PMC:7326463 / 1237-3295
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T2 | 462-466 | Body_part | denotes | body | http://purl.org/sig/ont/fma/fma256135 |
| T3 | 512-517 | Body_part | denotes | blood | http://purl.org/sig/ont/fma/fma9670 |
| T4 | 518-525 | Body_part | denotes | glucose | http://purl.org/sig/ont/fma/fma82743 |
| T5 | 643-646 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T4 | 512-517 | Body_part | denotes | blood | http://purl.obolibrary.org/obo/UBERON_0000178 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T23 | 150-175 | Disease | denotes | acute respiratory failure | http://purl.obolibrary.org/obo/MONDO_0001208|http://purl.obolibrary.org/obo/MONDO_0021113 |
| T25 | 263-265 | Disease | denotes | he | http://purl.obolibrary.org/obo/MONDO_0017319 |
| T26 | 387-403 | Disease | denotes | immunodeficiency | http://purl.obolibrary.org/obo/MONDO_0021094 |
| T27 | 422-441 | Disease | denotes | respiratory disease | http://purl.obolibrary.org/obo/MONDO_0005087 |
| T28 | 495-510 | Disease | denotes | type 2 diabetes | http://purl.obolibrary.org/obo/MONDO_0005148 |
| T29 | 502-510 | Disease | denotes | diabetes | http://purl.obolibrary.org/obo/MONDO_0005015 |
| T30 | 579-591 | Disease | denotes | hypertension | http://purl.obolibrary.org/obo/MONDO_0005044 |
| T31 | 610-624 | Disease | denotes | hypothyroidism | http://purl.obolibrary.org/obo/MONDO_0005420 |
| T32 | 626-634 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T33 | 847-854 | Disease | denotes | sterile | http://purl.obolibrary.org/obo/MONDO_0005047 |
| T34 | 1853-1863 | Disease | denotes | fusariosis | http://purl.obolibrary.org/obo/MONDO_0016426 |
| T35 | 1878-1886 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T7 | 0-1 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T8 | 512-517 | http://purl.obolibrary.org/obo/UBERON_0000178 | denotes | blood |
| T9 | 512-517 | http://www.ebi.ac.uk/efo/EFO_0000296 | denotes | blood |
| T10 | 596-597 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T11 | 663-664 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T12 | 737-738 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T13 | 769-770 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T14 | 785-786 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T15 | 909-910 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T16 | 999-1002 | http://purl.obolibrary.org/obo/CLO_0054060 | denotes | 102 |
| T17 | 1050-1058 | http://purl.obolibrary.org/obo/NCBITaxon_2 | denotes | bacteria |
| T18 | 1088-1089 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T19 | 1181-1188 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | testing |
| T20 | 1416-1417 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T21 | 1441-1442 | http://purl.obolibrary.org/obo/CLO_0001021 | denotes | B |
| T22 | 1548-1555 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | testing |
| T23 | 1759-1760 | http://purl.obolibrary.org/obo/CLO_0001021 | denotes | B |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T1 | 518-525 | Chemical | denotes | glucose | http://purl.obolibrary.org/obo/CHEBI_17234|http://purl.obolibrary.org/obo/CHEBI_4167 |
| T3 | 935-938 | Chemical | denotes | BAL | http://purl.obolibrary.org/obo/CHEBI_64198 |
| T4 | 1097-1100 | Chemical | denotes | BAL | http://purl.obolibrary.org/obo/CHEBI_64198 |
| T5 | 1193-1206 | Chemical | denotes | galactomannan | http://purl.obolibrary.org/obo/CHEBI_27680 |
| T6 | 1207-1214 | Chemical | denotes | antigen | http://purl.obolibrary.org/obo/CHEBI_59132 |
| T7 | 1428-1442 | Chemical | denotes | amphotericin B | http://purl.obolibrary.org/obo/CHEBI_2682 |
| T8 | 1682-1694 | Chemical | denotes | voriconazole | http://purl.obolibrary.org/obo/CHEBI_10023 |
| T9 | 1696-1708 | Chemical | denotes | posaconazole | http://purl.obolibrary.org/obo/CHEBI_64355 |
| T10 | 1713-1726 | Chemical | denotes | isavuconazole | http://purl.obolibrary.org/obo/CHEBI_85979 |
| T11 | 1732-1735 | Chemical | denotes | MIC | http://purl.obolibrary.org/obo/CHEBI_59059 |
| T12 | 1746-1760 | Chemical | denotes | amphotericin B | http://purl.obolibrary.org/obo/CHEBI_2682 |
| T13 | 1967-1970 | Chemical | denotes | BAL | http://purl.obolibrary.org/obo/CHEBI_64198 |
| T14 | 1996-1998 | Chemical | denotes | GM | http://purl.obolibrary.org/obo/CHEBI_74120 |
| T15 | 2000-2013 | Chemical | denotes | galactomannan | http://purl.obolibrary.org/obo/CHEBI_27680 |
| T16 | 2044-2050 | Chemical | denotes | glucan | http://purl.obolibrary.org/obo/CHEBI_37163 |
LitCovid-PD-GlycoEpitope
| Id | Subject | Object | Predicate | Lexical cue | glyco_epitope_db_id |
|---|---|---|---|---|---|
| T1 | 1193-1206 | GlycoEpitope | denotes | galactomannan | http://www.glycoepitope.jp/epitopes/EP0510 |
| T2 | 2000-2013 | GlycoEpitope | denotes | galactomannan | http://www.glycoepitope.jp/epitopes/EP0510 |
LitCovid-PD-HP
| Id | Subject | Object | Predicate | Lexical cue | hp_id |
|---|---|---|---|---|---|
| T3 | 59-64 | Phenotype | denotes | fever | http://purl.obolibrary.org/obo/HP_0001945 |
| T4 | 69-74 | Phenotype | denotes | cough | http://purl.obolibrary.org/obo/HP_0012735 |
| T5 | 156-175 | Phenotype | denotes | respiratory failure | http://purl.obolibrary.org/obo/HP_0002878 |
| T6 | 387-403 | Phenotype | denotes | immunodeficiency | http://purl.obolibrary.org/obo/HP_0002721 |
| T7 | 450-460 | Phenotype | denotes | overweight | http://purl.obolibrary.org/obo/HP_0025502 |
| T8 | 495-510 | Phenotype | denotes | type 2 diabetes | http://purl.obolibrary.org/obo/HP_0005978 |
| T9 | 542-552 | Phenotype | denotes | glycosuria | http://purl.obolibrary.org/obo/HP_0003076 |
| T10 | 579-591 | Phenotype | denotes | hypertension | http://purl.obolibrary.org/obo/HP_0000822 |
| T11 | 610-624 | Phenotype | denotes | hypothyroidism | http://purl.obolibrary.org/obo/HP_0000821 |
| T12 | 674-684 | Phenotype | denotes | aspiration | http://purl.obolibrary.org/obo/HP_0002835 |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 70 | 1812-1819 | Species | denotes | patient | Tax:9606 |
| 71 | 1909-1916 | Species | denotes | patient | Tax:9606 |
| 72 | 1996-1998 | Chemical | denotes | GM | MESH:D005839 |
| 73 | 2000-2013 | Chemical | denotes | galactomannan | MESH:C012990 |
| 74 | 2035-2038 | Chemical | denotes | BDG | |
| 75 | 2040-2050 | Chemical | denotes | β-D-glucan | |
| 76 | 1834-1863 | Disease | denotes | invasive pulmonary fusariosis | MESH:D060585 |
| 77 | 1878-1886 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 100 | 123-130 | Species | denotes | patient | Tax:9606 |
| 101 | 335-342 | Species | denotes | patient | Tax:9606 |
| 102 | 626-636 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 103 | 703-710 | Species | denotes | patient | Tax:9606 |
| 104 | 866-873 | Species | denotes | patient | Tax:9606 |
| 105 | 1329-1350 | Species | denotes | Fusarium proliferatum | Tax:948311 |
| 106 | 518-525 | Chemical | denotes | glucose | MESH:D005947 |
| 107 | 1193-1206 | Chemical | denotes | galactomannan | MESH:C012990 |
| 108 | 1428-1442 | Chemical | denotes | amphotericin B | MESH:D000666 |
| 109 | 1682-1694 | Chemical | denotes | voriconazole | MESH:D065819 |
| 110 | 1696-1708 | Chemical | denotes | posaconazole | MESH:C101425 |
| 111 | 1713-1726 | Chemical | denotes | isavuconazole | MESH:C508735 |
| 112 | 1746-1760 | Chemical | denotes | amphotericin B | MESH:D000666 |
| 113 | 59-64 | Disease | denotes | fever | MESH:D005334 |
| 114 | 69-74 | Disease | denotes | cough | MESH:D003371 |
| 115 | 150-175 | Disease | denotes | acute respiratory failure | MESH:D012120 |
| 116 | 377-403 | Disease | denotes | inherited immunodeficiency | MESH:D007153 |
| 117 | 422-441 | Disease | denotes | respiratory disease | MESH:D012140 |
| 118 | 495-510 | Disease | denotes | type 2 diabetes | MESH:D003924 |
| 119 | 542-552 | Disease | denotes | glycosuria | MESH:D006029 |
| 120 | 579-591 | Disease | denotes | hypertension | MESH:D006973 |
| 121 | 610-624 | Disease | denotes | hypothyroidism | MESH:D007037 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T10 | 0-105 | Sentence | denotes | A 57-year-old man was sent to our hospital after 7 days of fever and cough worsening over the last 24 hr. |
| T11 | 106-330 | Sentence | denotes | On admission the patient presented signs of acute respiratory failure and was rapidly transferred to our intensive care unit (ICU) on March 26 (day 1) where he was intubated and placed under mechanical ventilation (Fig. 1 ). |
| T12 | 331-442 | Sentence | denotes | The patient had no history of any acquired or inherited immunodeficiency and no underlying respiratory disease. |
| T13 | 443-625 | Sentence | denotes | He was overweight (body mass index 30.6 kg/m2) with type 2 diabetes (blood glucose 11.6 mmol/L and glycosuria 1.4 mmol/L on admission), hypertension and a substituted hypothyroidism. |
| T14 | 626-698 | Sentence | denotes | SARS-CoV-2 viral RNA was detected in a tracheal aspiration on admission. |
| T15 | 699-784 | Sentence | denotes | The patient's condition worsened with a PaO2/FiO2 ratio <90 mmHg with a FiO2 of 100%. |
| T16 | 785-855 | Sentence | denotes | A protected specimen brush sample performed on day 2 remained sterile. |
| T17 | 856-963 | Sentence | denotes | While the patient's condition showed no improvement, a bronchoalveolar lavage (BAL) was performed on day 7. |
| T18 | 964-1073 | Sentence | denotes | On day 9 this sample grew with 7 × 102/mL colony-forming unit (CFU) of mould while no bacteria were detected. |
| T19 | 1074-1235 | Sentence | denotes | The same day, a second BAL was performed: atypical fungal hyphae were detected on microscopic examination, testing for galactomannan antigen was positive (index: |
| T20 | 1236-1286 | Sentence | denotes | 1.7) and the sample grew with 103/mL CFU of mould. |
| T21 | 1287-1521 | Sentence | denotes | The different cultures were identified as Fusarium proliferatum using mass spectrometry (Bruker Microflex with MSI database) and a liposomal amphotericin B-based therapy was started on day 12 (5 mg/kg/day for 2 days then 7 mg/kg/day). |
| T22 | 1522-1727 | Sentence | denotes | Antifungal susceptibility testing determined using the gradient concentration strips method showed high minimal inhibitory concentrations (MICs) (>32 mg/L) for voriconazole, posaconazole and isavuconazole. |
| T23 | 1728-1772 | Sentence | denotes | The MIC value for amphotericin B was 2 mg/L. |
| T24 | 1773-1887 | Sentence | denotes | Fig. 1 Timeline for an immunocompetent patient who developed invasive pulmonary fusariosis during severe COVID-19. |
| T25 | 1888-1957 | Sentence | denotes | Day 1 is the day the patient was admitted to the intensive care unit. |
| T26 | 1958-2058 | Sentence | denotes | D, days; BAL, bronchoalveolar lavage; GM, galactomannan index determination; BDG, β-D-glucan dosage. |
LitCovid-PMC-OGER-BB
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T22 | 14-17 | NCBITaxon:9606 | denotes | man |
| T23 | 69-74 | UBERON:0001004 | denotes | cough |
| T24 | 156-167 | UBERON:0001004 | denotes | respiratory |
| T25 | 422-433 | UBERON:0001004 | denotes | respiratory |
| T26 | 512-517 | UBERON:0000178 | denotes | blood |
| T27 | 518-525 | CHEBI:17234;CHEBI:17234 | denotes | glucose |
| T28 | 626-636 | SP_7 | denotes | SARS-CoV-2 |
| T29 | 637-642 | NCBITaxon:10239 | denotes | viral |
| T30 | 665-673 | UBERON:0003126 | denotes | tracheal |
| T31 | 771-775 | CHEBI:16526;CHEBI:16526 | denotes | FiO2 |
| T32 | 911-926 | UBERON:0002186 | denotes | bronchoalveolar |
| T33 | 985-989 | GO:0040007 | denotes | grew |
| T34 | 1050-1058 | NCBITaxon:2 | denotes | bacteria |
| T35 | 1193-1206 | CHEBI:27680;CHEBI:27680 | denotes | galactomannan |
| T36 | 1207-1214 | CHEBI:59132;CHEBI:59132 | denotes | antigen |
| T37 | 1256-1260 | GO:0040007 | denotes | grew |
| T38 | 1329-1350 | NCBITaxon:948311 | denotes | Fusarium proliferatum |
| T39 | 1428-1442 | CHEBI:2682;CHEBI:2682 | denotes | amphotericin B |
| T40 | 1682-1694 | CHEBI:10023;CHEBI:10023 | denotes | voriconazole |
| T41 | 1696-1708 | CHEBI:64355;CHEBI:64355 | denotes | posaconazole |
| T42 | 1713-1726 | CHEBI:85979;CHEBI:85979 | denotes | isavuconazole |
| T43 | 1732-1735 | SO:0000154 | denotes | MIC |
| T44 | 1746-1760 | CHEBI:2682;CHEBI:2682 | denotes | amphotericin B |
| T45 | 1843-1852 | UBERON:0002048 | denotes | pulmonary |
| T46 | 1878-1886 | SP_7 | denotes | COVID-19 |
| T47 | 1947-1956 | UBERON:0007221 | denotes | care unit |
| T48 | 1972-1987 | UBERON:0002186 | denotes | bronchoalveolar |
| T49 | 2000-2013 | CHEBI:27680;CHEBI:27680 | denotes | galactomannan |
| T50 | 2044-2050 | CHEBI:28793;CHEBI:28793 | denotes | glucan |
| T84384 | 14-17 | NCBITaxon:9606 | denotes | man |
| T13089 | 69-74 | UBERON:0001004 | denotes | cough |
| T29928 | 156-167 | UBERON:0001004 | denotes | respiratory |
| T68878 | 422-433 | UBERON:0001004 | denotes | respiratory |
| T86378 | 512-517 | UBERON:0000178 | denotes | blood |
| T94726 | 518-525 | CHEBI:17234;CHEBI:17234 | denotes | glucose |
| T78314 | 626-636 | SP_7 | denotes | SARS-CoV-2 |
| T40427 | 637-642 | NCBITaxon:10239 | denotes | viral |
| T2505 | 665-673 | UBERON:0003126 | denotes | tracheal |
| T67814 | 771-775 | CHEBI:16526;CHEBI:16526 | denotes | FiO2 |
| T97680 | 911-926 | UBERON:0002186 | denotes | bronchoalveolar |
| T41320 | 985-989 | GO:0040007 | denotes | grew |
| T29670 | 1050-1058 | NCBITaxon:2 | denotes | bacteria |
| T41230 | 1193-1206 | CHEBI:27680;CHEBI:27680 | denotes | galactomannan |
| T76288 | 1207-1214 | CHEBI:59132;CHEBI:59132 | denotes | antigen |
| T91801 | 1256-1260 | GO:0040007 | denotes | grew |
| T24803 | 1329-1350 | NCBITaxon:948311 | denotes | Fusarium proliferatum |
| T75536 | 1428-1442 | CHEBI:2682;CHEBI:2682 | denotes | amphotericin B |
| T7769 | 1682-1694 | CHEBI:10023;CHEBI:10023 | denotes | voriconazole |
| T37012 | 1696-1708 | CHEBI:64355;CHEBI:64355 | denotes | posaconazole |
| T51161 | 1713-1726 | CHEBI:85979;CHEBI:85979 | denotes | isavuconazole |
| T30376 | 1732-1735 | SO:0000154 | denotes | MIC |
| T19946 | 1746-1760 | CHEBI:2682;CHEBI:2682 | denotes | amphotericin B |
| T13465 | 1843-1852 | UBERON:0002048 | denotes | pulmonary |
| T81946 | 1878-1886 | SP_7 | denotes | COVID-19 |
| T88494 | 1947-1956 | UBERON:0007221 | denotes | care unit |
| T46519 | 1972-1987 | UBERON:0002186 | denotes | bronchoalveolar |
| T16525 | 2000-2013 | CHEBI:27680;CHEBI:27680 | denotes | galactomannan |
| T97325 | 2044-2050 | CHEBI:28793;CHEBI:28793 | denotes | glucan |
| T53 | 1947-1956 | UBERON:0007221 | denotes | care unit |
| T54 | 1972-1987 | UBERON:0002186 | denotes | bronchoalveolar |
| T55 | 2000-2013 | CHEBI:27680;CHEBI:27680 | denotes | galactomannan |
| T56 | 2044-2050 | CHEBI:28793;CHEBI:28793 | denotes | glucan |