PMC:7306567 / 9911-13083
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T12 | 459-464 | Body_part | denotes | serum | http://purl.org/sig/ont/fma/fma63083 |
| T13 | 908-913 | Body_part | denotes | serum | http://purl.org/sig/ont/fma/fma63083 |
| T14 | 937-943 | Body_part | denotes | sputum | http://purl.org/sig/ont/fma/fma312401 |
| T15 | 1233-1238 | Body_part | denotes | chest | http://purl.org/sig/ont/fma/fma9576 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T10 | 459-464 | Body_part | denotes | serum | http://purl.obolibrary.org/obo/UBERON_0001977 |
| T11 | 908-913 | Body_part | denotes | serum | http://purl.obolibrary.org/obo/UBERON_0001977 |
| T12 | 937-943 | Body_part | denotes | sputum | http://purl.obolibrary.org/obo/UBERON_0007311 |
| T13 | 1233-1238 | Body_part | denotes | chest | http://purl.obolibrary.org/obo/UBERON_0001443 |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 98 | 434-436 | Chemical | denotes | GM | MESH:C012990 |
| 99 | 465-467 | Chemical | denotes | GM | MESH:C012990 |
| 100 | 785-787 | Chemical | denotes | GM | MESH:C012990 |
| 101 | 914-916 | Chemical | denotes | GM | MESH:C012990 |
| 102 | 487-498 | Disease | denotes | neutropenic | MESH:D009503 |
| 103 | 710-736 | Disease | denotes | invasive tracheobronchitis | MESH:D009361 |
| 113 | 1022-1035 | Disease | denotes | invasive mold | MESH:D009361 |
| 114 | 1058-1069 | Disease | denotes | neutropenic | MESH:D009503 |
| 115 | 1123-1137 | Disease | denotes | critically ill | MESH:D016638 |
| 116 | 1202-1231 | Disease | denotes | Aspergillus tracheobronchitis | MESH:D001228 |
| 117 | 1311-1356 | Disease | denotes | airway-invasive Aspergillus tracheobronchitis | MESH:D001228 |
| 118 | 1399-1405 | Disease | denotes | ulcers | MESH:D014456 |
| 119 | 1518-1539 | Disease | denotes | pulmonary infiltrates | MESH:D017254 |
| 120 | 1605-1609 | Disease | denotes | ARDS | MESH:D012128 |
| 121 | 1613-1632 | Disease | denotes | bacterial infection | MESH:D001424 |
| 124 | 2757-2762 | Chemical | denotes | azole | MESH:D001393 |
| 125 | 2845-2850 | Chemical | denotes | azole | MESH:D001393 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T54 | 77-86 | Disease | denotes | influenza | http://purl.obolibrary.org/obo/MONDO_0005812 |
| T55 | 341-350 | Disease | denotes | influenza | http://purl.obolibrary.org/obo/MONDO_0005812 |
| T56 | 719-736 | Disease | denotes | tracheobronchitis | http://purl.obolibrary.org/obo/MONDO_0021925 |
| T57 | 982-989 | Disease | denotes | sterile | http://purl.obolibrary.org/obo/MONDO_0005047 |
| T58 | 1214-1231 | Disease | denotes | tracheobronchitis | http://purl.obolibrary.org/obo/MONDO_0021925 |
| T59 | 1339-1356 | Disease | denotes | tracheobronchitis | http://purl.obolibrary.org/obo/MONDO_0021925 |
| T60 | 1399-1405 | Disease | denotes | ulcers | http://purl.obolibrary.org/obo/MONDO_0043839 |
| T61 | 1557-1566 | Disease | denotes | influenza | http://purl.obolibrary.org/obo/MONDO_0005812 |
| T62 | 1605-1609 | Disease | denotes | ARDS | http://purl.obolibrary.org/obo/MONDO_0006502 |
| T63 | 1613-1632 | Disease | denotes | bacterial infection | http://purl.obolibrary.org/obo/MONDO_0005113 |
| T64 | 1623-1632 | Disease | denotes | infection | http://purl.obolibrary.org/obo/MONDO_0005550 |
| T65 | 1844-1853 | Disease | denotes | influenza | http://purl.obolibrary.org/obo/MONDO_0005812 |
| T66 | 2517-2526 | Disease | denotes | influenza | http://purl.obolibrary.org/obo/MONDO_0005812 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T67 | 44-45 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T68 | 1233-1238 | http://www.ebi.ac.uk/efo/EFO_0000965 | denotes | chest |
| T69 | 1311-1317 | http://purl.obolibrary.org/obo/UBERON_0001005 | denotes | airway |
| T70 | 1360-1370 | http://purl.obolibrary.org/obo/CL_0000066 | denotes | epithelial |
| T71 | 1645-1646 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T72 | 2014-2019 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tests |
| T73 | 2270-2272 | http://purl.obolibrary.org/obo/CLO_0053799 | denotes | 45 |
| T74 | 2297-2301 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | test |
| T75 | 2395-2400 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tests |
| T76 | 2611-2618 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | testing |
| T77 | 2657-2661 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | test |
| T78 | 2774-2781 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | testing |
| T79 | 2869-2871 | http://purl.obolibrary.org/obo/CLO_0001302 | denotes | 34 |
| T80 | 2970-2972 | http://purl.obolibrary.org/obo/CLO_0001382 | denotes | 48 |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T46 | 430-433 | Chemical | denotes | BAL | http://purl.obolibrary.org/obo/CHEBI_64198 |
| T47 | 434-436 | Chemical | denotes | GM | http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680 |
| T49 | 465-467 | Chemical | denotes | GM | http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680 |
| T51 | 558-561 | Chemical | denotes | BAL | http://purl.obolibrary.org/obo/CHEBI_64198 |
| T52 | 781-784 | Chemical | denotes | BAL | http://purl.obolibrary.org/obo/CHEBI_64198 |
| T53 | 785-787 | Chemical | denotes | GM | http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680 |
| T55 | 850-853 | Chemical | denotes | BAL | http://purl.obolibrary.org/obo/CHEBI_64198 |
| T56 | 914-916 | Chemical | denotes | GM | http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680 |
| T58 | 1657-1670 | Chemical | denotes | antimicrobial | http://purl.obolibrary.org/obo/CHEBI_33281 |
| T59 | 1762-1772 | Chemical | denotes | antifungal | http://purl.obolibrary.org/obo/CHEBI_35718 |
| T60 | 1964-1974 | Chemical | denotes | antifungal | http://purl.obolibrary.org/obo/CHEBI_35718 |
| T61 | 2084-2087 | Chemical | denotes | IPA | http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802 |
| T63 | 2138-2140 | Chemical | denotes | GM | http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680 |
| T65 | 2583-2586 | Chemical | denotes | BAL | http://purl.obolibrary.org/obo/CHEBI_64198 |
| T66 | 2603-2610 | Chemical | denotes | antigen | http://purl.obolibrary.org/obo/CHEBI_59132 |
| T67 | 2713-2716 | Chemical | denotes | BAL | http://purl.obolibrary.org/obo/CHEBI_64198 |
| T68 | 2757-2762 | Chemical | denotes | azole | http://purl.obolibrary.org/obo/CHEBI_68452 |
| T69 | 2845-2850 | Chemical | denotes | azole | http://purl.obolibrary.org/obo/CHEBI_68452 |
| T70 | 2941-2951 | Chemical | denotes | antifungal | http://purl.obolibrary.org/obo/CHEBI_35718 |
| T71 | 3071-3081 | Chemical | denotes | antivirals | http://purl.obolibrary.org/obo/CHEBI_22587 |
| T72 | 3101-3112 | Chemical | denotes | antibiotics | http://purl.obolibrary.org/obo/CHEBI_33281 |
| T73 | 3132-3146 | Chemical | denotes | corticosteroid | http://purl.obolibrary.org/obo/CHEBI_50858 |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T11 | 548-554 | http://purl.obolibrary.org/obo/GO_0040007 | denotes | growth |
LitCovid-PD-GlycoEpitope
| Id | Subject | Object | Predicate | Lexical cue | glyco_epitope_db_id |
|---|---|---|---|---|---|
| T4 | 434-436 | GlycoEpitope | denotes | GM | http://www.glycoepitope.jp/epitopes/EP0510 |
| T5 | 465-467 | GlycoEpitope | denotes | GM | http://www.glycoepitope.jp/epitopes/EP0510 |
| T6 | 785-787 | GlycoEpitope | denotes | GM | http://www.glycoepitope.jp/epitopes/EP0510 |
| T7 | 914-916 | GlycoEpitope | denotes | GM | http://www.glycoepitope.jp/epitopes/EP0510 |
| T8 | 2138-2140 | GlycoEpitope | denotes | GM | http://www.glycoepitope.jp/epitopes/EP0510 |
LitCovid-PD-HP
| Id | Subject | Object | Predicate | Lexical cue | hp_id |
|---|---|---|---|---|---|
| T19 | 1518-1539 | Phenotype | denotes | pulmonary infiltrates | http://purl.obolibrary.org/obo/HP_0002113 |
| T20 | 2084-2087 | Phenotype | denotes | IPA | http://purl.obolibrary.org/obo/HP_0020103 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T64 | 0-43 | Sentence | denotes | Clinical presentation and diagnosis of IAPA |
| T65 | 44-194 | Sentence | denotes | A retrospective Belgian study of influenza patients admitted to ICU between September 2009 and March 2011 showed that 9 of 40 (23%) patients had IAPA. |
| T66 | 195-316 | Sentence | denotes | Four cases (44%) were proven despite not being immunocompromised according to the EORTC/MSGERC consensus definitions [7]. |
| T67 | 317-398 | Sentence | denotes | The median time between influenza diagnosis and IAPA was 2 days (range 0–4 days). |
| T68 | 399-499 | Sentence | denotes | All IAPA patients had positive BAL GM, and 78% had positive serum GM, despite not being neutropenic. |
| T69 | 500-741 | Sentence | denotes | Eighty-nine percent of patients had Aspergillus growth in BAL culture (almost exclusively Aspergillus fumigatus), and 55% of patients had endobronchial lesions observed during bronchoscopy, possibly indicating invasive tracheobronchitis [7]. |
| T70 | 742-849 | Sentence | denotes | Similar performance characteristics of BAL GM and culture were reported in two other cohort studies [8, 9]. |
| T71 | 850-990 | Sentence | denotes | BAL sampling is thus an important diagnostic procedure as serum GM can be negative and sputum/tracheal aspirate cultures can remain sterile. |
| T72 | 991-1147 | Sentence | denotes | Lesions that are suggestive of invasive mold disease on imaging in neutropenic patients, such as the halo sign, are often absent in critically ill patients. |
| T73 | 1148-1281 | Sentence | denotes | However, in some IAPA patients with autopsy-confirmed Aspergillus tracheobronchitis, chest CT demonstrated peribronchial infiltrates. |
| T74 | 1282-1491 | Sentence | denotes | The main diagnostic clue for airway-invasive Aspergillus tracheobronchitis is epithelial plaques, pseudomembranes or ulcers that can be visualized via bronchoscopy, as radiological features may be subtle [31]. |
| T75 | 1492-1725 | Sentence | denotes | Worsening of radiographic pulmonary infiltrates in patients with influenza is often attributed to progression of ARDS or bacterial infection, leading to a change of antimicrobial therapy without performing diagnostic procedures [32]. |
| T76 | 1726-2000 | Sentence | denotes | Patients who survived IAPA received antifungal therapy much earlier than those who did not (2 days after diagnosis of influenza among survivors versus 9 days among non-survivors) [8], suggesting that early diagnosis and administration of antifungal therapy may be important. |
| T77 | 2001-2209 | Sentence | denotes | Lateral flow tests have recently become available as an alternative for diagnosing IPA (AspLFD, OLM Diagnostics and the sōna Aspergillus GM, IMMY) showing overall good performance in hematology patients [33]. |
| T78 | 2210-2372 | Sentence | denotes | The very quick assessment, with results available within 30–45 min, makes this type of test very attractive for the management of IAPA and use in clinical trials. |
| T79 | 2373-2451 | Sentence | denotes | However, lateral flow tests have not yet been validated in the ICU population. |
| T80 | 2452-2643 | Sentence | denotes | IAPA needs to be considered in patients admitted to the ICU with influenza and where indicated these patients should undergo early BAL for Aspergillus antigen testing, culture and microscopy. |
| T81 | 2644-2873 | Sentence | denotes | Patients who test positive require anti-Aspergillus therapy, and the BAL fluid sample should be fast-tracked for azole resistance testing by PCR (and culture when positive) in regions with high (> 5%) azole resistance rates [34]. |
| T82 | 2874-2992 | Sentence | denotes | This would enable diagnostic assessment and initiation of adequate antifungal therapy within 24–48 h of ICU admission. |
| T83 | 2993-3172 | Sentence | denotes | Diagnostic workup for IAPA may be repeated in patients deteriorating while on antivirals and/or appropriate antibiotics or when initiating corticosteroid treatment is unavoidable. |
LitCovid-PMC-OGER-BB
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T70 | 290-299 | SO:0000993 | denotes | consensus |
| T71 | 459-464 | UBERON:0001977 | denotes | serum |
| T72 | 536-547 | NCBITaxon:5052 | denotes | Aspergillus |
| T73 | 590-611 | NCBITaxon:746128 | denotes | Aspergillus fumigatus |
| T74 | 638-651 | UBERON:0001852 | denotes | endobronchial |
| T75 | 719-736 | UBERON:0007196 | denotes | tracheobronchitis |
| T76 | 908-913 | UBERON:0001977 | denotes | serum |
| T77 | 937-943 | UBERON:0007311 | denotes | sputum |
| T78 | 944-952 | UBERON:0003126 | denotes | tracheal |
| T79 | 1202-1213 | NCBITaxon:5052 | denotes | Aspergillus |
| T80 | 1214-1231 | UBERON:0007196 | denotes | tracheobronchitis |
| T81 | 1233-1238 | UBERON:0001443 | denotes | chest |
| T82 | 1255-1268 | UBERON:0001845 | denotes | peribronchial |
| T83 | 1311-1317 | UBERON:0001005 | denotes | airway |
| T84 | 1327-1338 | NCBITaxon:5052 | denotes | Aspergillus |
| T85 | 1339-1356 | UBERON:0007196 | denotes | tracheobronchitis |
| T86 | 1360-1370 | UBERON:0000483 | denotes | epithelial |
| T87 | 1518-1527 | UBERON:0002048 | denotes | pulmonary |
| T88 | 1613-1622 | NCBITaxon:2 | denotes | bacterial |
| T89 | 1657-1670 | CHEBI:35718;CHEBI:35718 | denotes | antimicrobial |
| T90 | 2603-2610 | CHEBI:59132;CHEBI:59132 | denotes | antigen |
| T91 | 2713-2722 | UBERON:0006314 | denotes | BAL fluid |
| T92 | 2757-2762 | CHEBI:68452;CHEBI:68452 | denotes | azole |
| T93 | 2845-2850 | CHEBI:68452;CHEBI:68452 | denotes | azole |
| T94 | 3101-3112 | CHEBI:33282;CHEBI:33282 | denotes | antibiotics |
| T95 | 3132-3146 | CHEBI:50858;CHEBI:50858 | denotes | corticosteroid |
| T73706 | 290-299 | SO:0000993 | denotes | consensus |
| T23018 | 459-464 | UBERON:0001977 | denotes | serum |
| T97663 | 536-547 | NCBITaxon:5052 | denotes | Aspergillus |
| T79006 | 590-611 | NCBITaxon:746128 | denotes | Aspergillus fumigatus |
| T56081 | 638-651 | UBERON:0001852 | denotes | endobronchial |
| T28200 | 719-736 | UBERON:0007196 | denotes | tracheobronchitis |
| T83389 | 908-913 | UBERON:0001977 | denotes | serum |
| T54848 | 937-943 | UBERON:0007311 | denotes | sputum |
| T80836 | 944-952 | UBERON:0003126 | denotes | tracheal |
| T48603 | 1202-1213 | NCBITaxon:5052 | denotes | Aspergillus |
| T84469 | 1214-1231 | UBERON:0007196 | denotes | tracheobronchitis |
| T9111 | 1233-1238 | UBERON:0001443 | denotes | chest |
| T12913 | 1255-1268 | UBERON:0001845 | denotes | peribronchial |
| T37746 | 1311-1317 | UBERON:0001005 | denotes | airway |
| T32093 | 1327-1338 | NCBITaxon:5052 | denotes | Aspergillus |
| T90534 | 1339-1356 | UBERON:0007196 | denotes | tracheobronchitis |
| T78753 | 1360-1370 | UBERON:0000483 | denotes | epithelial |
| T63798 | 1518-1527 | UBERON:0002048 | denotes | pulmonary |
| T2169 | 1613-1622 | NCBITaxon:2 | denotes | bacterial |
| T80813 | 1657-1670 | CHEBI:35718;CHEBI:35718 | denotes | antimicrobial |
| T68219 | 2603-2610 | CHEBI:59132;CHEBI:59132 | denotes | antigen |
| T22792 | 2713-2722 | UBERON:0006314 | denotes | BAL fluid |
| T68159 | 2757-2762 | CHEBI:68452;CHEBI:68452 | denotes | azole |
| T29336 | 2845-2850 | CHEBI:68452;CHEBI:68452 | denotes | azole |
| T94543 | 3101-3112 | CHEBI:33282;CHEBI:33282 | denotes | antibiotics |
| T54450 | 3132-3146 | CHEBI:50858;CHEBI:50858 | denotes | corticosteroid |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32572532-22895826-47963419 | 313-314 | 22895826 | denotes | 7 |
| 32572532-22895826-47963420 | 738-739 | 22895826 | denotes | 7 |
| 32572532-28387526-47963421 | 843-844 | 28387526 | denotes | 8 |
| 32572532-30076119-47963422 | 846-847 | 30076119 | denotes | 9 |
| 32572532-31102782-47963423 | 1487-1489 | 31102782 | denotes | 31 |
| 32572532-27177530-47963424 | 1721-1723 | 27177530 | denotes | 32 |
| 32572532-28387526-47963425 | 1906-1907 | 28387526 | denotes | 8 |
| 32572532-31292663-47963426 | 2205-2207 | 31292663 | denotes | 33 |
| 32572532-30580035-47963427 | 2869-2871 | 30580035 | denotes | 34 |
| T80169 | 313-314 | 22895826 | denotes | 7 |
| T27000 | 738-739 | 22895826 | denotes | 7 |
| T8508 | 843-844 | 28387526 | denotes | 8 |
| T93633 | 846-847 | 30076119 | denotes | 9 |
| T30112 | 1487-1489 | 31102782 | denotes | 31 |
| T25822 | 1721-1723 | 27177530 | denotes | 32 |
| T48506 | 1906-1907 | 28387526 | denotes | 8 |
| T39271 | 2205-2207 | 31292663 | denotes | 33 |
| T67090 | 2869-2871 | 30580035 | denotes | 34 |