PMC:7340597 / 13626-15049
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T65 | 80-84 | Body_part | denotes | lung | http://purl.org/sig/ont/fma/fma7195 |
| T66 | 85-91 | Body_part | denotes | tissue | http://purl.org/sig/ont/fma/fma9637 |
| T67 | 155-167 | Body_part | denotes | fibroblastic | http://purl.org/sig/ont/fma/fma63877 |
| T68 | 219-230 | Body_part | denotes | histiocytes | http://purl.org/sig/ont/fma/fma83585 |
| T69 | 265-269 | Body_part | denotes | lung | http://purl.org/sig/ont/fma/fma7195 |
| T70 | 270-276 | Body_part | denotes | tissue | http://purl.org/sig/ont/fma/fma9637 |
| T71 | 362-370 | Body_part | denotes | alveolar | http://purl.org/sig/ont/fma/fma264783 |
| T72 | 423-436 | Body_part | denotes | blood vessels | http://purl.org/sig/ont/fma/fma63183 |
| T73 | 423-428 | Body_part | denotes | blood | http://purl.org/sig/ont/fma/fma9670 |
| T74 | 444-452 | Body_part | denotes | alveolar | http://purl.org/sig/ont/fma/fma264783 |
| T75 | 786-790 | Body_part | denotes | lung | http://purl.org/sig/ont/fma/fma7195 |
| T76 | 818-826 | Body_part | denotes | alveolar | http://purl.org/sig/ont/fma/fma264783 |
| T77 | 827-839 | Body_part | denotes | fibroblastic | http://purl.org/sig/ont/fma/fma63877 |
| T78 | 916-924 | Body_part | denotes | alveolar | http://purl.org/sig/ont/fma/fma264783 |
| T79 | 1013-1024 | Body_part | denotes | neutrophils | http://purl.org/sig/ont/fma/fma62860 |
| T80 | 1029-1040 | Body_part | denotes | lymphocytes | http://purl.org/sig/ont/fma/fma62863 |
| T81 | 1102-1110 | Body_part | denotes | alveolar | http://purl.org/sig/ont/fma/fma264783 |
| T82 | 1275-1286 | Body_part | denotes | pneumocytes | http://purl.org/sig/ont/fma/fma62499 |
| T83 | 1363-1368 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T33 | 80-84 | Body_part | denotes | lung | http://purl.obolibrary.org/obo/UBERON_0002048 |
| T34 | 85-91 | Body_part | denotes | tissue | http://purl.obolibrary.org/obo/UBERON_0000479 |
| T35 | 265-269 | Body_part | denotes | lung | http://purl.obolibrary.org/obo/UBERON_0002048 |
| T36 | 270-276 | Body_part | denotes | tissue | http://purl.obolibrary.org/obo/UBERON_0000479 |
| T37 | 381-388 | Body_part | denotes | exudate | http://purl.obolibrary.org/obo/UBERON_0007780 |
| T38 | 423-436 | Body_part | denotes | blood vessels | http://purl.obolibrary.org/obo/UBERON_0001981 |
| T39 | 423-428 | Body_part | denotes | blood | http://purl.obolibrary.org/obo/UBERON_0000178 |
| T40 | 429-436 | Body_part | denotes | vessels | http://purl.obolibrary.org/obo/UBERON_0000055 |
| T41 | 522-528 | Body_part | denotes | vessel | http://purl.obolibrary.org/obo/UBERON_0000055 |
| T42 | 786-790 | Body_part | denotes | lung | http://purl.obolibrary.org/obo/UBERON_0002048 |
| T43 | 1161-1168 | Body_part | denotes | exudate | http://purl.obolibrary.org/obo/UBERON_0007780 |
| T44 | 1229-1235 | Body_part | denotes | vessel | http://purl.obolibrary.org/obo/UBERON_0000055 |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 369 | 875-884 | Disease | denotes | pneumonia | MESH:D011014 |
| 370 | 953-961 | Disease | denotes | fibrosis | MESH:D005355 |
| 371 | 1102-1117 | Disease | denotes | alveolar damage | MESH:D055370 |
| 372 | 1294-1309 | Disease | denotes | viral infection | MESH:D001102 |
| 373 | 1329-1340 | Disease | denotes | hyperplasia | MESH:D006965 |
| 375 | 634-643 | Species | denotes | SARS-CoV2 | Tax:2697049 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T133 | 495-503 | Disease | denotes | thrombus | http://purl.obolibrary.org/obo/MONDO_0000831 |
| T134 | 634-638 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T135 | 644-653 | Disease | denotes | infection | http://purl.obolibrary.org/obo/MONDO_0005550 |
| T136 | 683-686 | Disease | denotes | PAS | http://purl.obolibrary.org/obo/MONDO_0004277 |
| T137 | 745-765 | Disease | denotes | organizing pneumonia | http://purl.obolibrary.org/obo/MONDO_0015265|http://purl.obolibrary.org/obo/MONDO_0056821 |
| T139 | 756-765 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
| T140 | 864-884 | Disease | denotes | organizing pneumonia | http://purl.obolibrary.org/obo/MONDO_0015265|http://purl.obolibrary.org/obo/MONDO_0056821 |
| T142 | 875-884 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
| T143 | 1210-1218 | Disease | denotes | thrombus | http://purl.obolibrary.org/obo/MONDO_0000831 |
| T144 | 1294-1309 | Disease | denotes | viral infection | http://purl.obolibrary.org/obo/MONDO_0005108 |
| T145 | 1300-1309 | Disease | denotes | infection | http://purl.obolibrary.org/obo/MONDO_0005550 |
| T146 | 1329-1340 | Disease | denotes | hyperplasia | http://purl.obolibrary.org/obo/MONDO_0005043 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T106 | 80-84 | http://purl.obolibrary.org/obo/UBERON_0002048 | denotes | lung |
| T107 | 80-84 | http://www.ebi.ac.uk/efo/EFO_0000934 | denotes | lung |
| T108 | 118-119 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T109 | 155-167 | http://purl.obolibrary.org/obo/CL_0000057 | denotes | fibroblastic |
| T110 | 219-230 | http://purl.obolibrary.org/obo/CL_0000235 | denotes | histiocytes |
| T111 | 237-239 | http://purl.obolibrary.org/obo/CLO_0001236 | denotes | 2A |
| T112 | 265-269 | http://purl.obolibrary.org/obo/UBERON_0002048 | denotes | lung |
| T113 | 265-269 | http://www.ebi.ac.uk/efo/EFO_0000934 | denotes | lung |
| T114 | 339-348 | http://purl.obolibrary.org/obo/UBERON_0000158 | denotes | membranes |
| T115 | 423-436 | http://purl.obolibrary.org/obo/UBERON_0001981 | denotes | blood vessels |
| T116 | 423-436 | http://www.ebi.ac.uk/efo/EFO_0000817 | denotes | blood vessels |
| T117 | 484-494 | http://purl.obolibrary.org/obo/OBI_0000245 | denotes | organizing |
| T118 | 507-508 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T119 | 522-528 | http://purl.obolibrary.org/obo/UBERON_0000055 | denotes | vessel |
| T120 | 594-604 | http://purl.obolibrary.org/obo/CL_0000066 | denotes | epithelial |
| T121 | 632-633 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T122 | 745-755 | http://purl.obolibrary.org/obo/OBI_0000245 | denotes | organizing |
| T123 | 786-790 | http://purl.obolibrary.org/obo/UBERON_0002048 | denotes | lung |
| T124 | 786-790 | http://www.ebi.ac.uk/efo/EFO_0000934 | denotes | lung |
| T125 | 801-802 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T126 | 827-839 | http://purl.obolibrary.org/obo/CL_0000057 | denotes | fibroblastic |
| T127 | 864-874 | http://purl.obolibrary.org/obo/OBI_0000245 | denotes | organizing |
| T128 | 897-898 | http://purl.obolibrary.org/obo/CLO_0001021 | denotes | B |
| T129 | 1059-1068 | http://purl.obolibrary.org/obo/UBERON_0000158 | denotes | membranes |
| T130 | 1122-1127 | http://purl.obolibrary.org/obo/CLO_0002850 | denotes | E, 20 |
| T131 | 1229-1235 | http://purl.obolibrary.org/obo/UBERON_0000055 | denotes | vessel |
| T132 | 1363-1368 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T84 | 683-686 | Chemical | denotes | PAS | http://purl.obolibrary.org/obo/CHEBI_27565 |
LitCovid-PD-HP
| Id | Subject | Object | Predicate | Lexical cue | hp_id |
|---|---|---|---|---|---|
| T36 | 756-765 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
| T37 | 875-884 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
| T38 | 1094-1117 | Phenotype | denotes | diffuse alveolar damage | http://purl.obolibrary.org/obo/HP_0033006 |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T3 | 1294-1309 | http://purl.obolibrary.org/obo/GO_0016032 | denotes | viral infection |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T110 | 0-108 | Sentence | denotes | Postmortem pathologic examination revealed that the overall architecture of the lung tissue remained intact. |
| T111 | 109-241 | Sentence | denotes | However, a prominent amount of fibromyxoid or fibroblastic bodies was present in the alveoli with surrounding histiocytes (Fig. 2A . |
| T112 | 242-315 | Sentence | denotes | The extent of involved lung tissue was estimated at around 25% (Table 2). |
| T113 | 316-400 | Sentence | denotes | No remnants of hyaline membranes or prominent alveolar fibrinous exudate were found. |
| T114 | 401-539 | Sentence | denotes | Microthrombi in small blood vessels of the alveolar septa were seen, as well as an organizing thrombus in a larger sized vessel (Fig. 2E). |
| T115 | 540-654 | Sentence | denotes | The histologic findings in this case point towards an epithelial, and vascular phenotype of a SARS-CoV2 infection. |
| T116 | 655-695 | Sentence | denotes | No fungi were present in de PAS-D stain. |
| T117 | 696-766 | Sentence | denotes | This histologic pattern is characteristic for an organizing pneumonia. |
| T118 | 767-800 | Sentence | denotes | Fig. 2 Microscopic lung findings. |
| T119 | 801-1423 | Sentence | denotes | A, case 1: intra-alveolar fibroblastic bodies, consistent with organizing pneumonia, (H&E, 10×) B, case 2: loss of alveolar architecture with extensive fibrosis (H&E; 10×) C, case 3: inflammatory infiltrate with neutrophils and lymphocytes, note the hyaline membranes (arrows), suggestive for diffuse alveolar damage. (H&E, 20×) D, case 4: prominent fibrinous exudate in alveoli as seen in AFOP (H&E; 10×) E: thrombus in larger vessel (H&E, 5×) F: cytopathogenic changes in pneumocytes due to viral infection seen in all cases: hyperplasia, multinucleated giant cells (asterisks), intranuclear inclusion bodies (H&E, 40×). |
LitCovid-PMC-OGER-BB
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T334 | 260-269 | UBERON:0002048 | denotes | lved lung |
| T335 | 602-618 | UBERON:0003215 | denotes | al, and vascular |
| T336 | 658-695 | CL:0000057 | denotes | fungi were present in de PAS-D stain. |
| T337 | 696-711 | UBERON:0000479 | denotes | This histologic |
| T338 | 1172-1179 | UBERON:0003215 | denotes | alveoli |
| T231 | 2-7 | NCBITaxon:4751 | denotes | stmor |
| T232 | 129-133 | UBERON:0002048 | denotes | amo |
| T233 | 161-169 | UBERON:0003215 | denotes | lastic b |
| T234 | 170-182 | CL:0000057 | denotes | dies was pre |
| T235 | 230-231 | CHEBI:51686;CHEBI:51686 | denotes | |
| T236 | 259-267 | UBERON:0003215 | denotes | olved lu |
| T237 | 304-305 | CHEBI:51686;CHEBI:51686 | denotes | |
| T74625 | 354-363 | CL:0000775 | denotes | ominent a |
| T239 | 368-379 | CL:0000542 | denotes | ar fibrinou |
| T79223 | 441-449 | UBERON:0003215 | denotes | he alveo |
| T241 | 459-460 | CHEBI:51686;CHEBI:51686 | denotes | w |
| T242 | 511-518 | UBERON:0003215 | denotes | rger si |
| T243 | 536-537 | CHEBI:51686;CHEBI:51686 | denotes | E |
| T244 | 549-557 | UBERON:0010210 | denotes | logic fi |
| T245 | 568-574 | UBERON:0000055 | denotes | his ca |
| T246 | 576-577 | CHEBI:51686;CHEBI:51686 | denotes | |
| T247 | 615-626 | CL:0000322 | denotes | lar phenoty |
| T55890 | 634-639 | NCBITaxon:10239 | denotes | SARS- |
| T46051 | 682-694 | GO:0005634;CL:0000647 | denotes | PAS-D stain |
| T11789 | 695-706 | CL:0000647 | denotes | This histo |
| T23332 | 720-731 | GO:0005634 | denotes | is characte |
| T84342 | 732-748 | GO:0016234 | denotes | istic for an org |
| T253 | 750-751 | CHEBI:51686;CHEBI:51686 | denotes | i |
| T81672 | 786-790 | UBERON:0002048 | denotes | lung |
| T27688 | 818-826 | UBERON:0003215 | denotes | alveolar |
| T256 | 827-839 | CL:0000057 | denotes | fibroblastic |
| T1033 | 887-888 | CHEBI:51686;CHEBI:51686 | denotes | H |
| T258 | 916-924 | UBERON:0003215 | denotes | alveolar |
| T259 | 963-964 | CHEBI:51686;CHEBI:51686 | denotes | H |
| T42968 | 1013-1024 | CL:0000775 | denotes | neutrophils |
| T261 | 1029-1040 | CL:0000542 | denotes | lymphocytes |
| T262 | 1102-1110 | UBERON:0003215 | denotes | alveolar |
| T263 | 1120-1121 | CHEBI:51686;CHEBI:51686 | denotes | H |
| T70845 | 1172-1179 | UBERON:0003215 | denotes | alveoli |
| T265 | 1197-1198 | CHEBI:51686;CHEBI:51686 | denotes | H |
| T266 | 1210-1218 | UBERON:0010210 | denotes | thrombus |
| T267 | 1229-1235 | UBERON:0000055 | denotes | vessel |
| T268 | 1237-1238 | CHEBI:51686;CHEBI:51686 | denotes | H |
| T269 | 1275-1286 | CL:0000322 | denotes | pneumocytes |
| T29843 | 1294-1299 | NCBITaxon:10239 | denotes | viral |
| T271 | 1342-1356 | GO:0005634;CL:0000647 | denotes | multinucleated |
| T25696 | 1357-1368 | CL:0000647 | denotes | giant cells |
| T273 | 1382-1394 | GO:0005634 | denotes | intranuclear |
| T99425 | 1395-1411 | GO:0016234 | denotes | inclusion bodies |
| T275 | 1413-1414 | CHEBI:51686;CHEBI:51686 | denotes | H |