PMC:7340597 / 4101-5681
Annnotations
LitCovid_Glycan-Motif-Structure
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T2 | 771-778 | https://glytoucan.org/Structures/Glycans/G00021MO | denotes | heparin |
| T3 | 771-778 | https://glytoucan.org/Structures/Glycans/G54161DR | denotes | heparin |
| T4 | 1061-1074 | https://glytoucan.org/Structures/Glycans/G93424OB | denotes | galactomannan |
| T5 | 1130-1143 | https://glytoucan.org/Structures/Glycans/G93424OB | denotes | galactomannan |
| T6 | 1145-1147 | https://glytoucan.org/Structures/Glycans/G93424OB | denotes | GM |
| T7 | 1499-1501 | https://glytoucan.org/Structures/Glycans/G93424OB | denotes | GM |
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T10 | 292-296 | Body_part | denotes | lung | http://purl.org/sig/ont/fma/fma7195 |
| T11 | 447-453 | Body_part | denotes | sputum | http://purl.org/sig/ont/fma/fma312401 |
| T12 | 545-560 | Body_part | denotes | digestive tract | http://purl.org/sig/ont/fma/fma317863 |
| T13 | 771-778 | Body_part | denotes | heparin | http://purl.org/sig/ont/fma/fma82839 |
| T14 | 1076-1081 | Body_part | denotes | serum | http://purl.org/sig/ont/fma/fma63083 |
| T15 | 1086-1092 | Body_part | denotes | sputum | http://purl.org/sig/ont/fma/fma312401 |
| T16 | 1535-1540 | Body_part | denotes | serum | http://purl.org/sig/ont/fma/fma63083 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T7 | 292-296 | Body_part | denotes | lung | http://purl.obolibrary.org/obo/UBERON_0002048 |
| T8 | 447-453 | Body_part | denotes | sputum | http://purl.obolibrary.org/obo/UBERON_0007311 |
| T9 | 545-560 | Body_part | denotes | digestive tract | http://purl.obolibrary.org/obo/UBERON_0001555 |
| T10 | 1076-1081 | Body_part | denotes | serum | http://purl.obolibrary.org/obo/UBERON_0001977 |
| T11 | 1086-1092 | Body_part | denotes | sputum | http://purl.obolibrary.org/obo/UBERON_0007311 |
| T12 | 1535-1540 | Body_part | denotes | serum | http://purl.obolibrary.org/obo/UBERON_0001977 |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 171 | 37-45 | Species | denotes | patients | Tax:9606 |
| 172 | 72-119 | Species | denotes | severe acute respiratory syndrome coronavirus 2 | Tax:2697049 |
| 173 | 121-131 | Species | denotes | SARS-COV-2 | Tax:2697049 |
| 174 | 346-356 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 175 | 1400-1408 | Species | denotes | patients | Tax:9606 |
| 176 | 1545-1556 | Species | denotes | Aspergillus | Tax:746128 |
| 177 | 584-595 | Chemical | denotes | chloroquine | MESH:D002738 |
| 178 | 771-778 | Chemical | denotes | heparin | MESH:D006493 |
| 179 | 780-784 | Chemical | denotes | LMWH | MESH:D006495 |
| 180 | 787-797 | Chemical | denotes | nadroparin | MESH:D017762 |
| 181 | 1061-1074 | Chemical | denotes | galactomannan | MESH:C012990 |
| 182 | 1130-1143 | Chemical | denotes | galactomannan | MESH:C012990 |
| 183 | 1145-1147 | Chemical | denotes | GM | MESH:C012990 |
| 184 | 1499-1501 | Chemical | denotes | GM | MESH:C012990 |
| 185 | 176-195 | Disease | denotes | respiratory failure | MESH:D012131 |
| 186 | 875-898 | Disease | denotes | pulmonary aspergillosis | MESH:D055732 |
| 187 | 960-983 | Disease | denotes | Pulmonary aspergillosis | MESH:D055732 |
| 188 | 1304-1327 | Disease | denotes | pulmonary aspergillosis | MESH:D055732 |
| 189 | 1460-1469 | Disease | denotes | infection | MESH:D007239 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T60 | 72-119 | Disease | denotes | severe acute respiratory syndrome coronavirus 2 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T61 | 72-105 | Disease | denotes | severe acute respiratory syndrome | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T62 | 121-125 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T63 | 176-195 | Disease | denotes | respiratory failure | http://purl.obolibrary.org/obo/MONDO_0021113 |
| T64 | 346-354 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T65 | 885-898 | Disease | denotes | aspergillosis | http://purl.obolibrary.org/obo/MONDO_0005657 |
| T66 | 970-983 | Disease | denotes | aspergillosis | http://purl.obolibrary.org/obo/MONDO_0005657 |
| T67 | 1283-1292 | Disease | denotes | influenza | http://purl.obolibrary.org/obo/MONDO_0005812 |
| T68 | 1314-1327 | Disease | denotes | aspergillosis | http://purl.obolibrary.org/obo/MONDO_0005657 |
| T69 | 1414-1418 | Disease | denotes | CAPA | http://purl.obolibrary.org/obo/MONDO_0007163 |
| T70 | 1460-1469 | Disease | denotes | infection | http://purl.obolibrary.org/obo/MONDO_0005550 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T23 | 204-206 | http://purl.obolibrary.org/obo/CLO_0050507 | denotes | 22 |
| T24 | 292-296 | http://purl.obolibrary.org/obo/UBERON_0002048 | denotes | lung |
| T25 | 292-296 | http://www.ebi.ac.uk/efo/EFO_0000934 | denotes | lung |
| T26 | 545-560 | http://purl.obolibrary.org/obo/UBERON_0001555 | denotes | digestive tract |
| T27 | 863-870 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | testing |
| T28 | 1149-1156 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | testing |
| T29 | 1261-1262 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T30 | 1497-1498 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T3 | 584-595 | Chemical | denotes | chloroquine | http://purl.obolibrary.org/obo/CHEBI_3638 |
| T4 | 771-778 | Chemical | denotes | heparin | http://purl.obolibrary.org/obo/CHEBI_28304 |
| T5 | 801-803 | Chemical | denotes | IE | http://purl.obolibrary.org/obo/CHEBI_137259 |
| T6 | 1061-1074 | Chemical | denotes | galactomannan | http://purl.obolibrary.org/obo/CHEBI_27680 |
| T7 | 1130-1143 | Chemical | denotes | galactomannan | http://purl.obolibrary.org/obo/CHEBI_27680 |
| T8 | 1145-1147 | Chemical | denotes | GM | http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680 |
| T10 | 1186-1189 | Chemical | denotes | BAL | http://purl.obolibrary.org/obo/CHEBI_64198 |
| T11 | 1218-1225 | Chemical | denotes | antigen | http://purl.obolibrary.org/obo/CHEBI_59132 |
| T12 | 1499-1501 | Chemical | denotes | GM | http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680 |
| T14 | 1517-1520 | Chemical | denotes | BAL | http://purl.obolibrary.org/obo/CHEBI_64198 |
| T15 | 1576-1579 | Chemical | denotes | BAL | http://purl.obolibrary.org/obo/CHEBI_64198 |
LitCovid-PD-HP
| Id | Subject | Object | Predicate | Lexical cue | hp_id |
|---|---|---|---|---|---|
| T12 | 176-195 | Phenotype | denotes | respiratory failure | http://purl.obolibrary.org/obo/HP_0002878 |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T1 | 387-408 | http://purl.obolibrary.org/obo/GO_0001171 | denotes | reverse transcription |
| T2 | 395-408 | http://purl.obolibrary.org/obo/GO_0006351 | denotes | transcription |
LitCovid-PD-GlycoEpitope
| Id | Subject | Object | Predicate | Lexical cue | glyco_epitope_db_id |
|---|---|---|---|---|---|
| T2 | 1061-1074 | GlycoEpitope | denotes | galactomannan | http://www.glycoepitope.jp/epitopes/EP0510 |
| T3 | 1130-1143 | GlycoEpitope | denotes | galactomannan | http://www.glycoepitope.jp/epitopes/EP0510 |
| T4 | 1145-1147 | GlycoEpitope | denotes | GM | http://www.glycoepitope.jp/epitopes/EP0510 |
| T5 | 1499-1501 | GlycoEpitope | denotes | GM | http://www.glycoepitope.jp/epitopes/EP0510 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T36 | 0-32 | Sentence | denotes | 2.1 Study population and design |
| T37 | 33-345 | Sentence | denotes | All patients with laboratory confirmed severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) admitted to the ICU due to acute hypoxemic respiratory failure between 22 March 2020 and 30 April 2020 and with available postmortem needle core biopsy of the lung were eligible for inclusion in this case series. |
| T38 | 346-481 | Sentence | denotes | SARS-CoV-2 was diagnosed using real-time reverse transcription polymerase chain reaction (RT-PCR) on sputum and/or bronchial aspirates. |
| T39 | 482-820 | Sentence | denotes | Routine ICU management included, among other things, selective digestive tract decontamination (SDD), chloroquine until the Dutch National Institute for Public Health and Environment advised against its use at the end of March 2020, and high dose anticoagulation with low-molecular-weight heparin (LMWH) (nadroparin 87 IE/kg twice daily). |
| T40 | 821-959 | Sentence | denotes | Bronchoscopy, with or without lavage, and testing for pulmonary aspergillosis were performed at the discretion of the attending physician. |
| T41 | 960-1125 | Sentence | denotes | Pulmonary aspergillosis was diagnosed using clinical, radiological and mycological data and included galactomannan (serum and sputum), tracheal or bronchial culture. |
| T42 | 1126-1250 | Sentence | denotes | For galactomannan (GM) testing from bronchoalveolar lavage (BAL) fluid Platelia Aspergillis antigen ELISA (Biorad) was used. |
| T43 | 1251-1424 | Sentence | denotes | Recently, a case definition for influenza associated pulmonary aspergillosis (IAPA) was proposed by an expert panel, which could be used to classify patients with CAPA [14]. |
| T44 | 1425-1580 | Sentence | denotes | Diagnostic criteria include proven infection with clinical symptoms and a GM index of ≥1 on BAL or of ≥0ꞏ5 on serum; or Aspergillus spp. cultured from BAL. |
LitCovid-PMC-OGER-BB
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T52 | 72-84 | SP_7 | denotes | severe acute |
| T53 | 85-96 | SP_7;UBERON:0001004 | denotes | respiratory |
| T54 | 97-119 | SP_7 | denotes | syndrome coronavirus 2 |
| T55 | 121-131 | SP_7 | denotes | SARS-COV-2 |
| T56 | 176-187 | UBERON:0001004 | denotes | respiratory |
| T57 | 255-265 | GO:0016265 | denotes | postmortem |
| T58 | 292-296 | UBERON:0002048 | denotes | lung |
| T59 | 346-356 | SP_7 | denotes | SARS-CoV-2 |
| T60 | 387-408 | GO:0001171 | denotes | reverse transcription |
| T61 | 447-453 | UBERON:0007311 | denotes | sputum |
| T62 | 461-470 | UBERON:0004242 | denotes | bronchial |
| T63 | 545-554 | GO:0007586;UBERON:0001555 | denotes | digestive |
| T64 | 555-560 | UBERON:0001555 | denotes | tract |
| T65 | 584-595 | CHEBI:3638;DG_10;CHEBI:3638 | denotes | chloroquine |
| T66 | 729-744 | GO:0050817 | denotes | anticoagulation |
| T67 | 771-778 | CHEBI:24505;CHEBI:24505 | denotes | heparin |
| T68 | 875-884 | UBERON:0002048 | denotes | pulmonary |
| T69 | 960-969 | UBERON:0002048 | denotes | Pulmonary |
| T70 | 1061-1074 | CHEBI:27680;CHEBI:27680 | denotes | galactomannan |
| T71 | 1076-1081 | UBERON:0001977 | denotes | serum |
| T72 | 1086-1092 | UBERON:0007311 | denotes | sputum |
| T73 | 1095-1103 | UBERON:0003126 | denotes | tracheal |
| T74 | 1107-1116 | UBERON:0004242 | denotes | bronchial |
| T75 | 1130-1143 | CHEBI:27680;CHEBI:27680 | denotes | galactomannan |
| T76 | 1162-1177 | UBERON:0002031 | denotes | bronchoalveolar |
| T77 | 1178-1184 | UBERON:0004821 | denotes | lavage |
| T78 | 1218-1225 | CHEBI:59132;CHEBI:59132 | denotes | antigen |
| T79 | 1304-1313 | UBERON:0002048 | denotes | pulmonary |
| T80 | 1535-1540 | UBERON:0001977 | denotes | serum |
| T81 | 1545-1556 | NCBITaxon:5052 | denotes | Aspergillus |
| T30595 | 87-93 | UBERON:0000170 | denotes | spirat |
| T75123 | 126-134 | CHEBI:16842;CHEBI:16842 | denotes | COV-2) a |
| T96536 | 187-198 | CHEBI:51686;CHEBI:51686 | denotes | failure be |
| T48493 | 210-211 | CHEBI:51686;CHEBI:51686 | denotes | c |
| T9930 | 220-233 | CHEBI:29149;CHEBI:29149 | denotes | d 30 April 20 |
| T72105 | 643-653 | GO:0016265 | denotes | ealth and |
| T2841 | 680-685 | UBERON:0000170 | denotes | its |
| T58291 | 821-830 | UBERON:0002048 | denotes | Bronchosc |
| T96902 | 857-873 | CHEBI:35705;CHEBI:35705 | denotes | , and testing fo |
| T96250 | 942-954 | CHEBI:8378;CHEBI:8378 | denotes | ending physi |
| T21854 | 1067-1072 | GO:0016265 | denotes | omann |
| T57492 | 1223-1232 | UBERON:0002048 | denotes | en ELISA |
| T41634 | 1466-1478 | CHEBI:10023;CHEBI:10023 | denotes | ion with cli |
| T55502 | 1544-1559 | CHEBI:50858;CHEBI:50858 | denotes | Aspergillus sp |
| T68620 | 1567-1579 | CHEBI:8378;CHEBI:8378 | denotes | red from BAL |