PMC:7341831 / 3059-7401
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T6 | 114-120 | Body_part | denotes | kidney | http://purl.org/sig/ont/fma/fma7203 |
| T7 | 560-571 | Body_part | denotes | extremities | http://purl.org/sig/ont/fma/fma7182 |
| T8 | 603-617 | Body_part | denotes | norepinephrine | http://purl.org/sig/ont/fma/fma61799 |
| T9 | 1252-1259 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T10 | 1367-1377 | Body_part | denotes | Leukocytes | http://purl.org/sig/ont/fma/fma62852 |
| T11 | 1388-1397 | Body_part | denotes | platelets | http://purl.org/sig/ont/fma/fma62851 |
| T12 | 1410-1420 | Body_part | denotes | hemoglobin | http://purl.org/sig/ont/fma/fma62293 |
| T13 | 1514-1519 | Body_part | denotes | Chest | http://purl.org/sig/ont/fma/fma9576 |
| T14 | 1578-1594 | Body_part | denotes | right lower lobe | http://purl.org/sig/ont/fma/fma7337 |
| T15 | 1622-1627 | Body_part | denotes | Blood | http://purl.org/sig/ont/fma/fma9670 |
| T16 | 2265-2269 | Body_part | denotes | lung | http://purl.org/sig/ont/fma/fma7195 |
| T17 | 2313-2329 | Body_part | denotes | right lower lobe | http://purl.org/sig/ont/fma/fma7337 |
| T18 | 2364-2368 | Body_part | denotes | lung | http://purl.org/sig/ont/fma/fma7195 |
| T19 | 2499-2503 | Body_part | denotes | head | http://purl.org/sig/ont/fma/fma7154 |
| T20 | 2598-2604 | Body_part | denotes | artery | http://purl.org/sig/ont/fma/fma50720 |
| T21 | 2664-2669 | Body_part | denotes | blood | http://purl.org/sig/ont/fma/fma9670 |
| T22 | 2813-2819 | Body_part | denotes | sputum | http://purl.org/sig/ont/fma/fma312401 |
| T23 | 2921-2925 | Body_part | denotes | lung | http://purl.org/sig/ont/fma/fma7195 |
| T24 | 3094-3098 | Body_part | denotes | head | http://purl.org/sig/ont/fma/fma7154 |
| T25 | 3461-3472 | Body_part | denotes | neutrophils | http://purl.org/sig/ont/fma/fma62860 |
| T26 | 3529-3535 | Body_part | denotes | artery | http://purl.org/sig/ont/fma/fma50720 |
| T27 | 3574-3599 | Body_part | denotes | alveolar epithelial cells | http://purl.org/sig/ont/fma/fma62499 |
| T28 | 3594-3599 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T29 | 3679-3689 | Body_part | denotes | nucleotide | http://purl.org/sig/ont/fma/fma82740 |
| T30 | 3773-3782 | Body_part | denotes | ribosomal | http://purl.org/sig/ont/fma/fma66867 |
| T31 | 3783-3786 | Body_part | denotes | DNA | http://purl.org/sig/ont/fma/fma74412 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T5 | 114-120 | Body_part | denotes | kidney | http://purl.obolibrary.org/obo/UBERON_0002113 |
| T6 | 716-720 | Body_part | denotes | tube | http://purl.obolibrary.org/obo/UBERON_0000025 |
| T7 | 977-981 | Body_part | denotes | tube | http://purl.obolibrary.org/obo/UBERON_0000025 |
| T8 | 1514-1519 | Body_part | denotes | Chest | http://purl.obolibrary.org/obo/UBERON_0001443 |
| T9 | 1590-1594 | Body_part | denotes | lobe | http://purl.obolibrary.org/obo/UBERON_3010752 |
| T10 | 1622-1627 | Body_part | denotes | Blood | http://purl.obolibrary.org/obo/UBERON_0000178 |
| T11 | 2265-2269 | Body_part | denotes | lung | http://purl.obolibrary.org/obo/UBERON_0002048 |
| T12 | 2325-2329 | Body_part | denotes | lobe | http://purl.obolibrary.org/obo/UBERON_3010752 |
| T13 | 2364-2368 | Body_part | denotes | lung | http://purl.obolibrary.org/obo/UBERON_0002048 |
| T14 | 2499-2503 | Body_part | denotes | head | http://purl.obolibrary.org/obo/UBERON_0000033 |
| T15 | 2598-2604 | Body_part | denotes | artery | http://purl.obolibrary.org/obo/UBERON_0001637 |
| T16 | 2664-2669 | Body_part | denotes | blood | http://purl.obolibrary.org/obo/UBERON_0000178 |
| T17 | 2813-2819 | Body_part | denotes | sputum | http://purl.obolibrary.org/obo/UBERON_0007311 |
| T18 | 2921-2925 | Body_part | denotes | lung | http://purl.obolibrary.org/obo/UBERON_0002048 |
| T19 | 3094-3098 | Body_part | denotes | head | http://purl.obolibrary.org/obo/UBERON_0000033 |
| T20 | 3529-3535 | Body_part | denotes | artery | http://purl.obolibrary.org/obo/UBERON_0001637 |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 115 | 31-38 | Species | denotes | patient | Tax:9606 |
| 116 | 241-249 | Species | denotes | patients | Tax:9606 |
| 117 | 279-286 | Species | denotes | patient | Tax:9606 |
| 118 | 862-869 | Species | denotes | patient | Tax:9606 |
| 119 | 603-617 | Chemical | denotes | norepinephrine | MESH:D009638 |
| 120 | 879-890 | Chemical | denotes | oseltamivir | MESH:D053139 |
| 121 | 915-926 | Chemical | denotes | chloroquine | MESH:D002738 |
| 122 | 986-998 | Chemical | denotes | azithromycin | MESH:D017963 |
| 123 | 1016-1027 | Chemical | denotes | ceftriaxone | MESH:D002443 |
| 124 | 1041-1051 | Chemical | denotes | furosemide | MESH:D005665 |
| 125 | 1094-1104 | Chemical | denotes | enoxaparin | MESH:D017984 |
| 126 | 61-73 | Disease | denotes | hypertension | MESH:D006973 |
| 127 | 75-100 | Disease | denotes | type II diabetes mellitus | MESH:D003924 |
| 128 | 106-128 | Disease | denotes | chronic kidney disease | MESH:D051436 |
| 129 | 255-263 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 130 | 367-375 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 131 | 542-571 | Disease | denotes | cyanosis and cold extremities | MESH:D003490 |
| 139 | 1241-1259 | Gene | denotes | C-reactive protein | Gene:1401 |
| 140 | 1192-1196 | Chemical | denotes | urea | MESH:D014508 |
| 141 | 1212-1222 | Chemical | denotes | creatinine | MESH:D003404 |
| 142 | 1299-1308 | Chemical | denotes | potassium | MESH:D011188 |
| 143 | 1313-1319 | Chemical | denotes | sodium | MESH:D012964 |
| 144 | 1450-1462 | Disease | denotes | neutrophilia | MESH:C563010 |
| 145 | 1474-1485 | Disease | denotes | lymphopenia | MESH:D008231 |
| 151 | 1710-1717 | Species | denotes | patient | Tax:9606 |
| 152 | 1950-1957 | Species | denotes | patient | Tax:9606 |
| 153 | 1796-1807 | Disease | denotes | hypotension | MESH:D007022 |
| 154 | 1812-1823 | Disease | denotes | bradycardia | MESH:D001919 |
| 155 | 1980-1985 | Disease | denotes | death | MESH:D003643 |
| 162 | 2408-2419 | Species | denotes | Aspergillus | Tax:746128 |
| 163 | 2487-2498 | Species | denotes | Aspergillus | Tax:746128 |
| 164 | 2694-2696 | Chemical | denotes | GM | MESH:C012990 |
| 165 | 2552-2568 | Disease | denotes | bronchopneumonia | MESH:D001996 |
| 166 | 2610-2629 | Disease | denotes | squamous metaplasia | MESH:D008679 |
| 167 | 2765-2778 | Disease | denotes | aspergillosis | MESH:D001228 |
| 172 | 3082-3093 | Species | denotes | Aspergillus | Tax:746128 |
| 173 | 2973-2976 | Chemical | denotes | H&E | MESH:D006371 |
| 174 | 3421-3437 | Disease | denotes | Bronchopneumonia | MESH:D001996 |
| 175 | 3551-3570 | Disease | denotes | Squamous metaplasia | MESH:D008679 |
| 178 | 4233-4259 | Species | denotes | Aspergillus penicillioides | Tax:41959 |
| 179 | 3646-3657 | Species | denotes | Aspergillus | Tax:746128 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T38 | 61-73 | Disease | denotes | hypertension | http://purl.obolibrary.org/obo/MONDO_0005044 |
| T39 | 75-100 | Disease | denotes | type II diabetes mellitus | http://purl.obolibrary.org/obo/MONDO_0005148 |
| T40 | 83-91 | Disease | denotes | diabetes | http://purl.obolibrary.org/obo/MONDO_0005015 |
| T41 | 106-128 | Disease | denotes | chronic kidney disease | http://purl.obolibrary.org/obo/MONDO_0005300 |
| T42 | 114-128 | Disease | denotes | kidney disease | http://purl.obolibrary.org/obo/MONDO_0001343|http://purl.obolibrary.org/obo/MONDO_0005240 |
| T44 | 255-263 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T45 | 332-334 | Disease | denotes | he | http://purl.obolibrary.org/obo/MONDO_0017319 |
| T46 | 367-375 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T47 | 417-419 | Disease | denotes | he | http://purl.obolibrary.org/obo/MONDO_0017319 |
| T48 | 1474-1485 | Disease | denotes | lymphopenia | http://purl.obolibrary.org/obo/MONDO_0003783 |
| T49 | 1796-1807 | Disease | denotes | hypotension | http://purl.obolibrary.org/obo/MONDO_0005468 |
| T50 | 2552-2568 | Disease | denotes | bronchopneumonia | http://purl.obolibrary.org/obo/MONDO_0005682 |
| T51 | 2765-2778 | Disease | denotes | aspergillosis | http://purl.obolibrary.org/obo/MONDO_0005657 |
| T52 | 3182-3185 | Disease | denotes | PAS | http://purl.obolibrary.org/obo/MONDO_0004277 |
| T53 | 3421-3437 | Disease | denotes | Bronchopneumonia | http://purl.obolibrary.org/obo/MONDO_0005682 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T18 | 12-13 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T19 | 14-16 | http://purl.obolibrary.org/obo/CLO_0054055 | denotes | 71 |
| T20 | 26-30 | http://purl.obolibrary.org/obo/UBERON_0003101 | denotes | male |
| T21 | 26-30 | http://www.ebi.ac.uk/efo/EFO_0000970 | denotes | male |
| T22 | 114-120 | http://purl.obolibrary.org/obo/UBERON_0002113 | denotes | kidney |
| T23 | 114-120 | http://www.ebi.ac.uk/efo/EFO_0000927 | denotes | kidney |
| T24 | 114-120 | http://www.ebi.ac.uk/efo/EFO_0000929 | denotes | kidney |
| T25 | 204-205 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T26 | 560-571 | http://www.ebi.ac.uk/efo/EFO_0000876 | denotes | extremities |
| T27 | 716-720 | http://purl.obolibrary.org/obo/UBERON_0000025 | denotes | tube |
| T28 | 963-964 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T29 | 977-981 | http://purl.obolibrary.org/obo/UBERON_0000025 | denotes | tube |
| T30 | 1514-1519 | http://www.ebi.ac.uk/efo/EFO_0000965 | denotes | Chest |
| T31 | 1622-1627 | http://purl.obolibrary.org/obo/UBERON_0000178 | denotes | Blood |
| T32 | 1622-1627 | http://www.ebi.ac.uk/efo/EFO_0000296 | denotes | Blood |
| T33 | 2265-2269 | http://purl.obolibrary.org/obo/UBERON_0002048 | denotes | lung |
| T34 | 2265-2269 | http://www.ebi.ac.uk/efo/EFO_0000934 | denotes | lung |
| T35 | 2364-2368 | http://purl.obolibrary.org/obo/UBERON_0002048 | denotes | lung |
| T36 | 2364-2368 | http://www.ebi.ac.uk/efo/EFO_0000934 | denotes | lung |
| T37 | 2472-2473 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T38 | 2499-2503 | http://purl.obolibrary.org/obo/UBERON_0000033 | denotes | head |
| T39 | 2499-2503 | http://www.ebi.ac.uk/efo/EFO_0000964 | denotes | head |
| T40 | 2598-2604 | http://purl.obolibrary.org/obo/UBERON_0001637 | denotes | artery |
| T41 | 2598-2604 | http://www.ebi.ac.uk/efo/EFO_0000814 | denotes | artery |
| T42 | 2664-2669 | http://purl.obolibrary.org/obo/UBERON_0000178 | denotes | blood |
| T43 | 2664-2669 | http://www.ebi.ac.uk/efo/EFO_0000296 | denotes | blood |
| T44 | 2670-2676 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tested |
| T45 | 2921-2925 | http://purl.obolibrary.org/obo/UBERON_0002048 | denotes | lung |
| T46 | 2921-2925 | http://www.ebi.ac.uk/efo/EFO_0000934 | denotes | lung |
| T47 | 2927-2928 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T48 | 3066-3067 | http://purl.obolibrary.org/obo/CLO_0001021 | denotes | B |
| T49 | 3094-3098 | http://purl.obolibrary.org/obo/UBERON_0000033 | denotes | head |
| T50 | 3094-3098 | http://www.ebi.ac.uk/efo/EFO_0000964 | denotes | head |
| T51 | 3514-3515 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T52 | 3529-3535 | http://purl.obolibrary.org/obo/UBERON_0001637 | denotes | artery |
| T53 | 3529-3535 | http://www.ebi.ac.uk/efo/EFO_0000814 | denotes | artery |
| T54 | 3583-3593 | http://purl.obolibrary.org/obo/CL_0000066 | denotes | epithelial |
| T55 | 3594-3599 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T29 | 26-30 | Chemical | denotes | male | http://purl.obolibrary.org/obo/CHEBI_30780 |
| T30 | 80-82 | Chemical | denotes | II | http://purl.obolibrary.org/obo/CHEBI_74067 |
| T31 | 491-496 | Chemical | denotes | drugs | http://purl.obolibrary.org/obo/CHEBI_23888 |
| T32 | 603-617 | Chemical | denotes | norepinephrine | http://purl.obolibrary.org/obo/CHEBI_18357|http://purl.obolibrary.org/obo/CHEBI_33569 |
| T34 | 777-781 | Chemical | denotes | PEEP | http://purl.obolibrary.org/obo/CHEBI_53359|http://purl.obolibrary.org/obo/CHEBI_60683 |
| T36 | 879-890 | Chemical | denotes | oseltamivir | http://purl.obolibrary.org/obo/CHEBI_7798 |
| T37 | 915-926 | Chemical | denotes | chloroquine | http://purl.obolibrary.org/obo/CHEBI_3638 |
| T38 | 983-985 | Chemical | denotes | IV | http://purl.obolibrary.org/obo/CHEBI_74327 |
| T39 | 986-998 | Chemical | denotes | azithromycin | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T40 | 1013-1015 | Chemical | denotes | IV | http://purl.obolibrary.org/obo/CHEBI_74327 |
| T41 | 1016-1027 | Chemical | denotes | ceftriaxone | http://purl.obolibrary.org/obo/CHEBI_29007 |
| T42 | 1038-1040 | Chemical | denotes | IV | http://purl.obolibrary.org/obo/CHEBI_74327 |
| T43 | 1041-1051 | Chemical | denotes | furosemide | http://purl.obolibrary.org/obo/CHEBI_47426 |
| T44 | 1121-1135 | Chemical | denotes | corticosteroid | http://purl.obolibrary.org/obo/CHEBI_50858 |
| T45 | 1136-1141 | Chemical | denotes | drugs | http://purl.obolibrary.org/obo/CHEBI_23888 |
| T46 | 1192-1196 | Chemical | denotes | urea | http://purl.obolibrary.org/obo/CHEBI_16199 |
| T47 | 1212-1222 | Chemical | denotes | creatinine | http://purl.obolibrary.org/obo/CHEBI_16737 |
| T48 | 1252-1259 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T49 | 1299-1308 | Chemical | denotes | potassium | http://purl.obolibrary.org/obo/CHEBI_26216 |
| T50 | 1313-1319 | Chemical | denotes | sodium | http://purl.obolibrary.org/obo/CHEBI_26708 |
| T51 | 1410-1420 | Chemical | denotes | hemoglobin | http://purl.obolibrary.org/obo/CHEBI_35143 |
| T52 | 2694-2696 | Chemical | denotes | GM | http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680 |
| T54 | 2697-2704 | Chemical | denotes | antigen | http://purl.obolibrary.org/obo/CHEBI_59132 |
| T55 | 2860-2876 | Chemical | denotes | antifungal drugs | http://purl.obolibrary.org/obo/CHEBI_35718|http://purl.obolibrary.org/obo/CHEBI_86327 |
| T57 | 2871-2876 | Chemical | denotes | drugs | http://purl.obolibrary.org/obo/CHEBI_23888 |
| T58 | 3182-3185 | Chemical | denotes | PAS | http://purl.obolibrary.org/obo/CHEBI_27565 |
| T59 | 3489-3495 | Chemical | denotes | Fibrin | http://purl.obolibrary.org/obo/CHEBI_5054 |
| T60 | 3679-3689 | Chemical | denotes | nucleotide | http://purl.obolibrary.org/obo/CHEBI_36976 |
| T61 | 3783-3786 | Chemical | denotes | DNA | http://purl.obolibrary.org/obo/CHEBI_16991 |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T4 | 1663-1669 | http://purl.obolibrary.org/obo/GO_0040007 | denotes | growth |
| T5 | 2619-2629 | http://purl.obolibrary.org/obo/GO_0036074 | denotes | metaplasia |
| T6 | 3358-3368 | http://purl.obolibrary.org/obo/GO_0000917 | denotes | septations |
| T7 | 3560-3570 | http://purl.obolibrary.org/obo/GO_0036074 | denotes | metaplasia |
LitCovid-PD-GlycoEpitope
| Id | Subject | Object | Predicate | Lexical cue | glyco_epitope_db_id |
|---|---|---|---|---|---|
| T5 | 2694-2696 | GlycoEpitope | denotes | GM | http://www.glycoepitope.jp/epitopes/EP0510 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T30 | 0-11 | Sentence | denotes | CASE REPORT |
| T31 | 12-274 | Sentence | denotes | A 71-year-old male patient with prior history of hypertension, type II diabetes mellitus, and chronic kidney disease was admitted to the Hospital e Pronto-Socorro Delphina Rinaldi Abdel Aziz, a referral unit for the treatment of patients with COVID-19 in Manaus. |
| T32 | 275-387 | Sentence | denotes | The patient was transferred from another hospital, where he had already been diagnosed with COVID-19 by RT-qPCR. |
| T33 | 388-572 | Sentence | denotes | Upon admission into the ICU, he was placed under orotracheal intubation, received high-dose vasoactive drugs, was hemodynamically unstable, and presented cyanosis and cold extremities. |
| T34 | 573-827 | Sentence | denotes | He was administered high-flow norepinephrine (1.41 µg/kg/min) and placed on invasive mechanical ventilation under aspiration of an orotracheal tube with high parameters (positive end-expiratory pressure [PEEP] 8/FiO2 60%/respiratory rate 26; volume 360). |
| T35 | 828-857 | Sentence | denotes | The PaO2/FiO2 ratio was 86.6. |
| T36 | 858-1117 | Sentence | denotes | The patient received oseltamivir (75 mg twice daily) and chloroquine (450 mg twice on the first day) via a nasoenteral tube, IV azithromycin (500 mg/day), IV ceftriaxone (2g/day), IV furosemide (20mg TID), and prophylactic subcutaneous enoxaparin (40 mg/day). |
| T37 | 1118-1152 | Sentence | denotes | No corticosteroid drugs were used. |
| T38 | 1153-1270 | Sentence | denotes | Laboratory parameters showed increased urea (360.7 mg/dL), creatinine (8.46 mg/dL), and C-reactive protein (12 mg/L). |
| T39 | 1271-1366 | Sentence | denotes | Normal values were seen for potassium and sodium (5.24 mmol/L; and 136.8 mmol/L, respectively). |
| T40 | 1367-1513 | Sentence | denotes | Leukocytes 6,530/µL, platelets 285x109/µL, hemoglobin 11.2 g/dL, hematocrit 34.5%, neutrophilia (84%), and lymphopenia (12,8%) were also observed. |
| T41 | 1514-1595 | Sentence | denotes | Chest x-rays showed infiltrate and nodular consolidation in the right lower lobe. |
| T42 | 1596-1621 | Sentence | denotes | No CT scan was performed. |
| T43 | 1622-1670 | Sentence | denotes | Blood culture was negative for bacterial growth. |
| T44 | 1671-1824 | Sentence | denotes | On day three, following admission, the patient progressed with hemodynamic worsening and refractory shock, with irreversible hypotension and bradycardia. |
| T45 | 1825-1851 | Sentence | denotes | He died the following day. |
| T46 | 1852-2140 | Sentence | denotes | The autopsy was authorized by legal representatives (an informed consent form was signed), as the patient was enrolled prior to death in the CloroCovid-19 Study (ClinicalTrials.gov Identifier: NCT04323527, approved by the Brazilian National Ethics Review Board CAAE 30152620.1.0000.0005). |
| T47 | 2141-2243 | Sentence | denotes | An autopsy was performed in the same hospital by trained technicians and under strict biosafety rules. |
| T48 | 2244-2330 | Sentence | denotes | Macroscopically, the lung showed focal areas of consolidation in the right lower lobe. |
| T49 | 2331-2641 | Sentence | denotes | Microscopic visualization of the lung showed the presence of clearly defined Aspergillus structures, including hyphae and fungal spores, and a well-defined Aspergillus head with phialides, conidia, and spores, as well as bronchopneumonia, fibrin thrombi occluding an artery, and squamous metaplasia (Figure 1). |
| T50 | 2642-2719 | Sentence | denotes | The stored peripheral blood tested positive for the GM antigen (index 4.290). |
| T51 | 2720-2887 | Sentence | denotes | Since the diagnosis was made postmortem, and aspergillosis was not considered antemortem, no sputum was collected for fungus culture and no antifungal drugs were used. |
| T52 | 2888-2897 | Sentence | denotes | FIGURE 1: |
| T53 | 2899-2926 | Sentence | denotes | Histopathology of the lung. |
| T54 | 2927-2929 | Sentence | denotes | A. |
| T55 | 2930-2986 | Sentence | denotes | Numerous hyphae and fungal spores shown by H&E staining. |
| T56 | 2987-3065 | Sentence | denotes | Microscopic cavitation surrounded by numerous hypahes and fungal spores (40x). |
| T57 | 3066-3068 | Sentence | denotes | B. |
| T58 | 3069-3193 | Sentence | denotes | Well-defined Aspergillus head, allowing the visualization of phialides and conidia, with numerous fungal spores (PAS, 400x). |
| T59 | 3194-3196 | Sentence | denotes | C. |
| T60 | 3197-3417 | Sentence | denotes | Well-defined aspergillary structure showing conidiophore, aspergillary vesicle, phialides, and conidia, as well as several hyphae of regular diameter, some with septations and dichotomous branches (Gomori-Grocott, 400x). |
| T61 | 3418-3420 | Sentence | denotes | D. |
| T62 | 3421-3485 | Sentence | denotes | Bronchopneumonia with alveoli filled by neutrophils (H&E, 400x). |
| T63 | 3486-3488 | Sentence | denotes | E. |
| T64 | 3489-3550 | Sentence | denotes | Fibrin thrombi occluding a medium-sized artery (H&E, 400x) F. |
| T65 | 3551-3612 | Sentence | denotes | Squamous metaplasia in alveolar epithelial cells (H&E, 400x). |
| T66 | 3613-3701 | Sentence | denotes | The histopathological finding of Aspergillus spp was confirmed by nucleotide sequencing. |
| T67 | 3702-3894 | Sentence | denotes | The internal transcribed spacer 1 (ITS1) and ITS2 regions and the 5.8S ribosomal DNA (rDNA) were amplified by polymerase chain reaction using the universal primers ITS1 and ITS4, as described. |
| T68 | 3895-4041 | Sentence | denotes | 10 Sequencing was performed using the BigDye® Terminator v3.1 Cycle Sequencing (Applied Biosystems) and the above primers on an individual basis. |
| T69 | 4042-4206 | Sentence | denotes | Only the best sequences were used to perform contig assembly and conduct comparative analysis with the GenBank database using the Basic Local Alignment Search Tool. |
| T70 | 4207-4260 | Sentence | denotes | The best hit returns were Aspergillus penicillioides. |
| T71 | 4261-4342 | Sentence | denotes | The sequence was submitted to GenBank and received the accession number MT582426. |
LitCovid-PD-HP
| Id | Subject | Object | Predicate | Lexical cue | hp_id |
|---|---|---|---|---|---|
| T15 | 61-73 | Phenotype | denotes | hypertension | http://purl.obolibrary.org/obo/HP_0000822 |
| T16 | 75-100 | Phenotype | denotes | type II diabetes mellitus | http://purl.obolibrary.org/obo/HP_0005978 |
| T17 | 106-128 | Phenotype | denotes | chronic kidney disease | http://purl.obolibrary.org/obo/HP_0012622 |
| T18 | 542-550 | Phenotype | denotes | cyanosis | http://purl.obolibrary.org/obo/HP_0000961 |
| T19 | 687-697 | Phenotype | denotes | aspiration | http://purl.obolibrary.org/obo/HP_0002835 |
| T20 | 1450-1462 | Phenotype | denotes | neutrophilia | http://purl.obolibrary.org/obo/HP_0011897 |
| T21 | 1474-1485 | Phenotype | denotes | lymphopenia | http://purl.obolibrary.org/obo/HP_0001888 |
| T22 | 1771-1776 | Phenotype | denotes | shock | http://purl.obolibrary.org/obo/HP_0031273 |
| T23 | 1796-1807 | Phenotype | denotes | hypotension | http://purl.obolibrary.org/obo/HP_0002615 |
| T24 | 1812-1823 | Phenotype | denotes | bradycardia | http://purl.obolibrary.org/obo/HP_0001662 |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32638890-20392915-134289067 | 3895-3897 | 20392915 | denotes | 10 |
LitCovid-PMC-OGER-BB
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T47 | 114-120 | UBERON:0002113 | denotes | kidney |
| T48 | 255-263 | SP_7 | denotes | COVID-19 |
| T49 | 367-375 | SP_7 | denotes | COVID-19 |
| T50 | 437-448 | UBERON:0006060 | denotes | orotracheal |
| T51 | 491-496 | CHEBI:23888;CHEBI:23888 | denotes | drugs |
| T52 | 716-720 | UBERON:0000025 | denotes | tube |
| T53 | 785-789 | CHEBI:16526;CHEBI:16526 | denotes | FiO2 |
| T54 | 794-805 | UBERON:0001004 | denotes | respiratory |
| T55 | 879-890 | CHEBI:7798;CHEBI:7798 | denotes | oseltamivir |
| T56 | 915-926 | CHEBI:3638;CHEBI:3638;DG_10 | denotes | chloroquine |
| T57 | 986-998 | CHEBI:2955;CHEBI:2955;DG_6 | denotes | azithromycin |
| T58 | 1016-1027 | CHEBI:29007;CHEBI:29007 | denotes | ceftriaxone |
| T59 | 1041-1051 | CHEBI:47426;CHEBI:47426 | denotes | furosemide |
| T60 | 1121-1135 | CHEBI:50858;CHEBI:50858 | denotes | corticosteroid |
| T61 | 1136-1141 | CHEBI:23888;CHEBI:23888 | denotes | drugs |
| T62 | 1192-1196 | CHEBI:16199;CHEBI:16199 | denotes | urea |
| T63 | 1212-1222 | CHEBI:16737;CHEBI:16737 | denotes | creatinine |
| T64 | 1241-1259 | PR:000005897 | denotes | C-reactive protein |
| T65 | 1367-1377 | CL:0000738 | denotes | Leukocytes |
| T66 | 1388-1397 | CL:0000233 | denotes | platelets |
| T67 | 1450-1462 | CL:0000775 | denotes | neutrophilia |
| T68 | 1590-1594 | UBERON:0002171 | denotes | lobe |
| T69 | 1622-1627 | UBERON:0000178 | denotes | Blood |
| T70 | 1653-1662 | NCBITaxon:2 | denotes | bacterial |
| T71 | 1828-1832 | GO:0016265 | denotes | died |
| T72 | 1980-1985 | GO:0016265 | denotes | death |
| T73 | 2265-2269 | UBERON:0002048 | denotes | lung |
| T74 | 2319-2324 | UBERON:0000101 | denotes | lower |
| T75 | 2325-2329 | UBERON:0002171 | denotes | lobe |
| T76 | 2364-2368 | UBERON:0002048 | denotes | lung |
| T77 | 2408-2419 | NCBITaxon:5052 | denotes | Aspergillus |
| T78 | 2453-2459 | NCBITaxon:4751 | denotes | fungal |
| T79 | 2499-2503 | UBERON:0000033 | denotes | head |
| T80 | 2570-2576 | UBERON:0010210;CHEBI:5054;CHEBI:5054 | denotes | fibrin |
| T81 | 2577-2584 | UBERON:0010210 | denotes | thrombi |
| T82 | 2598-2604 | UBERON:0001637 | denotes | artery |
| T83 | 2664-2669 | UBERON:0000178 | denotes | blood |
| T84 | 2697-2704 | CHEBI:59132;CHEBI:59132 | denotes | antigen |
| T85 | 2749-2759 | GO:0016265 | denotes | postmortem |
| T86 | 2798-2808 | GO:0016265 | denotes | antemortem |
| T87 | 2813-2819 | UBERON:0007311 | denotes | sputum |
| T88 | 2838-2844 | NCBITaxon:4751 | denotes | fungus |
| T89 | 2860-2870 | CHEBI:35718;CHEBI:35718 | denotes | antifungal |
| T90 | 2871-2876 | CHEBI:86327;CHEBI:86327 | denotes | drugs |
| T91 | 2921-2925 | UBERON:0002048 | denotes | lung |
| T92 | 2950-2956 | NCBITaxon:4751 | denotes | fungal |
| T93 | 2973-2974 | CHEBI:51686;CHEBI:51686 | denotes | H |
| T94 | 3045-3051 | NCBITaxon:4751 | denotes | fungal |
| T95 | 3082-3093 | NCBITaxon:5052 | denotes | Aspergillus |
| T96 | 3094-3098 | UBERON:0000033 | denotes | head |
| T97 | 3167-3173 | NCBITaxon:4751 | denotes | fungal |
| T98 | 3443-3450 | UBERON:0003215 | denotes | alveoli |
| T99 | 3461-3472 | CL:0000775 | denotes | neutrophils |
| T100 | 3474-3475 | CHEBI:51686;CHEBI:51686 | denotes | H |
| T101 | 3489-3495 | CHEBI:5054;CHEBI:5054;UBERON:0010210 | denotes | Fibrin |
| T102 | 3496-3503 | UBERON:0010210 | denotes | thrombi |
| T103 | 3529-3535 | UBERON:0001637 | denotes | artery |
| T104 | 3537-3538 | CHEBI:51686;CHEBI:51686 | denotes | H |
| T105 | 3574-3582 | UBERON:0003215;CL:0000322 | denotes | alveolar |
| T106 | 3583-3593 | CL:0000322;UBERON:0000483 | denotes | epithelial |
| T107 | 3594-3599 | CL:0000322 | denotes | cells |
| T108 | 3601-3602 | CHEBI:51686;CHEBI:51686 | denotes | H |
| T127 | 3646-3657 | NCBITaxon:5052 | denotes | Aspergillus |
| T128 | 3773-3782 | GO:0005840 | denotes | ribosomal |
| T129 | 3858-3865 | SO:0000112 | denotes | primers |
| T130 | 4010-4017 | SO:0000112 | denotes | primers |
| T131 | 4087-4093 | SO:0000149 | denotes | contig |
| T132 | 4233-4259 | NCBITaxon:41959 | denotes | Aspergillus penicillioides |
| T98313 | 114-120 | UBERON:0002113 | denotes | kidney |
| T14556 | 255-263 | SP_7 | denotes | COVID-19 |
| T45329 | 367-375 | SP_7 | denotes | COVID-19 |
| T62007 | 437-448 | UBERON:0006060 | denotes | orotracheal |
| T81053 | 491-496 | CHEBI:23888;CHEBI:23888 | denotes | drugs |
| T84418 | 716-720 | UBERON:0000025 | denotes | tube |
| T13632 | 785-789 | CHEBI:16526;CHEBI:16526 | denotes | FiO2 |
| T35862 | 794-805 | UBERON:0001004 | denotes | respiratory |
| T24320 | 879-890 | CHEBI:7798;CHEBI:7798 | denotes | oseltamivir |
| T83491 | 915-926 | CHEBI:3638;CHEBI:3638;DG_10 | denotes | chloroquine |
| T9292 | 986-998 | CHEBI:2955;CHEBI:2955;DG_6 | denotes | azithromycin |
| T19984 | 1016-1027 | CHEBI:29007;CHEBI:29007 | denotes | ceftriaxone |
| T4490 | 1041-1051 | CHEBI:47426;CHEBI:47426 | denotes | furosemide |
| T37947 | 1121-1135 | CHEBI:50858;CHEBI:50858 | denotes | corticosteroid |
| T19256 | 1136-1141 | CHEBI:23888;CHEBI:23888 | denotes | drugs |
| T6586 | 1192-1196 | CHEBI:16199;CHEBI:16199 | denotes | urea |
| T20602 | 1212-1222 | CHEBI:16737;CHEBI:16737 | denotes | creatinine |
| T37535 | 1241-1259 | PR:000005897 | denotes | C-reactive protein |
| T59138 | 1367-1377 | CL:0000738 | denotes | Leukocytes |
| T94991 | 1388-1397 | CL:0000233 | denotes | platelets |
| T9825 | 1450-1462 | CL:0000775 | denotes | neutrophilia |
| T4481 | 1590-1594 | UBERON:0002171 | denotes | lobe |
| T6767 | 1622-1627 | UBERON:0000178 | denotes | Blood |
| T5667 | 1653-1662 | NCBITaxon:2 | denotes | bacterial |
| T1728 | 1828-1832 | GO:0016265 | denotes | died |
| T27792 | 1980-1985 | GO:0016265 | denotes | death |
| T45015 | 2265-2269 | UBERON:0002048 | denotes | lung |
| T95141 | 2319-2324 | UBERON:0000101 | denotes | lower |
| T63510 | 2325-2329 | UBERON:0002171 | denotes | lobe |
| T50592 | 2364-2368 | UBERON:0002048 | denotes | lung |
| T54529 | 2408-2419 | NCBITaxon:5052 | denotes | Aspergillus |
| T53412 | 2453-2459 | NCBITaxon:4751 | denotes | fungal |
| T84391 | 2499-2503 | UBERON:0000033 | denotes | head |
| T7647 | 2570-2576 | UBERON:0010210;CHEBI:5054;CHEBI:5054 | denotes | fibrin |
| T64013 | 2577-2584 | UBERON:0010210 | denotes | thrombi |
| T81261 | 2598-2604 | UBERON:0001637 | denotes | artery |
| T18084 | 2664-2669 | UBERON:0000178 | denotes | blood |
| T70655 | 2697-2704 | CHEBI:59132;CHEBI:59132 | denotes | antigen |
| T71653 | 2749-2759 | GO:0016265 | denotes | postmortem |
| T7484 | 2798-2808 | GO:0016265 | denotes | antemortem |
| T96965 | 2813-2819 | UBERON:0007311 | denotes | sputum |
| T78632 | 2838-2844 | NCBITaxon:4751 | denotes | fungus |
| T68516 | 2860-2870 | CHEBI:35718;CHEBI:35718 | denotes | antifungal |
| T92277 | 2871-2876 | CHEBI:86327;CHEBI:86327 | denotes | drugs |
| T81207 | 2921-2925 | UBERON:0002048 | denotes | lung |
| T65437 | 2950-2956 | NCBITaxon:4751 | denotes | fungal |
| T92241 | 2973-2974 | CHEBI:51686;CHEBI:51686 | denotes | H |
| T64480 | 3045-3051 | NCBITaxon:4751 | denotes | fungal |
| T74480 | 3082-3093 | NCBITaxon:5052 | denotes | Aspergillus |
| T31521 | 3094-3098 | UBERON:0000033 | denotes | head |
| T29491 | 3167-3173 | NCBITaxon:4751 | denotes | fungal |
| T83684 | 3443-3450 | UBERON:0003215 | denotes | alveoli |
| T62000 | 3461-3472 | CL:0000775 | denotes | neutrophils |
| T43627 | 3474-3475 | CHEBI:51686;CHEBI:51686 | denotes | H |
| T39112 | 3489-3495 | CHEBI:5054;CHEBI:5054;UBERON:0010210 | denotes | Fibrin |
| T37990 | 3496-3503 | UBERON:0010210 | denotes | thrombi |
| T93077 | 3529-3535 | UBERON:0001637 | denotes | artery |
| T41475 | 3537-3538 | CHEBI:51686;CHEBI:51686 | denotes | H |
| T29535 | 3574-3582 | UBERON:0003215;CL:0000322 | denotes | alveolar |
| T32471 | 3583-3593 | CL:0000322;UBERON:0000483 | denotes | epithelial |
| T46776 | 3594-3599 | CL:0000322 | denotes | cells |
| T9064 | 3601-3602 | CHEBI:51686;CHEBI:51686 | denotes | H |
| T358 | 3646-3657 | NCBITaxon:5052 | denotes | Aspergillus |
| T55757 | 3773-3782 | GO:0005840 | denotes | ribosomal |
| T8859 | 3858-3865 | SO:0000112 | denotes | primers |
| T66811 | 4010-4017 | SO:0000112 | denotes | primers |
| T27374 | 4087-4093 | SO:0000149 | denotes | contig |
| T19455 | 4233-4259 | NCBITaxon:41959 | denotes | Aspergillus penicillioides |