PMC:7543426 / 11102-12515
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T66 | 18-22 | Body_part | denotes | lung | http://purl.org/sig/ont/fma/fma7195 |
| T67 | 250-258 | Body_part | denotes | alveolar | http://purl.org/sig/ont/fma/fma264783 |
| T68 | 324-334 | Body_part | denotes | pneumocyte | http://purl.org/sig/ont/fma/fma62499 |
| T69 | 360-369 | Body_part | denotes | cytoplasm | http://purl.org/sig/ont/fma/fma66835 |
| T70 | 483-495 | Body_part | denotes | Fibroblastic | http://purl.org/sig/ont/fma/fma63877 |
| T71 | 532-549 | Body_part | denotes | connective tissue | http://purl.org/sig/ont/fma/fma9640 |
| T72 | 564-577 | Body_part | denotes | alveolar duct | http://purl.org/sig/ont/fma/fma7341 |
| T73 | 813-818 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T74 | 833-845 | Body_part | denotes | granulocytes | http://purl.org/sig/ont/fma/fma62854 |
| T75 | 890-901 | Body_part | denotes | macrophages | http://purl.org/sig/ont/fma/fma63261 |
| T76 | 950-963 | Body_part | denotes | T lymphocytes | http://purl.org/sig/ont/fma/fma62870 |
| T77 | 989-997 | Body_part | denotes | alveolar | http://purl.org/sig/ont/fma/fma264783 |
| T78 | 1026-1035 | Body_part | denotes | capillary | http://purl.org/sig/ont/fma/fma63194 |
| T79 | 1128-1141 | Body_part | denotes | T lymphocytes | http://purl.org/sig/ont/fma/fma62870 |
| T80 | 1187-1198 | Body_part | denotes | lymphocytes | http://purl.org/sig/ont/fma/fma62863 |
| T81 | 1248-1261 | Body_part | denotes | B lymphocytes | http://purl.org/sig/ont/fma/fma62869 |
| T82 | 1332-1340 | Body_part | denotes | platelet | http://purl.org/sig/ont/fma/fma62851 |
| T83 | 1356-1370 | Body_part | denotes | megakaryocytes | http://purl.org/sig/ont/fma/fma83555 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T49 | 18-22 | Body_part | denotes | lung | http://purl.obolibrary.org/obo/UBERON_0002048 |
| T50 | 532-549 | Body_part | denotes | connective tissue | http://purl.obolibrary.org/obo/UBERON_0002384 |
| T51 | 543-549 | Body_part | denotes | tissue | http://purl.obolibrary.org/obo/UBERON_0000479 |
| T52 | 573-577 | Body_part | denotes | duct | http://purl.obolibrary.org/obo/UBERON_0000058 |
| T53 | 1026-1035 | Body_part | denotes | capillary | http://purl.obolibrary.org/obo/UBERON_0001982 |
| T54 | 1036-1043 | Body_part | denotes | vessels | http://purl.obolibrary.org/obo/UBERON_0000055 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T116 | 140-152 | Disease | denotes | inflammation | http://purl.obolibrary.org/obo/MONDO_0021166 |
| T117 | 277-297 | Disease | denotes | Organizing pneumonia | http://purl.obolibrary.org/obo/MONDO_0015265|http://purl.obolibrary.org/obo/MONDO_0056821 |
| T119 | 288-297 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
| T120 | 335-346 | Disease | denotes | hyperplasia | http://purl.obolibrary.org/obo/MONDO_0005043 |
| T121 | 693-699 | Disease | denotes | injury | http://purl.obolibrary.org/obo/MONDO_0021178 |
| T122 | 731-741 | Disease | denotes | vasculitis | http://purl.obolibrary.org/obo/MONDO_0018882 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T144 | 0-1 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T145 | 18-22 | http://purl.obolibrary.org/obo/UBERON_0002048 | denotes | lung |
| T146 | 18-22 | http://www.ebi.ac.uk/efo/EFO_0000934 | denotes | lung |
| T147 | 161-164 | http://purl.obolibrary.org/obo/CLO_0001146 | denotes | 1A2 |
| T148 | 188-197 | http://purl.obolibrary.org/obo/UBERON_0000158 | denotes | membranes |
| T149 | 227-228 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T150 | 277-287 | http://purl.obolibrary.org/obo/OBI_0000245 | denotes | Organizing |
| T151 | 439-444 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
| T152 | 483-495 | http://purl.obolibrary.org/obo/CL_0000057 | denotes | Fibroblastic |
| T153 | 521-531 | http://purl.obolibrary.org/obo/OBI_0000245 | denotes | organizing |
| T154 | 532-549 | http://purl.obolibrary.org/obo/UBERON_0002384 | denotes | connective tissue |
| T155 | 532-549 | http://www.ebi.ac.uk/efo/EFO_0000952 | denotes | connective tissue |
| T156 | 573-577 | http://purl.obolibrary.org/obo/UBERON_0000025 | denotes | duct |
| T157 | 573-577 | http://purl.obolibrary.org/obo/UBERON_0000058 | denotes | duct |
| T158 | 750-753 | http://purl.obolibrary.org/obo/CLO_0054085 | denotes | 1B3 |
| T159 | 756-757 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T160 | 813-818 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T161 | 884-887 | http://purl.obolibrary.org/obo/CLO_0001146 | denotes | 1A2 |
| T162 | 903-907 | http://purl.obolibrary.org/obo/PR_000002064 | denotes | CD68 |
| T163 | 965-968 | http://purl.obolibrary.org/obo/CLO_0052882 | denotes | CD3 |
| T164 | 965-968 | http://purl.obolibrary.org/obo/CLO_0053434 | denotes | CD3 |
| T165 | 1036-1043 | http://purl.obolibrary.org/obo/UBERON_0000055 | denotes | vessels |
| T166 | 1114-1117 | http://purl.obolibrary.org/obo/PR_000001004 | denotes | CD4 |
| T167 | 1123-1126 | http://purl.obolibrary.org/obo/CLO_0053438 | denotes | CD8 |
| T168 | 1172-1175 | http://purl.obolibrary.org/obo/CLO_0054085 | denotes | 1B3 |
| T169 | 1248-1249 | http://purl.obolibrary.org/obo/CLO_0001021 | denotes | B |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 333 | 847-851 | Gene | denotes | CD15 | Gene:2526 |
| 334 | 903-907 | Gene | denotes | CD68 | Gene:968 |
| 335 | 1114-1117 | Gene | denotes | CD4 | Gene:920 |
| 336 | 1123-1126 | Gene | denotes | CD8 | Gene:925 |
| 337 | 1204-1208 | Gene | denotes | CD20 | Gene:54474 |
| 338 | 1408-1411 | Gene | denotes | 1B4 | Gene:8847 |
| 339 | 678-681 | Gene | denotes | 1B4 | Gene:8847 |
| 340 | 140-152 | Disease | denotes | inflammation | MESH:D007249 |
| 341 | 250-265 | Disease | denotes | alveolar damage | MESH:D055370 |
| 342 | 288-297 | Disease | denotes | pneumonia | MESH:D011014 |
| 343 | 303-346 | Disease | denotes | fibrosis and type II pneumocyte hyperplasia | MESH:D005355 |
| 344 | 578-586 | Disease | denotes | fibrosis | MESH:D005355 |
| 345 | 653-669 | Disease | denotes | pleural fibrosis | MESH:D005355 |
| 346 | 684-699 | Disease | denotes | vascular injury | MESH:D057772 |
| 347 | 705-712 | Disease | denotes | thrombi | MESH:D013927 |
| 348 | 731-741 | Disease | denotes | vasculitis | MESH:D014657 |
| 349 | 1378-1385 | Disease | denotes | thrombi | MESH:D013927 |
LitCovid-PD-HP
| Id | Subject | Object | Predicate | Lexical cue | hp_id |
|---|---|---|---|---|---|
| T46 | 242-265 | Phenotype | denotes | diffuse alveolar damage | http://purl.obolibrary.org/obo/HP_0033006 |
| T47 | 288-297 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
| T48 | 316-346 | Phenotype | denotes | type II pneumocyte hyperplasia | http://purl.obolibrary.org/obo/HP_0033328 |
| T49 | 731-741 | Phenotype | denotes | vasculitis | http://purl.obolibrary.org/obo/HP_0002633 |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T5 | 140-152 | http://purl.obolibrary.org/obo/GO_0006954 | denotes | inflammation |
| T6 | 1332-1351 | http://purl.obolibrary.org/obo/GO_0070527 | denotes | platelet aggregates |
LitCovid-PD-GlycoEpitope
| Id | Subject | Object | Predicate | Lexical cue | glyco_epitope_db_id |
|---|---|---|---|---|---|
| T1 | 622-625 | GlycoEpitope | denotes | 1B1 | http://www.glycoepitope.jp/epitopes/AN0633 |
| T2 | 721-724 | GlycoEpitope | denotes | 1B2 | http://www.glycoepitope.jp/epitopes/AN0389 |
| T3 | 1059-1062 | GlycoEpitope | denotes | 1B1 | http://www.glycoepitope.jp/epitopes/AN0633 |
| T4 | 1164-1167 | GlycoEpitope | denotes | 1B2 | http://www.glycoepitope.jp/epitopes/AN0389 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T127 | 0-62 | Sentence | denotes | A range of common lung findings were seen on light microscopy. |
| T128 | 63-276 | Sentence | denotes | Parenchymal multifocal damage with intraalveolar exudative and proliferative inflammation (Figure 1A2), with fibrin, hyaline membranes (Figure 1A3) consistent with a diagnosis of diffuse alveolar damage (Table 3). |
| T129 | 277-482 | Sentence | denotes | Organizing pneumonia with fibrosis and type II pneumocyte hyperplasia, amphophilic cytoplasm, large nuclei, and prominent nucleoli, were indicative of cytopathic virus-induced changes (Figure 1A3 and 1A4). |
| T130 | 483-627 | Sentence | denotes | Fibroblastic foci consisting of loose organizing connective tissue reflective of alveolar duct fibrosis were seen (fibrotic phase) (Figure 1B1). |
| T131 | 628-755 | Sentence | denotes | Other findings included: pleural fibrosis (Figure 1B4), vascular injury with thrombi (Figure 1B2), and vasculitis (Figure 1B3). |
| T132 | 756-1064 | Sentence | denotes | A main feature was the presence of numerous inflammatory cells consisting of granulocytes (CD15+) (Supplementary Figure 1A1 and 1A2), macrophages (CD68+) (Supplementary Figure 1A3 and 1A4), and T lymphocytes (CD3+) infiltrating into alveolar septa and clustering around capillary vessels (Supplementary 1B1). |
| T133 | 1065-1177 | Sentence | denotes | Immunohistochemistry showed the presence of both CD4+ and CD8+ T lymphocytes (Supplementary Figure 1B2 and 1B3). |
| T134 | 1178-1262 | Sentence | denotes | Of note, lymphocytes were CD20− indicating an absence of infiltrating B lymphocytes. |
| T135 | 1263-1413 | Sentence | denotes | Thrombi were present and immunohistochemistry showed the presence of platelet aggregates and megakaryocytes within thrombi (Supplementary Figure 1B4). |