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PMC:7340597 / 15074-17065 JSONTXT

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LitCovid_Glycan-Motif-Structure

Id Subject Object Predicate Lexical cue
T19 949-951 https://glytoucan.org/Structures/Glycans/G93424OB denotes GM
T20 1087-1089 https://glytoucan.org/Structures/Glycans/G93424OB denotes GM

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T84 204-209 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T85 309-332 Body_part denotes bronchovascular bundles http://purl.org/sig/ont/fma/fma84474
T86 660-665 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T87 722-732 Body_part denotes right lung http://purl.org/sig/ont/fma/fma7309
T88 1247-1251 Body_part denotes head http://purl.org/sig/ont/fma/fma7154
T89 1361-1374 Body_part denotes frontal lobes http://purl.org/sig/ont/fma/fma61824
T90 1459-1463 Body_part denotes head http://purl.org/sig/ont/fma/fma7154
T91 1612-1616 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T92 1617-1623 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T93 1678-1682 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T94 1697-1705 Body_part denotes Alveolar http://purl.org/sig/ont/fma/fma264783
T95 1818-1829 Body_part denotes pneumocytes http://purl.org/sig/ont/fma/fma62499
T96 1831-1851 Body_part denotes bronchial epithelium http://purl.org/sig/ont/fma/fma67782
T97 1841-1851 Body_part denotes epithelium http://purl.org/sig/ont/fma/fma9639
T98 1857-1870 Body_part denotes blood vessels http://purl.org/sig/ont/fma/fma63183
T99 1857-1862 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T45 204-209 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T46 660-665 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T47 722-732 Body_part denotes right lung http://purl.obolibrary.org/obo/UBERON_0002167
T48 728-732 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T49 1247-1251 Body_part denotes head http://purl.obolibrary.org/obo/UBERON_0000033
T50 1361-1374 Body_part denotes frontal lobes http://purl.obolibrary.org/obo/UBERON_0016525
T51 1459-1463 Body_part denotes head http://purl.obolibrary.org/obo/UBERON_0000033
T52 1612-1616 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T53 1617-1623 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T54 1678-1682 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T55 1831-1851 Body_part denotes bronchial epithelium http://purl.obolibrary.org/obo/UBERON_0002031
T56 1841-1851 Body_part denotes epithelium http://purl.obolibrary.org/obo/UBERON_0000483
T57 1857-1870 Body_part denotes blood vessels http://purl.obolibrary.org/obo/UBERON_0001981
T58 1857-1862 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T59 1863-1870 Body_part denotes vessels http://purl.obolibrary.org/obo/UBERON_0000055

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
394 1134-1155 Species denotes Aspergillus fumigatus Tax:746128
395 1535-1542 Species denotes patient Tax:9606
396 1961-1968 Species denotes patient Tax:9606
397 586-598 Chemical denotes prednisolone MESH:D011239
398 949-951 Chemical denotes GM MESH:C012990
399 1168-1180 Chemical denotes prednisolone MESH:D011239
400 156-165 Disease denotes diarrhoea MESH:D003967
401 170-189 Disease denotes shortness of breath MESH:D004417
402 562-566 Disease denotes ARDS MESH:D012128
403 698-714 Disease denotes pulmonary emboli MESH:D011655
404 1001-1010 Disease denotes infection MESH:D007239
405 1299-1308 Disease denotes epileptic MESH:D004827
406 1341-1352 Disease denotes haemorrhage MESH:D006470
407 1422-1442 Disease denotes cerebral haemorrhage MESH:D002543
408 1763-1771 Disease denotes fibrosis MESH:D005355
409 1972-1990 Disease denotes pulmonary fibrosis MESH:D011658

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T147 156-165 Disease denotes diarrhoea http://purl.obolibrary.org/obo/MONDO_0001673
T148 420-434 Disease denotes bronchiectasis http://purl.obolibrary.org/obo/MONDO_0004822
T149 562-566 Disease denotes ARDS http://purl.obolibrary.org/obo/MONDO_0006502
T150 892-906 Disease denotes bronchiectasis http://purl.obolibrary.org/obo/MONDO_0004822
T151 994-1010 Disease denotes fungal infection http://purl.obolibrary.org/obo/MONDO_0002041
T152 1001-1010 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T153 1895-1898 Disease denotes PAS http://purl.obolibrary.org/obo/MONDO_0004277
T154 1972-1990 Disease denotes pulmonary fibrosis http://purl.obolibrary.org/obo/MONDO_0002771

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T133 0-1 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T134 14-20 http://purl.obolibrary.org/obo/UBERON_0003100 denotes female
T135 79-80 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T136 204-209 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T137 474-476 http://purl.obolibrary.org/obo/CLO_0001236 denotes 2A
T138 660-665 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T139 722-732 http://purl.obolibrary.org/obo/UBERON_0002167 denotes right lung
T140 809-810 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T141 1085-1086 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T142 1247-1251 http://purl.obolibrary.org/obo/UBERON_0000033 denotes head
T143 1247-1251 http://www.ebi.ac.uk/efo/EFO_0000964 denotes head
T144 1459-1463 http://purl.obolibrary.org/obo/UBERON_0000033 denotes head
T145 1459-1463 http://www.ebi.ac.uk/efo/EFO_0000964 denotes head
T146 1552-1554 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T147 1612-1616 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T148 1612-1616 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T149 1678-1682 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T150 1678-1682 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T151 1841-1851 http://purl.obolibrary.org/obo/UBERON_0000483 denotes epithelium
T152 1857-1870 http://purl.obolibrary.org/obo/UBERON_0001981 denotes blood vessels
T153 1857-1870 http://www.ebi.ac.uk/efo/EFO_0000817 denotes blood vessels

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T85 586-598 Chemical denotes prednisolone http://purl.obolibrary.org/obo/CHEBI_8378
T86 920-923 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T87 949-951 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680
T89 1040-1054 Chemical denotes glucocorticoid http://purl.obolibrary.org/obo/CHEBI_24261
T90 1063-1066 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T91 1087-1089 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680
T93 1168-1180 Chemical denotes prednisolone http://purl.obolibrary.org/obo/CHEBI_8378
T94 1212-1222 Chemical denotes antifungal http://purl.obolibrary.org/obo/CHEBI_35718
T95 1895-1898 Chemical denotes PAS http://purl.obolibrary.org/obo/CHEBI_27565

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T39 156-165 Phenotype denotes diarrhoea http://purl.obolibrary.org/obo/HP_0002014
T40 170-189 Phenotype denotes shortness of breath http://purl.obolibrary.org/obo/HP_0002098
T41 420-434 Phenotype denotes bronchiectasis http://purl.obolibrary.org/obo/HP_0002110
T42 883-906 Phenotype denotes traction bronchiectasis http://purl.obolibrary.org/obo/HP_0032969
T43 1422-1442 Phenotype denotes cerebral haemorrhage http://purl.obolibrary.org/obo/HP_0001342
T44 1972-1990 Phenotype denotes pulmonary fibrosis http://purl.obolibrary.org/obo/HP_0002206

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T4 1124-1130 http://purl.obolibrary.org/obo/GO_0040007 denotes growth

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T17 949-951 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T18 1087-1089 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T121 0-97 Sentence denotes A 73-year old female was transferred to our ICU due to shortage of ICU beds in a nearby hospital.
T122 98-190 Sentence denotes Prior to ICU admission, she was healthy but complained of diarrhoea and shortness of breath.
T123 191-347 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 348-412 Sentence denotes There were some small areas of consolidation in the upper lobes.
T125 413-478 Sentence denotes Subtle bronchiectasis were present in affected areas (Fig. 1-2A).
T126 479-567 Sentence denotes Her respiratory condition required mechanical ventilation in prone position due to ARDS.
T127 568-652 Sentence denotes After seven days, prednisolone treatment was started because of lack of improvement.
T128 653-733 Sentence denotes Repeat chest CT-angiography showed segmental pulmonary emboli in the right lung.
T129 734-808 Sentence denotes Ground-glass opacities persisted while the consolidations had disappeared.
T130 809-919 Sentence denotes A reticular pattern combined with GGO was more pronounced with increasing traction bronchiectasis (Fig. 1-2B).
T131 920-1011 Sentence denotes BAL was performed twice, but GM and culture showed no signs of additional fungal infection.
T132 1012-1100 Sentence denotes After one week of high dose glucocorticoid therapy BAL was repeated with a GM index 4.4.
T133 1101-1156 Sentence denotes Fungal cultures showed growth of Aspergillus fumigatus.
T134 1157-1243 Sentence denotes Therefore, prednisolone treatment was discontinued and antifungal treatment initiated.
T135 1244-1375 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 1376-1493 Sentence denotes Neurologic condition worsened and progressive cerebral haemorrhage on follow up CT head was seen with poor prognosis.
T137 1494-1584 Sentence denotes Palliative treatment was started and the patient deceased 27 days after onset of symptoms.
T138 1585-1696 Sentence denotes Microscopic examination of lung tissue of this case showed an almost complete loss of normal lung architecture.
T139 1697-1782 Sentence denotes Alveolar structures were unrecognizable and replaced by extensive fibrosis (Fig. 2B).
T140 1783-1887 Sentence denotes What remained were several foci of pneumocytes, bronchial epithelium, and blood vessels without thrombi.
T141 1888-1930 Sentence denotes In the PAS-D stain no fungi were observed.
T142 1931-1991 Sentence denotes The prominent pattern in this patient is pulmonary fibrosis.

LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T339 1215-1331 UBERON:0005169 denotes ifungal treatment initiated. CT head was performed because of the development of an epileptic insult and showed smal
T340 1461-1507 UBERON:0003215 denotes ad was seen with poor prognosis. Palliative tr
T341 1517-1548 UBERON:0003037 denotes s started and the patient decea
T342 1706-1809 UBERON:0003037 denotes structures were unrecognizable and replaced by extensive fibrosis (Fig. 2B). What remained were several
T343 1831-1870 UBERON:0001981 denotes bronchial epithelium, and blood vessels
T62375 204-209 UBERON:0001443 denotes chest
T96861 406-411 UBERON:3010752 denotes lobes
T278 483-494 UBERON:0001004 denotes respiratory
T890 586-598 CHEBI:8378;CHEBI:8378 denotes prednisolone
T280 660-665 UBERON:0001443 denotes chest
T281 698-707 UBERON:0002048 denotes pulmonary
T3895 722-732 UBERON:0002167 denotes right lung
T283 994-1000 NCBITaxon:4751 denotes fungal
T96203 1040-1054 CHEBI:24261;CHEBI:24261 denotes glucocorticoid
T285 1134-1155 NCBITaxon:746128 denotes Aspergillus fumigatus
T42190 1168-1180 CHEBI:8378;CHEBI:8378 denotes prednisolone
T85772 1247-1251 UBERON:0000033 denotes head
T288 1361-1374 UBERON:0016525 denotes frontal lobes
T90302 1376-1386 UBERON:0001016 denotes Neurologic
T55602 1422-1430 UBERON:0001893 denotes cerebral
T84549 1459-1463 UBERON:0000033 denotes head
T87751 1612-1616 UBERON:0002048 denotes lung
T56185 1617-1623 UBERON:0000479 denotes tissue
T88680 1678-1682 UBERON:0002048 denotes lung
T295 1697-1705 UBERON:0003215 denotes Alveolar
T296 1818-1829 CL:0000322 denotes pneumocytes
T297 1831-1851 UBERON:0002031 denotes bronchial epithelium
T87358 1857-1870 UBERON:0001981 denotes blood vessels
T299 1910-1915 NCBITaxon:4751 denotes fungi
T300 1972-1981 UBERON:0002048 denotes pulmonary