PMC:7340597 / 19065-21011
Annnotations
LitCovid_Glycan-Motif-Structure
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T22 | 393-395 | https://glytoucan.org/Structures/Glycans/G93424OB | denotes | GM |
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T113 | 512-517 | Body_part | denotes | Chest | http://purl.org/sig/ont/fma/fma9576 |
| T114 | 872-876 | Body_part | denotes | head | http://purl.org/sig/ont/fma/fma7154 |
| T115 | 1178-1182 | Body_part | denotes | lung | http://purl.org/sig/ont/fma/fma7195 |
| T116 | 1245-1253 | Body_part | denotes | alveolar | http://purl.org/sig/ont/fma/fma264783 |
| T117 | 1269-1281 | Body_part | denotes | fibroblastic | http://purl.org/sig/ont/fma/fma63877 |
| T118 | 1282-1288 | Body_part | denotes | tissue | http://purl.org/sig/ont/fma/fma9637 |
| T119 | 1626-1634 | Body_part | denotes | alveolar | http://purl.org/sig/ont/fma/fma264783 |
| T120 | 1671-1684 | Body_part | denotes | blood vessels | http://purl.org/sig/ont/fma/fma63183 |
| T121 | 1671-1676 | Body_part | denotes | blood | http://purl.org/sig/ont/fma/fma9670 |
| T122 | 1754-1765 | Body_part | denotes | eosinophils | http://purl.org/sig/ont/fma/fma62861 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T67 | 512-517 | Body_part | denotes | Chest | http://purl.obolibrary.org/obo/UBERON_0001443 |
| T68 | 872-876 | Body_part | denotes | head | http://purl.obolibrary.org/obo/UBERON_0000033 |
| T69 | 1178-1182 | Body_part | denotes | lung | http://purl.obolibrary.org/obo/UBERON_0002048 |
| T70 | 1282-1288 | Body_part | denotes | tissue | http://purl.obolibrary.org/obo/UBERON_0000479 |
| T71 | 1394-1401 | Body_part | denotes | exudate | http://purl.obolibrary.org/obo/UBERON_0007780 |
| T72 | 1671-1684 | Body_part | denotes | blood vessels | http://purl.obolibrary.org/obo/UBERON_0001981 |
| T73 | 1671-1676 | Body_part | denotes | blood | http://purl.obolibrary.org/obo/UBERON_0000178 |
| T74 | 1677-1684 | Body_part | denotes | vessels | http://purl.obolibrary.org/obo/UBERON_0000055 |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 437 | 45-54 | Disease | denotes | pneumonia | MESH:D011014 |
| 450 | 199-206 | Species | denotes | Patient | Tax:9606 |
| 451 | 409-430 | Species | denotes | Aspergillus fumigatus | Tax:746128 |
| 452 | 799-806 | Species | denotes | patient | Tax:9606 |
| 453 | 1087-1094 | Species | denotes | patient | Tax:9606 |
| 454 | 435-447 | Species | denotes | Enterococcus | Tax:1351 |
| 455 | 393-395 | Chemical | denotes | GM | MESH:C012990 |
| 456 | 101-124 | Disease | denotes | cardiopulmonary disease | MESH:D006323 |
| 457 | 179-184 | Disease | denotes | fever | MESH:D005334 |
| 458 | 189-197 | Disease | denotes | dyspnoea | MESH:D004417 |
| 459 | 340-349 | Disease | denotes | infection | MESH:D007239 |
| 460 | 550-566 | Disease | denotes | pulmonary emboli | MESH:D011655 |
| 461 | 894-923 | Disease | denotes | bilateral cerebellar ischemia | MESH:D007511 |
| 466 | 1178-1189 | Disease | denotes | lung injury | MESH:D055370 |
| 467 | 1328-1337 | Disease | denotes | pneumonia | MESH:D011014 |
| 468 | 1496-1505 | Disease | denotes | pneumonia | MESH:D011014 |
| 469 | 1920-1929 | Disease | denotes | pneumonia | MESH:D011014 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T158 | 34-54 | Disease | denotes | organizing pneumonia | http://purl.obolibrary.org/obo/MONDO_0015265|http://purl.obolibrary.org/obo/MONDO_0056821 |
| T160 | 45-54 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
| T161 | 101-124 | Disease | denotes | cardiopulmonary disease | http://purl.obolibrary.org/obo/MONDO_0004596 |
| T162 | 340-349 | Disease | denotes | infection | http://purl.obolibrary.org/obo/MONDO_0005550 |
| T163 | 767-781 | Disease | denotes | bronchiectasis | http://purl.obolibrary.org/obo/MONDO_0004822 |
| T164 | 915-923 | Disease | denotes | ischemia | http://purl.obolibrary.org/obo/MONDO_0005053 |
| T165 | 1183-1189 | Disease | denotes | injury | http://purl.obolibrary.org/obo/MONDO_0021178 |
| T166 | 1317-1337 | Disease | denotes | organizing pneumonia | http://purl.obolibrary.org/obo/MONDO_0015265|http://purl.obolibrary.org/obo/MONDO_0056821 |
| T168 | 1328-1337 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
| T169 | 1485-1505 | Disease | denotes | organizing pneumonia | http://purl.obolibrary.org/obo/MONDO_0015265|http://purl.obolibrary.org/obo/MONDO_0056821 |
| T171 | 1496-1505 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
| T172 | 1791-1794 | Disease | denotes | PAS | http://purl.obolibrary.org/obo/MONDO_0004277 |
| T173 | 1909-1929 | Disease | denotes | organizing pneumonia | http://purl.obolibrary.org/obo/MONDO_0015265|http://purl.obolibrary.org/obo/MONDO_0056821 |
| T175 | 1920-1929 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T168 | 34-44 | http://purl.obolibrary.org/obo/OBI_0000245 | denotes | organizing |
| T169 | 55-56 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T170 | 69-73 | http://purl.obolibrary.org/obo/UBERON_0003101 | denotes | male |
| T171 | 69-73 | http://www.ebi.ac.uk/efo/EFO_0000970 | denotes | male |
| T172 | 153-154 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T173 | 382-383 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T174 | 512-517 | http://www.ebi.ac.uk/efo/EFO_0000965 | denotes | Chest |
| T175 | 872-876 | http://purl.obolibrary.org/obo/UBERON_0000033 | denotes | head |
| T176 | 872-876 | http://www.ebi.ac.uk/efo/EFO_0000964 | denotes | head |
| T177 | 1165-1166 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T178 | 1178-1182 | http://purl.obolibrary.org/obo/UBERON_0002048 | denotes | lung |
| T179 | 1178-1182 | http://www.ebi.ac.uk/efo/EFO_0000934 | denotes | lung |
| T180 | 1269-1281 | http://purl.obolibrary.org/obo/CL_0000057 | denotes | fibroblastic |
| T181 | 1317-1327 | http://purl.obolibrary.org/obo/OBI_0000245 | denotes | organizing |
| T182 | 1348-1349 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T183 | 1485-1495 | http://purl.obolibrary.org/obo/OBI_0000245 | denotes | organizing |
| T184 | 1538-1539 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T185 | 1671-1684 | http://purl.obolibrary.org/obo/UBERON_0001981 | denotes | blood vessels |
| T186 | 1671-1684 | http://www.ebi.ac.uk/efo/EFO_0000817 | denotes | blood vessels |
| T187 | 1730-1739 | http://purl.obolibrary.org/obo/UBERON_0000158 | denotes | membranes |
| T188 | 1909-1919 | http://purl.obolibrary.org/obo/OBI_0000245 | denotes | organizing |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T103 | 69-73 | Chemical | denotes | male | http://purl.obolibrary.org/obo/CHEBI_30780 |
| T104 | 147-149 | Chemical | denotes | ED | http://purl.obolibrary.org/obo/CHEBI_73503 |
| T105 | 351-354 | Chemical | denotes | BAL | http://purl.obolibrary.org/obo/CHEBI_64198 |
| T106 | 393-395 | Chemical | denotes | GM | http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680 |
| T108 | 848-856 | Chemical | denotes | sedative | http://purl.obolibrary.org/obo/CHEBI_35717 |
| T109 | 1791-1794 | Chemical | denotes | PAS | http://purl.obolibrary.org/obo/CHEBI_27565 |
LitCovid-PD-HP
| Id | Subject | Object | Predicate | Lexical cue | hp_id |
|---|---|---|---|---|---|
| T48 | 45-54 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
| T49 | 179-184 | Phenotype | denotes | fever | http://purl.obolibrary.org/obo/HP_0001945 |
| T50 | 189-197 | Phenotype | denotes | dyspnoea | http://purl.obolibrary.org/obo/HP_0002094 |
| T51 | 767-781 | Phenotype | denotes | bronchiectasis | http://purl.obolibrary.org/obo/HP_0002110 |
| T52 | 1328-1337 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
| T53 | 1496-1505 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
| T54 | 1920-1929 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
LitCovid-PD-GlycoEpitope
| Id | Subject | Object | Predicate | Lexical cue | glyco_epitope_db_id |
|---|---|---|---|---|---|
| T20 | 393-395 | GlycoEpitope | denotes | GM | http://www.glycoepitope.jp/epitopes/EP0510 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T161 | 0-54 | Sentence | denotes | 3.5 Case 4 – Acute fibrinous and organizing pneumonia |
| T162 | 55-198 | Sentence | denotes | A 68-year old male without medical history of cardiopulmonary disease, was presented at the ED in a critical condition with fever and dyspnoea. |
| T163 | 199-318 | Sentence | denotes | Patient was in need of endotracheal intubation and mechanical ventilation in prone position to improve his oxygenation. |
| T164 | 319-456 | Sentence | denotes | To exclude secondary infection, BAL was performed and revealed a positive GM and cultured Aspergillus fumigatus and Enterococcus faecium. |
| T165 | 457-511 | Sentence | denotes | Antifungal therapy was added to his treatment regimen. |
| T166 | 512-706 | Sentence | denotes | Chest CT-angiography showed segmental pulmonary emboli along with extensive bilateral areas of ground-glass opacity with reticulation and multiple patchy non-dependant peripheral consolidations. |
| T167 | 707-794 | Sentence | denotes | In contrast to normal areas, the abnormal areas showed mild bronchiectasis (Fig. 1-4A). |
| T168 | 795-868 | Sentence | denotes | The patient remained unresponsive after cessation of sedative medication. |
| T169 | 869-959 | Sentence | denotes | CT head showed extensive bilateral cerebellar ischemia with small haemorrhagic components. |
| T170 | 960-1082 | Sentence | denotes | After three weeks of mechanical ventilation his respiratory status worsened and treatment was ended due to poor prognosis. |
| T171 | 1083-1140 | Sentence | denotes | The patient passed away 21 days after hospital admission. |
| T172 | 1141-1238 | Sentence | denotes | Biopsy specimens showed a pattern of lung injury, that was partially identical to that of case 1. |
| T173 | 1239-1338 | Sentence | denotes | Intra-alveolar depositions of fibroblastic tissue were found, consistent with organizing pneumonia. |
| T174 | 1339-1506 | Sentence | denotes | However, a predominant, diffuse component of fibrinous exudate in the alveoli was present, which was not the case in the aforementioned case with organizing pneumonia. |
| T175 | 1507-1641 | Sentence | denotes | Other histologic findings were a chronic inflammatory infiltrate, and mild interstitial changes, including widening of alveolar septa. |
| T176 | 1642-1704 | Sentence | denotes | Microthrombi in small septal blood vessels were also observed. |
| T177 | 1705-1779 | Sentence | denotes | Neither remnants hyaline membranes nor prominent eosinophils were present. |
| T178 | 1780-1826 | Sentence | denotes | Additional PAS-D stain did not show any fungi. |
| T179 | 1827-1946 | Sentence | denotes | The overall histologic pattern of this case was classified as acute fibrinous and organizing pneumonia (AFOP), Fig. 2D. |
LitCovid-PMC-OGER-BB
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T31499 | 222-234 | UBERON:0001852 | denotes | endotracheal |
| T16403 | 306-317 | GO:0015671 | denotes | oxygenation |
| T14517 | 409-430 | NCBITaxon:746128 | denotes | Aspergillus fumigatus |
| T4434 | 435-455 | NCBITaxon:1352 | denotes | Enterococcus faecium |
| T32949 | 550-559 | UBERON:0002048 | denotes | pulmonary |
| T23048 | 872-876 | UBERON:0000033 | denotes | head |
| T39092 | 904-914 | UBERON:0002037 | denotes | cerebellar |
| T74431 | 1008-1019 | UBERON:0001004 | denotes | respiratory |
| T28835 | 1178-1182 | UBERON:0002048 | denotes | lung |
| T46508 | 1245-1253 | UBERON:0003215 | denotes | alveolar |
| T32950 | 1269-1281 | CL:0000057 | denotes | fibroblastic |
| T85905 | 1282-1288 | UBERON:0000479 | denotes | tissue |
| T72453 | 1409-1416 | UBERON:0003215 | denotes | alveoli |
| T83892 | 1582-1594 | UBERON:0005169 | denotes | interstitial |
| T50871 | 1626-1634 | UBERON:0003215 | denotes | alveolar |
| T65185 | 1635-1640 | UBERON:0003037 | denotes | septa |
| T3448 | 1664-1670 | UBERON:0003037 | denotes | septal |
| T58151 | 1671-1684 | UBERON:0001981 | denotes | blood vessels |
| T66331 | 1730-1739 | GO:0016020 | denotes | membranes |
| T96825 | 1754-1765 | CL:0000771 | denotes | eosinophils |
| T62230 | 1820-1825 | NCBITaxon:4751 | denotes | fungi |