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PMC:7340597 / 15051-17065 JSONTXT

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LitCovid_Glycan-Motif-Structure

Id Subject Object Predicate Lexical cue
T19 972-974 https://glytoucan.org/Structures/Glycans/G93424OB denotes GM
T20 1110-1112 https://glytoucan.org/Structures/Glycans/G93424OB denotes GM

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T84 227-232 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T85 332-355 Body_part denotes bronchovascular bundles http://purl.org/sig/ont/fma/fma84474
T86 683-688 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T87 745-755 Body_part denotes right lung http://purl.org/sig/ont/fma/fma7309
T88 1270-1274 Body_part denotes head http://purl.org/sig/ont/fma/fma7154
T89 1384-1397 Body_part denotes frontal lobes http://purl.org/sig/ont/fma/fma61824
T90 1482-1486 Body_part denotes head http://purl.org/sig/ont/fma/fma7154
T91 1635-1639 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T92 1640-1646 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T93 1701-1705 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T94 1720-1728 Body_part denotes Alveolar http://purl.org/sig/ont/fma/fma264783
T95 1841-1852 Body_part denotes pneumocytes http://purl.org/sig/ont/fma/fma62499
T96 1854-1874 Body_part denotes bronchial epithelium http://purl.org/sig/ont/fma/fma67782
T97 1864-1874 Body_part denotes epithelium http://purl.org/sig/ont/fma/fma9639
T98 1880-1893 Body_part denotes blood vessels http://purl.org/sig/ont/fma/fma63183
T99 1880-1885 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T45 227-232 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T46 683-688 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T47 745-755 Body_part denotes right lung http://purl.obolibrary.org/obo/UBERON_0002167
T48 751-755 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T49 1270-1274 Body_part denotes head http://purl.obolibrary.org/obo/UBERON_0000033
T50 1384-1397 Body_part denotes frontal lobes http://purl.obolibrary.org/obo/UBERON_0016525
T51 1482-1486 Body_part denotes head http://purl.obolibrary.org/obo/UBERON_0000033
T52 1635-1639 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T53 1640-1646 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T54 1701-1705 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T55 1854-1874 Body_part denotes bronchial epithelium http://purl.obolibrary.org/obo/UBERON_0002031
T56 1864-1874 Body_part denotes epithelium http://purl.obolibrary.org/obo/UBERON_0000483
T57 1880-1893 Body_part denotes blood vessels http://purl.obolibrary.org/obo/UBERON_0001981
T58 1880-1885 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T59 1886-1893 Body_part denotes vessels http://purl.obolibrary.org/obo/UBERON_0000055

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
377 14-22 Disease denotes Fibrosis MESH:D005355
394 1157-1178 Species denotes Aspergillus fumigatus Tax:746128
395 1558-1565 Species denotes patient Tax:9606
396 1984-1991 Species denotes patient Tax:9606
397 609-621 Chemical denotes prednisolone MESH:D011239
398 972-974 Chemical denotes GM MESH:C012990
399 1191-1203 Chemical denotes prednisolone MESH:D011239
400 179-188 Disease denotes diarrhoea MESH:D003967
401 193-212 Disease denotes shortness of breath MESH:D004417
402 585-589 Disease denotes ARDS MESH:D012128
403 721-737 Disease denotes pulmonary emboli MESH:D011655
404 1024-1033 Disease denotes infection MESH:D007239
405 1322-1331 Disease denotes epileptic MESH:D004827
406 1364-1375 Disease denotes haemorrhage MESH:D006470
407 1445-1465 Disease denotes cerebral haemorrhage MESH:D002543
408 1786-1794 Disease denotes fibrosis MESH:D005355
409 1995-2013 Disease denotes pulmonary fibrosis MESH:D011658

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T147 179-188 Disease denotes diarrhoea http://purl.obolibrary.org/obo/MONDO_0001673
T148 443-457 Disease denotes bronchiectasis http://purl.obolibrary.org/obo/MONDO_0004822
T149 585-589 Disease denotes ARDS http://purl.obolibrary.org/obo/MONDO_0006502
T150 915-929 Disease denotes bronchiectasis http://purl.obolibrary.org/obo/MONDO_0004822
T151 1017-1033 Disease denotes fungal infection http://purl.obolibrary.org/obo/MONDO_0002041
T152 1024-1033 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T153 1918-1921 Disease denotes PAS http://purl.obolibrary.org/obo/MONDO_0004277
T154 1995-2013 Disease denotes pulmonary fibrosis http://purl.obolibrary.org/obo/MONDO_0002771

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T133 23-24 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T134 37-43 http://purl.obolibrary.org/obo/UBERON_0003100 denotes female
T135 102-103 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T136 227-232 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T137 497-499 http://purl.obolibrary.org/obo/CLO_0001236 denotes 2A
T138 683-688 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T139 745-755 http://purl.obolibrary.org/obo/UBERON_0002167 denotes right lung
T140 832-833 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T141 1108-1109 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T142 1270-1274 http://purl.obolibrary.org/obo/UBERON_0000033 denotes head
T143 1270-1274 http://www.ebi.ac.uk/efo/EFO_0000964 denotes head
T144 1482-1486 http://purl.obolibrary.org/obo/UBERON_0000033 denotes head
T145 1482-1486 http://www.ebi.ac.uk/efo/EFO_0000964 denotes head
T146 1575-1577 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T147 1635-1639 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T148 1635-1639 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T149 1701-1705 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T150 1701-1705 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T151 1864-1874 http://purl.obolibrary.org/obo/UBERON_0000483 denotes epithelium
T152 1880-1893 http://purl.obolibrary.org/obo/UBERON_0001981 denotes blood vessels
T153 1880-1893 http://www.ebi.ac.uk/efo/EFO_0000817 denotes blood vessels

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T85 609-621 Chemical denotes prednisolone http://purl.obolibrary.org/obo/CHEBI_8378
T86 943-946 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T87 972-974 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680
T89 1063-1077 Chemical denotes glucocorticoid http://purl.obolibrary.org/obo/CHEBI_24261
T90 1086-1089 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T91 1110-1112 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680
T93 1191-1203 Chemical denotes prednisolone http://purl.obolibrary.org/obo/CHEBI_8378
T94 1235-1245 Chemical denotes antifungal http://purl.obolibrary.org/obo/CHEBI_35718
T95 1918-1921 Chemical denotes PAS http://purl.obolibrary.org/obo/CHEBI_27565

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T39 179-188 Phenotype denotes diarrhoea http://purl.obolibrary.org/obo/HP_0002014
T40 193-212 Phenotype denotes shortness of breath http://purl.obolibrary.org/obo/HP_0002098
T41 443-457 Phenotype denotes bronchiectasis http://purl.obolibrary.org/obo/HP_0002110
T42 906-929 Phenotype denotes traction bronchiectasis http://purl.obolibrary.org/obo/HP_0032969
T43 1445-1465 Phenotype denotes cerebral haemorrhage http://purl.obolibrary.org/obo/HP_0001342
T44 1995-2013 Phenotype denotes pulmonary fibrosis http://purl.obolibrary.org/obo/HP_0002206

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T4 1147-1153 http://purl.obolibrary.org/obo/GO_0040007 denotes growth

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T17 972-974 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T18 1110-1112 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T120 0-22 Sentence denotes 3.3 Case 2 – Fibrosis
T121 23-120 Sentence denotes A 73-year old female was transferred to our ICU due to shortage of ICU beds in a nearby hospital.
T122 121-213 Sentence denotes Prior to ICU admission, she was healthy but complained of diarrhoea and shortness of breath.
T123 214-370 Sentence denotes Non-contrast chest CT at initial hospital admission showed multiple bilateral areas of ground-glass opacity along the bronchovascular bundles and periphery.
T124 371-435 Sentence denotes There were some small areas of consolidation in the upper lobes.
T125 436-501 Sentence denotes Subtle bronchiectasis were present in affected areas (Fig. 1-2A).
T126 502-590 Sentence denotes Her respiratory condition required mechanical ventilation in prone position due to ARDS.
T127 591-675 Sentence denotes After seven days, prednisolone treatment was started because of lack of improvement.
T128 676-756 Sentence denotes Repeat chest CT-angiography showed segmental pulmonary emboli in the right lung.
T129 757-831 Sentence denotes Ground-glass opacities persisted while the consolidations had disappeared.
T130 832-942 Sentence denotes A reticular pattern combined with GGO was more pronounced with increasing traction bronchiectasis (Fig. 1-2B).
T131 943-1034 Sentence denotes BAL was performed twice, but GM and culture showed no signs of additional fungal infection.
T132 1035-1123 Sentence denotes After one week of high dose glucocorticoid therapy BAL was repeated with a GM index 4.4.
T133 1124-1179 Sentence denotes Fungal cultures showed growth of Aspergillus fumigatus.
T134 1180-1266 Sentence denotes Therefore, prednisolone treatment was discontinued and antifungal treatment initiated.
T135 1267-1398 Sentence denotes CT head was performed because of the development of an epileptic insult and showed small foci of haemorrhage in both frontal lobes.
T136 1399-1516 Sentence denotes Neurologic condition worsened and progressive cerebral haemorrhage on follow up CT head was seen with poor prognosis.
T137 1517-1607 Sentence denotes Palliative treatment was started and the patient deceased 27 days after onset of symptoms.
T138 1608-1719 Sentence denotes Microscopic examination of lung tissue of this case showed an almost complete loss of normal lung architecture.
T139 1720-1805 Sentence denotes Alveolar structures were unrecognizable and replaced by extensive fibrosis (Fig. 2B).
T140 1806-1910 Sentence denotes What remained were several foci of pneumocytes, bronchial epithelium, and blood vessels without thrombi.
T141 1911-1953 Sentence denotes In the PAS-D stain no fungi were observed.
T142 1954-2014 Sentence denotes The prominent pattern in this patient is pulmonary fibrosis.

LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T339 1238-1354 UBERON:0005169 denotes ifungal treatment initiated. CT head was performed because of the development of an epileptic insult and showed smal
T340 1484-1530 UBERON:0003215 denotes ad was seen with poor prognosis. Palliative tr
T341 1540-1571 UBERON:0003037 denotes s started and the patient decea
T342 1729-1832 UBERON:0003037 denotes structures were unrecognizable and replaced by extensive fibrosis (Fig. 2B). What remained were several
T343 1854-1893 UBERON:0001981 denotes bronchial epithelium, and blood vessels
T62375 227-232 UBERON:0001443 denotes chest
T96861 429-434 UBERON:3010752 denotes lobes
T278 506-517 UBERON:0001004 denotes respiratory
T890 609-621 CHEBI:8378;CHEBI:8378 denotes prednisolone
T280 683-688 UBERON:0001443 denotes chest
T281 721-730 UBERON:0002048 denotes pulmonary
T3895 745-755 UBERON:0002167 denotes right lung
T283 1017-1023 NCBITaxon:4751 denotes fungal
T96203 1063-1077 CHEBI:24261;CHEBI:24261 denotes glucocorticoid
T285 1157-1178 NCBITaxon:746128 denotes Aspergillus fumigatus
T42190 1191-1203 CHEBI:8378;CHEBI:8378 denotes prednisolone
T85772 1270-1274 UBERON:0000033 denotes head
T288 1384-1397 UBERON:0016525 denotes frontal lobes
T90302 1399-1409 UBERON:0001016 denotes Neurologic
T55602 1445-1453 UBERON:0001893 denotes cerebral
T84549 1482-1486 UBERON:0000033 denotes head
T87751 1635-1639 UBERON:0002048 denotes lung
T56185 1640-1646 UBERON:0000479 denotes tissue
T88680 1701-1705 UBERON:0002048 denotes lung
T295 1720-1728 UBERON:0003215 denotes Alveolar
T296 1841-1852 CL:0000322 denotes pneumocytes
T297 1854-1874 UBERON:0002031 denotes bronchial epithelium
T87358 1880-1893 UBERON:0001981 denotes blood vessels
T299 1933-1938 NCBITaxon:4751 denotes fungi
T300 1995-2004 UBERON:0002048 denotes pulmonary