PMC:7560789 / 95-3238
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T1 | 131-147 | Body_part | denotes | bronchial mucosa | http://purl.org/sig/ont/fma/fma62652 |
| T2 | 141-147 | Body_part | denotes | mucosa | http://purl.org/sig/ont/fma/fma85355 |
| T3 | 2201-2208 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T4 | 2711-2713 | Body_part | denotes | Ag | http://purl.org/sig/ont/fma/fma61898 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T1 | 131-147 | Body_part | denotes | bronchial mucosa | http://purl.obolibrary.org/obo/UBERON_0000410 |
| T2 | 141-147 | Body_part | denotes | mucosa | http://purl.obolibrary.org/obo/UBERON_0000344 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T3 | 19-32 | Disease | denotes | aspergillosis | http://purl.obolibrary.org/obo/MONDO_0005657 |
| T4 | 54-63 | Disease | denotes | influenza | http://purl.obolibrary.org/obo/MONDO_0005812 |
| T5 | 64-73 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
| T6 | 306-315 | Disease | denotes | influenza | http://purl.obolibrary.org/obo/MONDO_0005812 |
| T7 | 437-446 | Disease | denotes | influenza | http://purl.obolibrary.org/obo/MONDO_0005812 |
| T8 | 494-502 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T9 | 541-550 | Disease | denotes | influenza | http://purl.obolibrary.org/obo/MONDO_0005812 |
| T10 | 593-601 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T11 | 840-848 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T12 | 1118-1126 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T13 | 1423-1431 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T14 | 1839-1854 | Disease | denotes | viral infection | http://purl.obolibrary.org/obo/MONDO_0005108 |
| T15 | 1845-1854 | Disease | denotes | infection | http://purl.obolibrary.org/obo/MONDO_0005550 |
| T16 | 2563-2570 | Disease | denotes | sterile | http://purl.obolibrary.org/obo/MONDO_0005047 |
| T17 | 2723-2726 | Disease | denotes | RAD | http://purl.obolibrary.org/obo/MONDO_0007483 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T1 | 141-147 | http://purl.obolibrary.org/obo/UBERON_0000344 | denotes | mucosa |
| T2 | 552-553 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T3 | 622-625 | http://purl.obolibrary.org/obo/CLO_0051582 | denotes | has |
| T4 | 734-735 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T5 | 853-854 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T6 | 1042-1043 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T7 | 1148-1149 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T8 | 1184-1185 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T9 | 1206-1207 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T10 | 1315-1316 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T11 | 1397-1398 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T12 | 1556-1559 | http://purl.obolibrary.org/obo/CLO_0001577 | denotes | a 3 |
| T13 | 1787-1799 | http://purl.obolibrary.org/obo/UBERON_0001155 | denotes | colonization |
| T14 | 1862-1863 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T15 | 2010-2017 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | testing |
| T16 | 2023-2024 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T17 | 2299-2300 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T18 | 2393-2394 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T19 | 2422-2423 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T20 | 2444-2445 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T21 | 2803-2804 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T22 | 2970-2976 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tested |
| T23 | 2994-2998 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | test |
| T24 | 3031-3035 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | test |
| T25 | 3051-3055 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | test |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T2 | 34-37 | Chemical | denotes | IPA | http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802 |
| T4 | 275-278 | Chemical | denotes | IPA | http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802 |
| T6 | 385-388 | Chemical | denotes | IPA | http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802 |
| T8 | 572-575 | Chemical | denotes | IPA | http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802 |
| T10 | 754-757 | Chemical | denotes | BAL | http://purl.obolibrary.org/obo/CHEBI_64198 |
| T11 | 823-826 | Chemical | denotes | IPA | http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802 |
| T13 | 855-858 | Chemical | denotes | BAL | http://purl.obolibrary.org/obo/CHEBI_64198 |
| T14 | 898-911 | Chemical | denotes | galactomannan | http://purl.obolibrary.org/obo/CHEBI_27680 |
| T15 | 913-915 | Chemical | denotes | GM | http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680 |
| T17 | 958-961 | Chemical | denotes | IPA | http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802 |
| T19 | 1082-1085 | Chemical | denotes | BAL | http://purl.obolibrary.org/obo/CHEBI_64198 |
| T20 | 1198-1201 | Chemical | denotes | BAL | http://purl.obolibrary.org/obo/CHEBI_64198 |
| T21 | 1298-1301 | Chemical | denotes | BAL | http://purl.obolibrary.org/obo/CHEBI_64198 |
| T22 | 1390-1393 | Chemical | denotes | IPA | http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802 |
| T24 | 1778-1781 | Chemical | denotes | IPA | http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802 |
| T26 | 1945-1948 | Chemical | denotes | IPA | http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802 |
| T28 | 2003-2006 | Chemical | denotes | BAL | http://purl.obolibrary.org/obo/CHEBI_64198 |
| T29 | 2007-2009 | Chemical | denotes | GM | http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680 |
| T31 | 2201-2208 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T32 | 2278-2281 | Chemical | denotes | BAL | http://purl.obolibrary.org/obo/CHEBI_64198 |
| T33 | 2571-2575 | Chemical | denotes | NaCl | http://purl.obolibrary.org/obo/CHEBI_26710 |
| T34 | 2676-2678 | Chemical | denotes | GM | http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680 |
| T36 | 2711-2713 | Chemical | denotes | Ag | http://purl.obolibrary.org/obo/CHEBI_30512|http://purl.obolibrary.org/obo/CHEBI_9141 |
| T38 | 2821-2839 | Chemical | denotes | hydroxychloroquine | http://purl.obolibrary.org/obo/CHEBI_5801 |
| T39 | 2844-2863 | Chemical | denotes | lopinavir/ritonavir | http://purl.obolibrary.org/obo/CHEBI_145924 |
| T40 | 2844-2853 | Chemical | denotes | lopinavir | http://purl.obolibrary.org/obo/CHEBI_31781 |
| T41 | 2854-2863 | Chemical | denotes | ritonavir | http://purl.obolibrary.org/obo/CHEBI_45409 |
| T42 | 2949-2952 | Chemical | denotes | IPA | http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802 |
| T44 | 2961-2964 | Chemical | denotes | IPA | http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802 |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T1 | 1839-1854 | http://purl.obolibrary.org/obo/GO_0016032 | denotes | viral infection |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T3 | 0-244 | Sentence | denotes | Invasive pulmonary aspergillosis (IPA) can complicate influenza pneumonia in critically ill patients owing to viral destruction of bronchial mucosa, facilitating invasion of Aspergillus species, and compromised host defenses to Aspergillus (1). |
| T4 | 245-451 | Sentence | denotes | Given the association between IPA and increased mortality in influenza, rapid diagnostic investigations and early (preemptive) treatment of IPA are recommended in critically ill patients with influenza (2). |
| T5 | 452-551 | Sentence | denotes | In ICU patients with coronavirus disease (COVID-19), the same principles may apply as in influenza. |
| T6 | 552-706 | Sentence | denotes | A high incidence of IPA in patients with COVID-19 admitted to the ICU has been reported in small cohorts of patients, some of which appeared online (3–7). |
| T7 | 707-994 | Sentence | denotes | However, in these studies, a bronchoscopy with BAL was not consistently applied, which may hamper estimation of the IPA incidence in COVID-19, as a BAL to obtain material for culture and for galactomannan (GM) measurement is generally recommended for IPA diagnosis in the critically ill. |
| T8 | 995-1131 | Sentence | denotes | However, owing to risk of aerosolization, only a restricted role for bronchoscopy with BAL is recommended in patients with COVID-19 (8). |
| T9 | 1132-1274 | Sentence | denotes | We have applied a diagnostic approach by performing a nondirected BAL via a closed-circuit suction catheter, which we describe in this letter. |
| T10 | 1275-1590 | Sentence | denotes | Using this nondirected BAL technique as a standard approach, we aimed to determine the proportion of patients with IPA in a cohort of patients with COVID-19 (PCR confirmed) requiring mechanical ventilation who were consecutively admitted to the ICU of our teaching hospital during a 3-week time frame in April 2020. |
| T11 | 1591-1720 | Sentence | denotes | The institutional review board of the Amsterdam University Medical Center considered the study as not requiring informed consent. |
| T12 | 1721-1940 | Sentence | denotes | The clinical AspICU algorithm can be used to distinguish IPA from colonization in critically ill patients (9), but as viral infection is not a classified host risk factor in this definition, the host factor was omitted. |
| T13 | 1941-2265 | Sentence | denotes | The IPA definition used in this paper is based on nondirected BAL GM testing with a cutoff of 1 optical density index, for which sensitivity and specificity are 86% and 95%, respectively, combined with worsening clinical symptoms (i.e., increase in C-reactive protein, worsening PaO2/FiO2 ratio, persistent or rising fever). |
| T14 | 2266-2543 | Sentence | denotes | Nondirected BAL was performed at a median of 2 days (range, 0–8 d) after ICU admission, in nonparalyzed patients, by advancing a 12-F suction catheter with a length of 54 cm via a closed circuit until bronchial wedging (Halyard Turbo-cleaning closed suction system for adults). |
| T15 | 2544-2653 | Sentence | denotes | Then, 2 × 20 ml of sterile NaCl 0.9% was given via the closed circuit and retrieved via the suction catheter. |
| T16 | 2654-2780 | Sentence | denotes | Samples were sent for GM (by ELISA, Platelia Aspergillus Ag from BIO-RAD) and culture only if it yielded nontransparent fluid. |
| T17 | 2781-2928 | Sentence | denotes | All patients received a 5-day course of hydroxychloroquine and lopinavir/ritonavir, either of which was stopped upon the emergence of side effects. |
| T18 | 2929-3087 | Sentence | denotes | Differences between IPA and non-IPA were tested with Student’s t test or Mann-Whitney U or chi-square test/Fisher’s exact test depending on data distribution. |
| T19 | 3088-3143 | Sentence | denotes | P value <0.05 was considered statistically significant. |
LitCovid-PD-GlycoEpitope
| Id | Subject | Object | Predicate | Lexical cue | glyco_epitope_db_id |
|---|---|---|---|---|---|
| T1 | 898-911 | GlycoEpitope | denotes | galactomannan | http://www.glycoepitope.jp/epitopes/EP0510 |
| T2 | 913-915 | GlycoEpitope | denotes | GM | http://www.glycoepitope.jp/epitopes/EP0510 |
| T3 | 2007-2009 | GlycoEpitope | denotes | GM | http://www.glycoepitope.jp/epitopes/EP0510 |
| T4 | 2676-2678 | GlycoEpitope | denotes | GM | http://www.glycoepitope.jp/epitopes/EP0510 |
LitCovid-PD-HP
| Id | Subject | Object | Predicate | Lexical cue | hp_id |
|---|---|---|---|---|---|
| T2 | 0-32 | Phenotype | denotes | Invasive pulmonary aspergillosis | http://purl.obolibrary.org/obo/HP_0020103 |
| T3 | 34-37 | Phenotype | denotes | IPA | http://purl.obolibrary.org/obo/HP_0020103 |
| T4 | 64-73 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
| T5 | 275-278 | Phenotype | denotes | IPA | http://purl.obolibrary.org/obo/HP_0020103 |
| T6 | 385-388 | Phenotype | denotes | IPA | http://purl.obolibrary.org/obo/HP_0020103 |
| T7 | 572-575 | Phenotype | denotes | IPA | http://purl.obolibrary.org/obo/HP_0020103 |
| T8 | 823-826 | Phenotype | denotes | IPA | http://purl.obolibrary.org/obo/HP_0020103 |
| T9 | 958-961 | Phenotype | denotes | IPA | http://purl.obolibrary.org/obo/HP_0020103 |
| T10 | 1390-1393 | Phenotype | denotes | IPA | http://purl.obolibrary.org/obo/HP_0020103 |
| T11 | 1778-1781 | Phenotype | denotes | IPA | http://purl.obolibrary.org/obo/HP_0020103 |
| T12 | 1945-1948 | Phenotype | denotes | IPA | http://purl.obolibrary.org/obo/HP_0020103 |
| T13 | 2258-2263 | Phenotype | denotes | fever | http://purl.obolibrary.org/obo/HP_0001945 |
| T14 | 2949-2952 | Phenotype | denotes | IPA | http://purl.obolibrary.org/obo/HP_0020103 |
| T15 | 2961-2964 | Phenotype | denotes | IPA | http://purl.obolibrary.org/obo/HP_0020103 |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 41 | 2190-2208 | Gene | denotes | C-reactive protein | Gene:1401 |
| 42 | 92-100 | Species | denotes | patients | Tax:9606 |
| 43 | 423-431 | Species | denotes | patients | Tax:9606 |
| 44 | 459-467 | Species | denotes | patients | Tax:9606 |
| 45 | 579-587 | Species | denotes | patients | Tax:9606 |
| 46 | 660-668 | Species | denotes | patients | Tax:9606 |
| 47 | 1104-1112 | Species | denotes | patients | Tax:9606 |
| 48 | 1376-1384 | Species | denotes | patients | Tax:9606 |
| 49 | 1409-1417 | Species | denotes | patients | Tax:9606 |
| 50 | 1818-1826 | Species | denotes | patients | Tax:9606 |
| 51 | 2370-2378 | Species | denotes | patients | Tax:9606 |
| 52 | 2785-2793 | Species | denotes | patients | Tax:9606 |
| 53 | 174-185 | Species | denotes | Aspergillus | Tax:746128 |
| 54 | 228-239 | Species | denotes | Aspergillus | Tax:746128 |
| 55 | 2699-2710 | Species | denotes | Aspergillus | Tax:746128 |
| 56 | 898-911 | Chemical | denotes | galactomannan | MESH:C012990 |
| 57 | 913-915 | Chemical | denotes | GM | MESH:C012990 |
| 58 | 2571-2575 | Chemical | denotes | NaCl | MESH:D012965 |
| 59 | 2676-2678 | Chemical | denotes | GM | MESH:C012990 |
| 60 | 2821-2839 | Chemical | denotes | hydroxychloroquine | MESH:D006886 |
| 61 | 2844-2863 | Chemical | denotes | lopinavir/ritonavir | MESH:C558899 |
| 62 | 0-32 | Disease | denotes | Invasive pulmonary aspergillosis | MESH:D055744 |
| 63 | 64-73 | Disease | denotes | pneumonia | MESH:D011014 |
| 64 | 77-91 | Disease | denotes | critically ill | MESH:D016638 |
| 65 | 293-302 | Disease | denotes | mortality | MESH:D003643 |
| 66 | 408-422 | Disease | denotes | critically ill | MESH:D016638 |
| 67 | 473-492 | Disease | denotes | coronavirus disease | MESH:D018352 |
| 68 | 494-502 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 69 | 593-601 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 70 | 840-848 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 71 | 979-993 | Disease | denotes | critically ill | MESH:D016638 |
| 72 | 1118-1126 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 73 | 1423-1431 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 74 | 1803-1817 | Disease | denotes | critically ill | MESH:D016638 |
| 75 | 1839-1854 | Disease | denotes | viral infection | MESH:D001102 |
| 76 | 2258-2263 | Disease | denotes | fever | MESH:D005334 |
| 77 | 2357-2369 | Disease | denotes | nonparalyzed |