> top > docs > PMC:7340597 > spans > 12575-15049 > annotations

PMC:7340597 / 12575-15049 JSONTXT

Annnotations TAB JSON ListView MergeView

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T59 202-207 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T60 610-615 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T61 719-723 Body_part denotes dens http://purl.org/sig/ont/fma/fma24043
T62 892-896 Body_part denotes head http://purl.org/sig/ont/fma/fma7154
T63 906-911 Body_part denotes brain http://purl.org/sig/ont/fma/fma50801
T64 976-1007 Body_part denotes right posterior cerebral artery http://purl.org/sig/ont/fma/fma50584
T65 1131-1135 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T66 1136-1142 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T67 1206-1218 Body_part denotes fibroblastic http://purl.org/sig/ont/fma/fma63877
T68 1270-1281 Body_part denotes histiocytes http://purl.org/sig/ont/fma/fma83585
T69 1316-1320 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T70 1321-1327 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T71 1413-1421 Body_part denotes alveolar http://purl.org/sig/ont/fma/fma264783
T72 1474-1487 Body_part denotes blood vessels http://purl.org/sig/ont/fma/fma63183
T73 1474-1479 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T74 1495-1503 Body_part denotes alveolar http://purl.org/sig/ont/fma/fma264783
T75 1837-1841 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T76 1869-1877 Body_part denotes alveolar http://purl.org/sig/ont/fma/fma264783
T77 1878-1890 Body_part denotes fibroblastic http://purl.org/sig/ont/fma/fma63877
T78 1967-1975 Body_part denotes alveolar http://purl.org/sig/ont/fma/fma264783
T79 2064-2075 Body_part denotes neutrophils http://purl.org/sig/ont/fma/fma62860
T80 2080-2091 Body_part denotes lymphocytes http://purl.org/sig/ont/fma/fma62863
T81 2153-2161 Body_part denotes alveolar http://purl.org/sig/ont/fma/fma264783
T82 2326-2337 Body_part denotes pneumocytes http://purl.org/sig/ont/fma/fma62499
T83 2414-2419 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T26 202-207 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T27 610-615 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T28 892-896 Body_part denotes head http://purl.obolibrary.org/obo/UBERON_0000033
T29 906-911 Body_part denotes brain http://purl.obolibrary.org/obo/UBERON_0000955
T30 982-1007 Body_part denotes posterior cerebral artery http://purl.obolibrary.org/obo/UBERON_0001636
T31 992-1007 Body_part denotes cerebral artery http://purl.obolibrary.org/obo/UBERON_0004449
T32 1001-1007 Body_part denotes artery http://purl.obolibrary.org/obo/UBERON_0001637
T33 1131-1135 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T34 1136-1142 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T35 1316-1320 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T36 1321-1327 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T37 1432-1439 Body_part denotes exudate http://purl.obolibrary.org/obo/UBERON_0007780
T38 1474-1487 Body_part denotes blood vessels http://purl.obolibrary.org/obo/UBERON_0001981
T39 1474-1479 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T40 1480-1487 Body_part denotes vessels http://purl.obolibrary.org/obo/UBERON_0000055
T41 1573-1579 Body_part denotes vessel http://purl.obolibrary.org/obo/UBERON_0000055
T42 1837-1841 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T43 2212-2219 Body_part denotes exudate http://purl.obolibrary.org/obo/UBERON_0007780
T44 2280-2286 Body_part denotes vessel http://purl.obolibrary.org/obo/UBERON_0000055

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
337 25-34 Disease denotes pneumonia MESH:D011014
351 430-437 Species denotes patient Tax:9606
352 844-851 Species denotes Patient Tax:9606
353 1013-1020 Species denotes patient Tax:9606
354 719-723 Chemical denotes dens MESH:D004052
355 164-172 Disease denotes weakness MESH:D018908
356 174-179 Disease denotes fever MESH:D005334
357 184-192 Disease denotes dyspnoea MESH:D004417
358 498-517 Disease denotes acute renal failure MESH:D058186
359 638-654 Disease denotes pulmonary emboli MESH:D011655
360 787-807 Disease denotes nosocomial infection MESH:D003428
361 906-920 Disease denotes brain ischemia MESH:D002545
362 928-938 Disease denotes infarction MESH:D007238
363 1021-1025 Disease denotes died MESH:D003643
369 1926-1935 Disease denotes pneumonia MESH:D011014
370 2004-2012 Disease denotes fibrosis MESH:D005355
371 2153-2168 Disease denotes alveolar damage MESH:D055370
372 2345-2360 Disease denotes viral infection MESH:D001102
373 2380-2391 Disease denotes hyperplasia MESH:D006965
375 1685-1694 Species denotes SARS-CoV2 Tax:2697049

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T124 14-34 Disease denotes Organizing pneumonia http://purl.obolibrary.org/obo/MONDO_0015265|http://purl.obolibrary.org/obo/MONDO_0056821
T126 25-34 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T127 498-517 Disease denotes acute renal failure http://purl.obolibrary.org/obo/MONDO_0002492
T128 504-517 Disease denotes renal failure http://purl.obolibrary.org/obo/MONDO_0001106
T129 787-807 Disease denotes nosocomial infection http://purl.obolibrary.org/obo/MONDO_0043544
T130 798-807 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T131 906-920 Disease denotes brain ischemia http://purl.obolibrary.org/obo/MONDO_0005299
T132 912-920 Disease denotes ischemia http://purl.obolibrary.org/obo/MONDO_0005053
T133 1546-1554 Disease denotes thrombus http://purl.obolibrary.org/obo/MONDO_0000831
T134 1685-1689 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T135 1695-1704 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T136 1734-1737 Disease denotes PAS http://purl.obolibrary.org/obo/MONDO_0004277
T137 1796-1816 Disease denotes organizing pneumonia http://purl.obolibrary.org/obo/MONDO_0015265|http://purl.obolibrary.org/obo/MONDO_0056821
T139 1807-1816 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T140 1915-1935 Disease denotes organizing pneumonia http://purl.obolibrary.org/obo/MONDO_0015265|http://purl.obolibrary.org/obo/MONDO_0056821
T142 1926-1935 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T143 2261-2269 Disease denotes thrombus http://purl.obolibrary.org/obo/MONDO_0000831
T144 2345-2360 Disease denotes viral infection http://purl.obolibrary.org/obo/MONDO_0005108
T145 2351-2360 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T146 2380-2391 Disease denotes hyperplasia http://purl.obolibrary.org/obo/MONDO_0005043

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T92 14-24 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organizing
T93 35-36 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T94 49-53 http://purl.obolibrary.org/obo/UBERON_0003101 denotes male
T95 49-53 http://www.ebi.ac.uk/efo/EFO_0000970 denotes male
T96 202-207 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T97 610-615 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T98 785-786 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T99 892-896 http://purl.obolibrary.org/obo/UBERON_0000033 denotes head
T100 892-896 http://www.ebi.ac.uk/efo/EFO_0000964 denotes head
T101 906-911 http://purl.obolibrary.org/obo/UBERON_0000955 denotes brain
T102 906-911 http://www.ebi.ac.uk/efo/EFO_0000302 denotes brain
T103 982-991 http://purl.obolibrary.org/obo/UBERON_0001353 denotes posterior
T104 1001-1007 http://purl.obolibrary.org/obo/UBERON_0001637 denotes artery
T105 1001-1007 http://www.ebi.ac.uk/efo/EFO_0000814 denotes artery
T106 1131-1135 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T107 1131-1135 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T108 1169-1170 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T109 1206-1218 http://purl.obolibrary.org/obo/CL_0000057 denotes fibroblastic
T110 1270-1281 http://purl.obolibrary.org/obo/CL_0000235 denotes histiocytes
T111 1288-1290 http://purl.obolibrary.org/obo/CLO_0001236 denotes 2A
T112 1316-1320 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T113 1316-1320 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T114 1390-1399 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membranes
T115 1474-1487 http://purl.obolibrary.org/obo/UBERON_0001981 denotes blood vessels
T116 1474-1487 http://www.ebi.ac.uk/efo/EFO_0000817 denotes blood vessels
T117 1535-1545 http://purl.obolibrary.org/obo/OBI_0000245 denotes organizing
T118 1558-1559 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T119 1573-1579 http://purl.obolibrary.org/obo/UBERON_0000055 denotes vessel
T120 1645-1655 http://purl.obolibrary.org/obo/CL_0000066 denotes epithelial
T121 1683-1684 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T122 1796-1806 http://purl.obolibrary.org/obo/OBI_0000245 denotes organizing
T123 1837-1841 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T124 1837-1841 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T125 1852-1853 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T126 1878-1890 http://purl.obolibrary.org/obo/CL_0000057 denotes fibroblastic
T127 1915-1925 http://purl.obolibrary.org/obo/OBI_0000245 denotes organizing
T128 1948-1949 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T129 2110-2119 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membranes
T130 2173-2178 http://purl.obolibrary.org/obo/CLO_0002850 denotes E, 20
T131 2280-2286 http://purl.obolibrary.org/obo/UBERON_0000055 denotes vessel
T132 2414-2419 http://purl.obolibrary.org/obo/GO_0005623 denotes cells

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T82 49-53 Chemical denotes male http://purl.obolibrary.org/obo/CHEBI_30780
T83 133-135 Chemical denotes ED http://purl.obolibrary.org/obo/CHEBI_73503
T84 1734-1737 Chemical denotes PAS http://purl.obolibrary.org/obo/CHEBI_27565

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T30 25-34 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T31 156-172 Phenotype denotes general weakness http://purl.obolibrary.org/obo/HP_0003324
T32 174-179 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T33 184-192 Phenotype denotes dyspnoea http://purl.obolibrary.org/obo/HP_0002094
T34 498-517 Phenotype denotes acute renal failure http://purl.obolibrary.org/obo/HP_0001919
T35 906-920 Phenotype denotes brain ischemia http://purl.obolibrary.org/obo/HP_0002637
T36 1807-1816 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T37 1926-1935 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T38 2145-2168 Phenotype denotes diffuse alveolar damage http://purl.obolibrary.org/obo/HP_0033006

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T3 2345-2360 http://purl.obolibrary.org/obo/GO_0016032 denotes viral infection

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T102 0-34 Sentence denotes 3.2 Case 1 – Organizing pneumonia
T103 35-193 Sentence denotes A 77-year old male without significant medical history was evaluated in our emergency department (ED) with complaints of general weakness, fever and dyspnoea.
T104 194-408 Sentence denotes Initial chest CT showed extensive bilateral areas of ground-glass opacity with both central and peripheral distribution, patchy subpleural non-dependant consolidations and areas with subpleural sparing (Fig. 1-1A).
T105 409-568 Sentence denotes Soon after admission patient was in need of mechanical ventilatory support and developed acute renal failure for which renal replacement therapy was initiated.
T106 569-784 Sentence denotes After six days of mechanical ventilation chest CT-angiography showed pulmonary emboli along with new areas of ground-glass opacity and progression of dens subpleural consolidations with air-bronchograms (Fig. 1-1B).
T107 785-843 Sentence denotes A nosocomial infection was ruled out by bronchial culture.
T108 844-1008 Sentence denotes Patient's neurologic status deteriorated and CT head revealed brain ischemia due to infarction of the area supplied by the left and right posterior cerebral artery.
T109 1009-1050 Sentence denotes The patient died 12 days after admission.
T110 1051-1159 Sentence denotes Postmortem pathologic examination revealed that the overall architecture of the lung tissue remained intact.
T111 1160-1292 Sentence denotes However, a prominent amount of fibromyxoid or fibroblastic bodies was present in the alveoli with surrounding histiocytes (Fig. 2A .
T112 1293-1366 Sentence denotes The extent of involved lung tissue was estimated at around 25% (Table 2).
T113 1367-1451 Sentence denotes No remnants of hyaline membranes or prominent alveolar fibrinous exudate were found.
T114 1452-1590 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 1591-1705 Sentence denotes The histologic findings in this case point towards an epithelial, and vascular phenotype of a SARS-CoV2 infection.
T116 1706-1746 Sentence denotes No fungi were present in de PAS-D stain.
T117 1747-1817 Sentence denotes This histologic pattern is characteristic for an organizing pneumonia.
T118 1818-1851 Sentence denotes Fig. 2 Microscopic lung findings.
T119 1852-2474 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
T331 203-207 UBERON:0000033 denotes hest
T332 238-293 UBERON:0002037 denotes areas of ground-glass opacity with both central and per
T333 625-699 UBERON:0001004 denotes raphy showed pulmonary emboli along with new areas of ground-glass opacity
T334 1311-1320 UBERON:0002048 denotes lved lung
T335 1653-1669 UBERON:0003215 denotes al, and vascular
T336 1709-1746 CL:0000057 denotes fungi were present in de PAS-D stain.
T337 1747-1762 UBERON:0000479 denotes This histologic
T338 2223-2230 UBERON:0003215 denotes alveoli
T209 66-70 UBERON:0004096 denotes ific
T210 199-209 UBERON:0001016 denotes al chest C
T211 237-241 UBERON:0000033 denotes are
T212 251-256 UBERON:0000955 denotes nd-gl
T213 337-352 UBERON:0001636 denotes dependant conso
T214 366-370 GO:0016265 denotes area
T215 396-406 GO:0016265 denotes (Fig. 1-1A
T216 474-478 UBERON:0002048 denotes y su
T217 479-485 UBERON:0000479 denotes port a
T81145 549-561 CL:0000057 denotes rapy was ini
T219 588-595 UBERON:0003215 denotes echanic
T220 613-624 CL:0000235 denotes st CT-angio
T221 659-663 UBERON:0002048 denotes g wi
T222 664-670 UBERON:0000479 denotes h new
T223 756-764 UBERON:0003215 denotes ir-bronc
T224 817-832 UBERON:0001981 denotes out by bronchi
T225 840-848 UBERON:0003215 denotes re. Pati
T226 849-854 UBERON:0003037 denotes nt's
T28263 891-899 UBERON:0010210 denotes head re
T40605 918-924 UBERON:0000055 denotes ia due
T229 990-999 UBERON:0000483 denotes r cerebra
T34853 1029-1038 SP_7 denotes days afte
T231 1053-1058 NCBITaxon:4751 denotes stmor
T232 1180-1184 UBERON:0002048 denotes amo
T233 1212-1220 UBERON:0003215 denotes lastic b
T234 1221-1233 CL:0000057 denotes dies was pre
T235 1281-1282 CHEBI:51686;CHEBI:51686 denotes
T236 1310-1318 UBERON:0003215 denotes olved lu
T237 1355-1356 CHEBI:51686;CHEBI:51686 denotes
T74625 1405-1414 CL:0000775 denotes ominent a
T239 1419-1430 CL:0000542 denotes ar fibrinou
T79223 1492-1500 UBERON:0003215 denotes he alveo
T241 1510-1511 CHEBI:51686;CHEBI:51686 denotes w
T242 1562-1569 UBERON:0003215 denotes rger si
T243 1587-1588 CHEBI:51686;CHEBI:51686 denotes E
T244 1600-1608 UBERON:0010210 denotes logic fi
T245 1619-1625 UBERON:0000055 denotes his ca
T246 1627-1628 CHEBI:51686;CHEBI:51686 denotes
T247 1666-1677 CL:0000322 denotes lar phenoty
T55890 1685-1690 NCBITaxon:10239 denotes SARS-
T46051 1733-1745 GO:0005634;CL:0000647 denotes PAS-D stain
T11789 1746-1757 CL:0000647 denotes This histo
T23332 1771-1782 GO:0005634 denotes is characte
T84342 1783-1799 GO:0016234 denotes istic for an org
T253 1801-1802 CHEBI:51686;CHEBI:51686 denotes i
T81672 1837-1841 UBERON:0002048 denotes lung
T27688 1869-1877 UBERON:0003215 denotes alveolar
T256 1878-1890 CL:0000057 denotes fibroblastic
T1033 1938-1939 CHEBI:51686;CHEBI:51686 denotes H
T258 1967-1975 UBERON:0003215 denotes alveolar
T259 2014-2015 CHEBI:51686;CHEBI:51686 denotes H
T42968 2064-2075 CL:0000775 denotes neutrophils
T261 2080-2091 CL:0000542 denotes lymphocytes
T262 2153-2161 UBERON:0003215 denotes alveolar
T263 2171-2172 CHEBI:51686;CHEBI:51686 denotes H
T70845 2223-2230 UBERON:0003215 denotes alveoli
T265 2248-2249 CHEBI:51686;CHEBI:51686 denotes H
T266 2261-2269 UBERON:0010210 denotes thrombus
T267 2280-2286 UBERON:0000055 denotes vessel
T268 2288-2289 CHEBI:51686;CHEBI:51686 denotes H
T269 2326-2337 CL:0000322 denotes pneumocytes
T29843 2345-2350 NCBITaxon:10239 denotes viral
T271 2393-2407 GO:0005634;CL:0000647 denotes multinucleated
T25696 2408-2419 CL:0000647 denotes giant cells
T273 2433-2445 GO:0005634 denotes intranuclear
T99425 2446-2462 GO:0016234 denotes inclusion bodies
T275 2464-2465 CHEBI:51686;CHEBI:51686 denotes H