413-4603 Sentence denotes Of course, the limitation of this work is the relatively small number of patients and should be evaluated on larger cohorts in order to correctly analyze the performance of this alternative.
T136 4604-4775 Sentence denotes A remaining question is also to determine the place of the serum biomarker (1,3)-β-d-glucan in ICU patients, a question that has recently been raised by Honoré et al. [27]
T137 4776-4972 Sentence denotes In conclusion, molecular techniques are now key tools for monitoring IFD, particularly IA as recently updated in the EORTC/MSG definitions, but also Pneumocystis jirovecii or mucorales infections.
T138 4973-5079 Sentence denotes Here, we suggest some adaptations of the AspICU clinical algorithm to gain in sensitivity and specificity.
T139 5080-5154 Sentence denotes Large multicentric data are needed to confirm this proof of concept study.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
324 189-197 Species denotes patients Tax:9606
325 318-328 Species denotes Sars-CoV-2 Tax:2697049
326 53-69 Disease denotes fungal infection MESH:D009181
327 176-185 Disease denotes mortality MESH:D003643
328 249-257 Disease denotes COVID-19 MESH:C000657245
329 343-353 Disease denotes infections MESH:D007239
341 699-707 Species denotes patients Tax:9606
342 729-737 Species denotes patients Tax:9606
343 1218-1226 Species denotes patients Tax:9606
344 1277-1285 Species denotes patients Tax:9606
345 1376-1384 Species denotes patients Tax:9606
346 929-940 Species denotes Aspergillus Tax:746128
347 739-747 Species denotes patients Tax:9606
348 717-728 Disease denotes neutropenic MESH:D009503
349 1058-1071 Disease denotes aspergillosis MESH:D001228
350 1240-1257 Disease denotes FUNgal infections MESH:D009181
351 1361-1375 Disease denotes critically ill MESH:D016638
368 1411-1421 Species denotes SARS-CoV-2 Tax:2697049
369 1528-1536 Species denotes patients Tax:9606
370 1556-1564 Species denotes patients Tax:9606
371 2141-2149 Species denotes patients Tax:9606
372 1939-1950 Species denotes Aspergillus Tax:746128
373 1425-1434 Disease denotes infection MESH:D007239
374 1519-1527 Disease denotes COVID-19 MESH:C000657245
375 1551-1555 Disease denotes ARDS MESH:D012128
376 1674-1679 Disease denotes fever MESH:D005334
377 1681-1701 Disease denotes pleuritic chest pain MESH:D002637
378 1711-1718 Disease denotes dyspnea MESH:D004417
379 1720-1730 Disease denotes hemoptysis MESH:D006469
380 1745-1770 Disease denotes respiratory insufficiency MESH:D012131
381 1853-1861 Disease denotes COVID-19 MESH:C000657245
382 1968-1977 Disease denotes infection MESH:D007239
383 2010-2018 Disease denotes COVID-19 MESH:C000657245
403 2229-2236 Species denotes patient Tax:9606
404 2372-2384 Species denotes A. fumigatus Tax:746128
405 2742-2750 Species denotes patients Tax:9606
406 2774-2782 Species denotes patients Tax:9606
407 3025-3033 Species denotes patients Tax:9606
408 2583-2594 Species denotes Aspergillus Tax:746128
409 2685-2696 Species denotes Aspergillus Tax:746128
410 3103-3114 Species denotes Aspergillus Tax:746128
411 3327-3338 Species denotes Aspergillus Tax:746128
412 3381-3392 Species denotes Aspergillus Tax:746128
413 3734-3745 Species denotes Aspergillus Tax:746128
414 2506-2508 Chemical denotes GM MESH:C012990
415 2915-2920 Chemical denotes azole MESH:D001393
416 2969-2971 Chemical denotes GM MESH:C012990
417 3601-3603 Chemical denotes GM MESH:C012990
418 3776-3778 Chemical denotes GM MESH:C012990
419 3039-3065 Disease denotes hematological malignancies MESH:D019337
420 3805-3825 Disease denotes respiratory diseases MESH:D012140
421 3871-3894 Disease denotes pulmonary aspergillosis MESH:D055732
428 3985-3993 Species denotes patients Tax:9606
429 4393-4400 Species denotes patient Tax:9606
430 4486-4494 Species denotes patients Tax:9606
431 4703-4711 Species denotes patients Tax:9606
432 4679-4695 Chemical denotes (1,3)-β-d-glucan MESH:C480180
433 4014-4023 Disease denotes infection MESH:D007239
436 4925-4947 Species denotes Pneumocystis jirovecii Tax:42068
437 4961-4971 Disease denotes infections MESH:D007239

2_test

Id Subject Object Predicate Lexical cue
32664423-27887809-60101700 135-137 27887809 denotes 13
32664423-24960557-60101701 233-235 24960557 denotes 14
32664423-32835328-60101702 404-406 32835328 denotes 15
32664423-32307254-60101703 407-409 32307254 denotes 16
32664423-32339350-60101704 492-494 32339350 denotes 19
32664423-32396381-60101705 498-500 32396381 denotes 21
32664423-32224310-60101706 501-503 32224310 denotes 22
32664423-22517788-60101707 1022-1023 22517788 denotes 3
32664423-22517788-60101708 1777-1778 22517788 denotes 3
32664423-32339350-60101709 1979-1981 32339350 denotes 19
32664423-32488446-60101710 1982-1984 32488446 denotes 23
32664423-29248586-60101711 2784-2786 29248586 denotes 11
32664423-29248586-60101712 2933-2935 29248586 denotes 11
32664423-25903571-60101713 2936-2938 25903571 denotes 24
32664423-17906086-60101714 3911-3913 17906086 denotes 25
32664423-26699723-60101715 3914-3916 26699723 denotes 26
32664423-32503673-60101716 4772-4774 32503673 denotes 27