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PMC:7543426 / 11080-13688 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T66 40-44 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T67 272-280 Body_part denotes alveolar http://purl.org/sig/ont/fma/fma264783
T68 346-356 Body_part denotes pneumocyte http://purl.org/sig/ont/fma/fma62499
T69 382-391 Body_part denotes cytoplasm http://purl.org/sig/ont/fma/fma66835
T70 505-517 Body_part denotes Fibroblastic http://purl.org/sig/ont/fma/fma63877
T71 554-571 Body_part denotes connective tissue http://purl.org/sig/ont/fma/fma9640
T72 586-599 Body_part denotes alveolar duct http://purl.org/sig/ont/fma/fma7341
T73 835-840 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T74 855-867 Body_part denotes granulocytes http://purl.org/sig/ont/fma/fma62854
T75 912-923 Body_part denotes macrophages http://purl.org/sig/ont/fma/fma63261
T76 972-985 Body_part denotes T lymphocytes http://purl.org/sig/ont/fma/fma62870
T77 1011-1019 Body_part denotes alveolar http://purl.org/sig/ont/fma/fma264783
T78 1048-1057 Body_part denotes capillary http://purl.org/sig/ont/fma/fma63194
T79 1150-1163 Body_part denotes T lymphocytes http://purl.org/sig/ont/fma/fma62870
T80 1209-1220 Body_part denotes lymphocytes http://purl.org/sig/ont/fma/fma62863
T81 1270-1283 Body_part denotes B lymphocytes http://purl.org/sig/ont/fma/fma62869
T82 1354-1362 Body_part denotes platelet http://purl.org/sig/ont/fma/fma62851
T83 1378-1392 Body_part denotes megakaryocytes http://purl.org/sig/ont/fma/fma83555
T84 1532-1536 Body_part denotes Lung http://purl.org/sig/ont/fma/fma7195
T85 1600-1610 Body_part denotes pneumocyte http://purl.org/sig/ont/fma/fma62499
T86 1632-1640 Body_part denotes Alveolar http://purl.org/sig/ont/fma/fma264783
T87 1666-1674 Body_part denotes Alveolar http://purl.org/sig/ont/fma/fma264783
T88 1757-1762 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T89 1792-1800 Body_part denotes alveolar http://purl.org/sig/ont/fma/fma264783
T90 1933-1938 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T91 2454-2462 Body_part denotes red pulp http://purl.org/sig/ont/fma/fma15844
T92 2524-2535 Body_part denotes Bone marrow http://purl.org/sig/ont/fma/fma9608
T93 2537-2551 Body_part denotes Megakaryocytes http://purl.org/sig/ont/fma/fma83555
T94 2578-2588 Body_part denotes Adipocytes http://purl.org/sig/ont/fma/fma63880

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T49 40-44 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T50 554-571 Body_part denotes connective tissue http://purl.obolibrary.org/obo/UBERON_0002384
T51 565-571 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T52 595-599 Body_part denotes duct http://purl.obolibrary.org/obo/UBERON_0000058
T53 1048-1057 Body_part denotes capillary http://purl.obolibrary.org/obo/UBERON_0001982
T54 1058-1065 Body_part denotes vessels http://purl.obolibrary.org/obo/UBERON_0000055
T55 1532-1536 Body_part denotes Lung http://purl.obolibrary.org/obo/UBERON_0002048
T56 2524-2535 Body_part denotes Bone marrow http://purl.obolibrary.org/obo/UBERON_0002371

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T116 162-174 Disease denotes inflammation http://purl.obolibrary.org/obo/MONDO_0021166
T117 299-319 Disease denotes Organizing pneumonia http://purl.obolibrary.org/obo/MONDO_0015265|http://purl.obolibrary.org/obo/MONDO_0056821
T119 310-319 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T120 357-368 Disease denotes hyperplasia http://purl.obolibrary.org/obo/MONDO_0005043
T121 715-721 Disease denotes injury http://purl.obolibrary.org/obo/MONDO_0021178
T122 753-763 Disease denotes vasculitis http://purl.obolibrary.org/obo/MONDO_0018882
T123 1577-1588 Disease denotes Hyperplasia http://purl.obolibrary.org/obo/MONDO_0005043
T124 1881-1891 Disease denotes Vasculitis http://purl.obolibrary.org/obo/MONDO_0018882
T125 1968-1979 Disease denotes Myocarditis http://purl.obolibrary.org/obo/MONDO_0004496
T126 2001-2011 Disease denotes Vasculitis http://purl.obolibrary.org/obo/MONDO_0018882
T127 2115-2127 Disease denotes Pericarditis http://purl.obolibrary.org/obo/MONDO_0005904
T128 2354-2372 Disease denotes Glomerulosclerosis http://purl.obolibrary.org/obo/MONDO_0000490
T129 2552-2563 Disease denotes hyperplasia http://purl.obolibrary.org/obo/MONDO_0005043

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T144 22-23 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T145 40-44 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T146 40-44 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T147 183-186 http://purl.obolibrary.org/obo/CLO_0001146 denotes 1A2
T148 210-219 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membranes
T149 249-250 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T150 299-309 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organizing
T151 461-466 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T152 505-517 http://purl.obolibrary.org/obo/CL_0000057 denotes Fibroblastic
T153 543-553 http://purl.obolibrary.org/obo/OBI_0000245 denotes organizing
T154 554-571 http://purl.obolibrary.org/obo/UBERON_0002384 denotes connective tissue
T155 554-571 http://www.ebi.ac.uk/efo/EFO_0000952 denotes connective tissue
T156 595-599 http://purl.obolibrary.org/obo/UBERON_0000025 denotes duct
T157 595-599 http://purl.obolibrary.org/obo/UBERON_0000058 denotes duct
T158 772-775 http://purl.obolibrary.org/obo/CLO_0054085 denotes 1B3
T159 778-779 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T160 835-840 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T161 906-909 http://purl.obolibrary.org/obo/CLO_0001146 denotes 1A2
T162 925-929 http://purl.obolibrary.org/obo/PR_000002064 denotes CD68
T163 987-990 http://purl.obolibrary.org/obo/CLO_0052882 denotes CD3
T164 987-990 http://purl.obolibrary.org/obo/CLO_0053434 denotes CD3
T165 1058-1065 http://purl.obolibrary.org/obo/UBERON_0000055 denotes vessels
T166 1136-1139 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T167 1145-1148 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T168 1194-1197 http://purl.obolibrary.org/obo/CLO_0054085 denotes 1B3
T169 1270-1271 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T170 1498-1504 http://purl.obolibrary.org/obo/CLO_0007919 denotes n = 18
T171 1498-1504 http://purl.obolibrary.org/obo/CLO_0007920 denotes n = 18
T172 1532-1536 http://purl.obolibrary.org/obo/UBERON_0002048 denotes Lung
T173 1532-1536 http://www.ebi.ac.uk/efo/EFO_0000934 denotes Lung
T174 1546-1555 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membranes
T175 1612-1614 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T176 1757-1762 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T177 1933-1938 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T178 2505-2507 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T179 2524-2528 http://purl.obolibrary.org/obo/UBERON_0002481 denotes Bone
T180 2578-2588 http://purl.obolibrary.org/obo/CL_0000136 denotes Adipocytes

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
333 869-873 Gene denotes CD15 Gene:2526
334 925-929 Gene denotes CD68 Gene:968
335 1136-1139 Gene denotes CD4 Gene:920
336 1145-1148 Gene denotes CD8 Gene:925
337 1226-1230 Gene denotes CD20 Gene:54474
338 1430-1433 Gene denotes 1B4 Gene:8847
339 700-703 Gene denotes 1B4 Gene:8847
340 162-174 Disease denotes inflammation MESH:D007249
341 272-287 Disease denotes alveolar damage MESH:D055370
342 310-319 Disease denotes pneumonia MESH:D011014
343 325-368 Disease denotes fibrosis and type II pneumocyte hyperplasia MESH:D005355
344 600-608 Disease denotes fibrosis MESH:D005355
345 675-691 Disease denotes pleural fibrosis MESH:D005355
346 706-721 Disease denotes vascular injury MESH:D057772
347 727-734 Disease denotes thrombi MESH:D013927
348 753-763 Disease denotes vasculitis MESH:D014657
349 1400-1407 Disease denotes thrombi MESH:D013927
364 1577-1610 Disease denotes Hyperplasia of type II pneumocyte MESH:D006965
365 1711-1721 Disease denotes Hemorrhage MESH:D006470
366 1792-1807 Disease denotes alveolar damage MESH:D055370
367 1881-1891 Disease denotes Vasculitis MESH:D014657
368 1968-1979 Disease denotes Myocarditis MESH:D009205
369 2001-2011 Disease denotes Vasculitis MESH:D014657
370 2085-2093 Disease denotes necrosis MESH:D009336
371 2115-2127 Disease denotes Pericarditis MESH:D010493
372 2157-2165 Disease denotes fibrosis MESH:D005355
373 2272-2281 Disease denotes Steatosis MESH:D005234
374 2354-2372 Disease denotes Glomerulosclerosis MESH:D005921
375 2407-2415 Disease denotes fibrosis MESH:D005355
376 2484-2503 Disease denotes Lymphoid hypoplasia MESH:D008224
377 2552-2563 Disease denotes hyperplasia MESH:D006965

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T46 264-287 Phenotype denotes diffuse alveolar damage http://purl.obolibrary.org/obo/HP_0033006
T47 310-319 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T48 338-368 Phenotype denotes type II pneumocyte hyperplasia http://purl.obolibrary.org/obo/HP_0033328
T49 753-763 Phenotype denotes vasculitis http://purl.obolibrary.org/obo/HP_0002633
T50 1784-1807 Phenotype denotes Diffuse alveolar damage http://purl.obolibrary.org/obo/HP_0033006
T51 1881-1891 Phenotype denotes Vasculitis http://purl.obolibrary.org/obo/HP_0002633
T52 1968-1979 Phenotype denotes Myocarditis http://purl.obolibrary.org/obo/HP_0012819
T53 2001-2011 Phenotype denotes Vasculitis http://purl.obolibrary.org/obo/HP_0002633
T54 2115-2127 Phenotype denotes Pericarditis http://purl.obolibrary.org/obo/HP_0001701
T55 2272-2281 Phenotype denotes Steatosis http://purl.obolibrary.org/obo/HP_0001397
T56 2354-2372 Phenotype denotes Glomerulosclerosis http://purl.obolibrary.org/obo/HP_0000096

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T5 162-174 http://purl.obolibrary.org/obo/GO_0006954 denotes inflammation
T6 1354-1373 http://purl.obolibrary.org/obo/GO_0070527 denotes platelet aggregates
T7 2085-2093 http://purl.obolibrary.org/obo/GO_0070265 denotes necrosis
T8 2085-2093 http://purl.obolibrary.org/obo/GO_0019835 denotes necrosis
T9 2085-2093 http://purl.obolibrary.org/obo/GO_0008219 denotes necrosis
T10 2085-2093 http://purl.obolibrary.org/obo/GO_0001906 denotes necrosis

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T1 644-647 GlycoEpitope denotes 1B1 http://www.glycoepitope.jp/epitopes/AN0633
T2 743-746 GlycoEpitope denotes 1B2 http://www.glycoepitope.jp/epitopes/AN0389
T3 1081-1084 GlycoEpitope denotes 1B1 http://www.glycoepitope.jp/epitopes/AN0633
T4 1186-1189 GlycoEpitope denotes 1B2 http://www.glycoepitope.jp/epitopes/AN0389

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T126 0-21 Sentence denotes Microscopic Findings.
T127 22-84 Sentence denotes A range of common lung findings were seen on light microscopy.
T128 85-298 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 299-504 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 505-649 Sentence denotes Fibroblastic foci consisting of loose organizing connective tissue reflective of alveolar duct fibrosis were seen (fibrotic phase) (Figure 1B1).
T131 650-777 Sentence denotes Other findings included: pleural fibrosis (Figure 1B4), vascular injury with thrombi (Figure 1B2), and vasculitis (Figure 1B3).
T132 778-1086 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 1087-1199 Sentence denotes Immunohistochemistry showed the presence of both CD4+ and CD8+ T lymphocytes (Supplementary Figure 1B2 and 1B3).
T134 1200-1284 Sentence denotes Of note, lymphocytes were CD20− indicating an absence of infiltrating B lymphocytes.
T135 1285-1435 Sentence denotes Thrombi were present and immunohistochemistry showed the presence of platelet aggregates and megakaryocytes within thrombi (Supplementary Figure 1B4).
T136 1436-1444 Sentence denotes Table 3.
T137 1446-1469 Sentence denotes Histopathology Findings
T138 1470-1531 Sentence denotes Findings Group 1, No. (%) (n = 18) Group 2, No. (%) (n = 4)
T139 1532-1536 Sentence denotes Lung
T140 1537-1575 Sentence denotes  Hyaline membranes 8 (44.4) 2 (50.0)
T141 1576-1630 Sentence denotes  Hyperplasia of type II pneumocyte 11 (61.2) 4 (100)
T142 1631-1664 Sentence denotes  Alveolar plug 8 (44.4) 4 (100)
T143 1665-1709 Sentence denotes  Alveolar fibrin deposit 9 (50.0) 3 (75.0)
T144 1710-1742 Sentence denotes  Hemorrhage 10 (55.6) 2 (50.0)
T145 1743-1782 Sentence denotes  Inflammatory cells 13 (72.3) 4 (100)
T146 1783-1844 Sentence denotes  Diffuse alveolar damage, fibrotic phase 12 (66.7) 1 (25.0)
T147 1845-1879 Sentence denotes  Microthrombi 14 (77.8) 2 (50.0)
T148 1880-1910 Sentence denotes  Vasculitis 8 (44.4) 4 (100)
T149 1911-1958 Sentence denotes  Multinucleated giant cells 4 (22.3) 2 (50.0)
T150 1959-1966 Sentence denotes Cardiac
T151 1967-1999 Sentence denotes  Myocarditis 9 (50.0) 3 (75.0)
T152 2000-2031 Sentence denotes  Vasculitis 5 (27.8) 3 (75.0)
T153 2032-2077 Sentence denotes  Inflammatory infiltrate 13 (72.3) 3 (75.0)
T154 2078-2113 Sentence denotes  Focal necrosis 6 (33.4) 2 (50.0)
T155 2114-2146 Sentence denotes  Pericarditis 9 (50.0) 4 (100)
T156 2147-2185 Sentence denotes  Vascular fibrosis 4 (22.3) 2 (50.0)
T157 2186-2193 Sentence denotes Hepatic
T158 2194-2238 Sentence denotes  Inflammatory infiltrate 8 (44.4) 3 (75.0)
T159 2239-2270 Sentence denotes  Congestion 8 (44.4) 2 (50.0)
T160 2271-2301 Sentence denotes  Steatosis 9 (50.0) 3 (75.0)
T161 2302-2307 Sentence denotes Renal
T162 2308-2352 Sentence denotes  Inflammatory infiltrate 9 (50.0) 3 (75.0)
T163 2353-2392 Sentence denotes  Glomerulosclerosis 9 (50.0) 3 (75.0)
T164 2393-2434 Sentence denotes  Interstitial fibrosis 9 (50.0) 4 (100)
T165 2435-2442 Sentence denotes Splenic
T166 2443-2482 Sentence denotes  Congested red pulp 15 (83.4) 4 (100)
T167 2483-2523 Sentence denotes  Lymphoid hypoplasia 11 (61.2) 4 (100)
T168 2524-2535 Sentence denotes Bone marrow
T169 2536-2576 Sentence denotes  Megakaryocytes hyperplasia 0 2 (50.0)
T170 2577-2608 Sentence denotes  Adipocytes 7 (38.9) 1 (25.0)