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PMC:7340597 / 19065-21011 JSONTXT

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LitCovid_Glycan-Motif-Structure

Id Subject Object Predicate Lexical cue
T22 393-395 https://glytoucan.org/Structures/Glycans/G93424OB denotes GM

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T113 512-517 Body_part denotes Chest http://purl.org/sig/ont/fma/fma9576
T114 872-876 Body_part denotes head http://purl.org/sig/ont/fma/fma7154
T115 1178-1182 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T116 1245-1253 Body_part denotes alveolar http://purl.org/sig/ont/fma/fma264783
T117 1269-1281 Body_part denotes fibroblastic http://purl.org/sig/ont/fma/fma63877
T118 1282-1288 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T119 1626-1634 Body_part denotes alveolar http://purl.org/sig/ont/fma/fma264783
T120 1671-1684 Body_part denotes blood vessels http://purl.org/sig/ont/fma/fma63183
T121 1671-1676 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T122 1754-1765 Body_part denotes eosinophils http://purl.org/sig/ont/fma/fma62861

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T67 512-517 Body_part denotes Chest http://purl.obolibrary.org/obo/UBERON_0001443
T68 872-876 Body_part denotes head http://purl.obolibrary.org/obo/UBERON_0000033
T69 1178-1182 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T70 1282-1288 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T71 1394-1401 Body_part denotes exudate http://purl.obolibrary.org/obo/UBERON_0007780
T72 1671-1684 Body_part denotes blood vessels http://purl.obolibrary.org/obo/UBERON_0001981
T73 1671-1676 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T74 1677-1684 Body_part denotes vessels http://purl.obolibrary.org/obo/UBERON_0000055

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
437 45-54 Disease denotes pneumonia MESH:D011014
450 199-206 Species denotes Patient Tax:9606
451 409-430 Species denotes Aspergillus fumigatus Tax:746128
452 799-806 Species denotes patient Tax:9606
453 1087-1094 Species denotes patient Tax:9606
454 435-447 Species denotes Enterococcus Tax:1351
455 393-395 Chemical denotes GM MESH:C012990
456 101-124 Disease denotes cardiopulmonary disease MESH:D006323
457 179-184 Disease denotes fever MESH:D005334
458 189-197 Disease denotes dyspnoea MESH:D004417
459 340-349 Disease denotes infection MESH:D007239
460 550-566 Disease denotes pulmonary emboli MESH:D011655
461 894-923 Disease denotes bilateral cerebellar ischemia MESH:D007511
466 1178-1189 Disease denotes lung injury MESH:D055370
467 1328-1337 Disease denotes pneumonia MESH:D011014
468 1496-1505 Disease denotes pneumonia MESH:D011014
469 1920-1929 Disease denotes pneumonia MESH:D011014

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T158 34-54 Disease denotes organizing pneumonia http://purl.obolibrary.org/obo/MONDO_0015265|http://purl.obolibrary.org/obo/MONDO_0056821
T160 45-54 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T161 101-124 Disease denotes cardiopulmonary disease http://purl.obolibrary.org/obo/MONDO_0004596
T162 340-349 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T163 767-781 Disease denotes bronchiectasis http://purl.obolibrary.org/obo/MONDO_0004822
T164 915-923 Disease denotes ischemia http://purl.obolibrary.org/obo/MONDO_0005053
T165 1183-1189 Disease denotes injury http://purl.obolibrary.org/obo/MONDO_0021178
T166 1317-1337 Disease denotes organizing pneumonia http://purl.obolibrary.org/obo/MONDO_0015265|http://purl.obolibrary.org/obo/MONDO_0056821
T168 1328-1337 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T169 1485-1505 Disease denotes organizing pneumonia http://purl.obolibrary.org/obo/MONDO_0015265|http://purl.obolibrary.org/obo/MONDO_0056821
T171 1496-1505 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T172 1791-1794 Disease denotes PAS http://purl.obolibrary.org/obo/MONDO_0004277
T173 1909-1929 Disease denotes organizing pneumonia http://purl.obolibrary.org/obo/MONDO_0015265|http://purl.obolibrary.org/obo/MONDO_0056821
T175 1920-1929 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T168 34-44 http://purl.obolibrary.org/obo/OBI_0000245 denotes organizing
T169 55-56 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T170 69-73 http://purl.obolibrary.org/obo/UBERON_0003101 denotes male
T171 69-73 http://www.ebi.ac.uk/efo/EFO_0000970 denotes male
T172 153-154 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T173 382-383 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T174 512-517 http://www.ebi.ac.uk/efo/EFO_0000965 denotes Chest
T175 872-876 http://purl.obolibrary.org/obo/UBERON_0000033 denotes head
T176 872-876 http://www.ebi.ac.uk/efo/EFO_0000964 denotes head
T177 1165-1166 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T178 1178-1182 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T179 1178-1182 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T180 1269-1281 http://purl.obolibrary.org/obo/CL_0000057 denotes fibroblastic
T181 1317-1327 http://purl.obolibrary.org/obo/OBI_0000245 denotes organizing
T182 1348-1349 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T183 1485-1495 http://purl.obolibrary.org/obo/OBI_0000245 denotes organizing
T184 1538-1539 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T185 1671-1684 http://purl.obolibrary.org/obo/UBERON_0001981 denotes blood vessels
T186 1671-1684 http://www.ebi.ac.uk/efo/EFO_0000817 denotes blood vessels
T187 1730-1739 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membranes
T188 1909-1919 http://purl.obolibrary.org/obo/OBI_0000245 denotes organizing

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T103 69-73 Chemical denotes male http://purl.obolibrary.org/obo/CHEBI_30780
T104 147-149 Chemical denotes ED http://purl.obolibrary.org/obo/CHEBI_73503
T105 351-354 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T106 393-395 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680
T108 848-856 Chemical denotes sedative http://purl.obolibrary.org/obo/CHEBI_35717
T109 1791-1794 Chemical denotes PAS http://purl.obolibrary.org/obo/CHEBI_27565

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T48 45-54 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T49 179-184 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T50 189-197 Phenotype denotes dyspnoea http://purl.obolibrary.org/obo/HP_0002094
T51 767-781 Phenotype denotes bronchiectasis http://purl.obolibrary.org/obo/HP_0002110
T52 1328-1337 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T53 1496-1505 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T54 1920-1929 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T20 393-395 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T161 0-54 Sentence denotes 3.5 Case 4 – Acute fibrinous and organizing pneumonia
T162 55-198 Sentence denotes A 68-year old male without medical history of cardiopulmonary disease, was presented at the ED in a critical condition with fever and dyspnoea.
T163 199-318 Sentence denotes Patient was in need of endotracheal intubation and mechanical ventilation in prone position to improve his oxygenation.
T164 319-456 Sentence denotes To exclude secondary infection, BAL was performed and revealed a positive GM and cultured Aspergillus fumigatus and Enterococcus faecium.
T165 457-511 Sentence denotes Antifungal therapy was added to his treatment regimen.
T166 512-706 Sentence denotes Chest CT-angiography showed segmental pulmonary emboli along with extensive bilateral areas of ground-glass opacity with reticulation and multiple patchy non-dependant peripheral consolidations.
T167 707-794 Sentence denotes In contrast to normal areas, the abnormal areas showed mild bronchiectasis (Fig. 1-4A).
T168 795-868 Sentence denotes The patient remained unresponsive after cessation of sedative medication.
T169 869-959 Sentence denotes CT head showed extensive bilateral cerebellar ischemia with small haemorrhagic components.
T170 960-1082 Sentence denotes After three weeks of mechanical ventilation his respiratory status worsened and treatment was ended due to poor prognosis.
T171 1083-1140 Sentence denotes The patient passed away 21 days after hospital admission.
T172 1141-1238 Sentence denotes Biopsy specimens showed a pattern of lung injury, that was partially identical to that of case 1.
T173 1239-1338 Sentence denotes Intra-alveolar depositions of fibroblastic tissue were found, consistent with organizing pneumonia.
T174 1339-1506 Sentence denotes However, a predominant, diffuse component of fibrinous exudate in the alveoli was present, which was not the case in the aforementioned case with organizing pneumonia.
T175 1507-1641 Sentence denotes Other histologic findings were a chronic inflammatory infiltrate, and mild interstitial changes, including widening of alveolar septa.
T176 1642-1704 Sentence denotes Microthrombi in small septal blood vessels were also observed.
T177 1705-1779 Sentence denotes Neither remnants hyaline membranes nor prominent eosinophils were present.
T178 1780-1826 Sentence denotes Additional PAS-D stain did not show any fungi.
T179 1827-1946 Sentence denotes The overall histologic pattern of this case was classified as acute fibrinous and organizing pneumonia (AFOP), Fig. 2D.

LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T31499 222-234 UBERON:0001852 denotes endotracheal
T16403 306-317 GO:0015671 denotes oxygenation
T14517 409-430 NCBITaxon:746128 denotes Aspergillus fumigatus
T4434 435-455 NCBITaxon:1352 denotes Enterococcus faecium
T32949 550-559 UBERON:0002048 denotes pulmonary
T23048 872-876 UBERON:0000033 denotes head
T39092 904-914 UBERON:0002037 denotes cerebellar
T74431 1008-1019 UBERON:0001004 denotes respiratory
T28835 1178-1182 UBERON:0002048 denotes lung
T46508 1245-1253 UBERON:0003215 denotes alveolar
T32950 1269-1281 CL:0000057 denotes fibroblastic
T85905 1282-1288 UBERON:0000479 denotes tissue
T72453 1409-1416 UBERON:0003215 denotes alveoli
T83892 1582-1594 UBERON:0005169 denotes interstitial
T50871 1626-1634 UBERON:0003215 denotes alveolar
T65185 1635-1640 UBERON:0003037 denotes septa
T3448 1664-1670 UBERON:0003037 denotes septal
T58151 1671-1684 UBERON:0001981 denotes blood vessels
T66331 1730-1739 GO:0016020 denotes membranes
T96825 1754-1765 CL:0000771 denotes eosinophils
T62230 1820-1825 NCBITaxon:4751 denotes fungi