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PMC:7537941 / 16200-19834 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T87 10-17 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T88 306-313 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T89 333-340 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T90 417-424 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T91 447-454 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T92 749-755 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T93 809-813 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T94 872-876 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T95 910-928 Body_part denotes lipopolysaccharide http://purl.org/sig/ont/fma/fma82785
T96 941-945 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T97 1273-1292 Body_part denotes alveolar epithelium http://purl.org/sig/ont/fma/fma63915
T98 1282-1292 Body_part denotes epithelium http://purl.org/sig/ont/fma/fma9639
T99 1985-1989 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T30 749-755 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T31 809-813 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T32 872-876 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T33 941-945 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T34 1282-1292 Body_part denotes epithelium http://purl.obolibrary.org/obo/UBERON_0000483
T35 1985-1989 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T127 756-762 Disease denotes injury http://purl.obolibrary.org/obo/MONDO_0021178
T128 814-820 Disease denotes injury http://purl.obolibrary.org/obo/MONDO_0021178
T129 877-883 Disease denotes injury http://purl.obolibrary.org/obo/MONDO_0021178
T130 946-952 Disease denotes injury http://purl.obolibrary.org/obo/MONDO_0021178
T131 954-988 Disease denotes Streptococcus pneumoniae infection http://purl.obolibrary.org/obo/MONDO_0005114
T132 979-988 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T133 1746-1765 Disease denotes respiratory failure http://purl.obolibrary.org/obo/MONDO_0021113
T134 1793-1803 Disease denotes Infectious http://purl.obolibrary.org/obo/MONDO_0005550
T135 1990-1996 Disease denotes injury http://purl.obolibrary.org/obo/MONDO_0021178
T136 2035-2039 Disease denotes ARDS http://purl.obolibrary.org/obo/MONDO_0006502
T137 2139-2143 Disease denotes ARDS http://purl.obolibrary.org/obo/MONDO_0006502
T138 2908-2916 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T139 2917-2926 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T140 3367-3375 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T159 0-9 http://purl.obolibrary.org/obo/CLO_0001658 denotes Activated
T160 30-31 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T161 131-134 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T162 226-235 http://purl.obolibrary.org/obo/CLO_0001658 denotes activated
T163 346-355 http://purl.obolibrary.org/obo/CLO_0001658 denotes activated
T164 676-677 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T165 809-813 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T166 809-813 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T167 872-876 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T168 872-876 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T169 941-945 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T170 941-945 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T171 1149-1157 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T172 1282-1292 http://purl.obolibrary.org/obo/UBERON_0000483 denotes epithelium
T173 1348-1358 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T174 1464-1467 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T175 1591-1600 http://purl.obolibrary.org/obo/CLO_0001658 denotes activated
T176 1767-1769 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T177 1970-1980 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T178 1985-1989 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T179 1985-1989 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T180 2007-2008 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T181 2018-2020 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T182 2053-2054 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T183 2229-2230 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T184 2713-2716 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T185 2748-2749 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T186 2846-2847 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T187 2857-2858 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T188 3213-3221 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T189 3347-3348 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T190 3364-3366 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
495 20-23 Gene denotes APC Gene:324
496 237-245 Gene denotes thrombin Gene:2147
497 255-269 Gene denotes thrombomodulin Gene:7056
498 294-324 Gene denotes endothelial protein C receptor Gene:10544
499 326-330 Gene denotes EPCR Gene:10544
500 357-360 Gene denotes APC Gene:324
501 379-383 Gene denotes EPCR Gene:10544
502 554-562 Gene denotes thrombin Gene:2147
503 699-702 Gene denotes APC Gene:324
504 1113-1121 Gene denotes thrombin Gene:2147
505 1050-1058 Gene denotes thrombin Gene:2147
506 575-578 Gene denotes APC Gene:324
507 846-852 Species denotes murine Tax:10090
508 443-446 Gene denotes APC Gene:324
509 438-442 Gene denotes EPCR Gene:10544
510 910-928 Chemical denotes lipopolysaccharide MESH:D008070
511 178-184 Disease denotes sepsis MESH:D018805
512 732-762 Disease denotes rhAPC attenuates tissue injury MESH:C538265
513 798-804 Disease denotes sepsis MESH:D018805
514 809-820 Disease denotes lung injury MESH:D055370
515 872-883 Disease denotes lung injury MESH:D055370
516 941-952 Disease denotes lung injury MESH:D055370
517 954-988 Disease denotes Streptococcus pneumoniae infection MESH:D011008
551 1460-1463 Gene denotes APC Gene:324
552 2304-2307 Gene denotes APC Gene:324
553 3287-3290 Gene denotes APC Gene:11789
554 2094-2097 Gene denotes APC Gene:324
555 1946-1949 Gene denotes APC Gene:324
556 1871-1874 Gene denotes APC Gene:324
557 1664-1672 Species denotes patients Tax:9606
558 2021-2029 Species denotes patients Tax:9606
559 2144-2152 Species denotes patients Tax:9606
560 2164-2172 Species denotes patients Tax:9606
561 2276-2288 Species denotes participants Tax:9606
562 2378-2386 Species denotes patients Tax:9606
563 2522-2530 Species denotes patients Tax:9606
564 2662-2669 Species denotes patient Tax:9606
565 3316-3320 Species denotes mice Tax:10090
566 1651-1660 Disease denotes mortality MESH:D003643
567 1678-1684 Disease denotes sepsis MESH:D018805
568 1746-1765 Disease denotes respiratory failure MESH:D012131
569 1793-1812 Disease denotes Infectious Diseases MESH:D003141
570 1907-1919 Disease denotes septic shock MESH:D012772
571 1985-1996 Disease denotes lung injury MESH:D055370
572 2035-2039 Disease denotes ARDS MESH:D012128
573 2139-2143 Disease denotes ARDS MESH:D012128
574 2178-2184 Disease denotes sepsis MESH:D018805
575 2204-2209 Disease denotes death MESH:D003643
576 2343-2351 Disease denotes bleeding MESH:D006470
577 2399-2405 Disease denotes sepsis MESH:D018805
578 2409-2421 Disease denotes septic shock MESH:D012772
579 2536-2548 Disease denotes septic shock MESH:D012772
580 2908-2926 Disease denotes COVID-19 pneumonia MESH:C000657245
581 3009-3017 Disease denotes bleeding MESH:D006470
582 3133-3141 Disease denotes bleeding MESH:D006470
583 3324-3330 Disease denotes sepsis MESH:D018805
592 3416-3419 Gene denotes APC Gene:324
593 3466-3469 Gene denotes APC Gene:324
594 3376-3384 Species denotes patients Tax:9606
595 3447-3455 Species denotes patients Tax:9606
596 3501-3509 Species denotes patients Tax:9606
597 3367-3375 Disease denotes COVID-19 MESH:C000657245
598 3535-3547 Disease denotes septic shock MESH:D012772
599 3567-3572 Disease denotes death MESH:D003643

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T86 61-72 http://purl.obolibrary.org/obo/GO_0050817 denotes coagulation
T87 203-214 http://purl.obolibrary.org/obo/GO_0050817 denotes coagulation
T88 1336-1347 http://purl.obolibrary.org/obo/GO_0050817 denotes coagulation
T89 1958-1969 http://purl.obolibrary.org/obo/GO_0050817 denotes coagulation
T90 3199-3221 http://purl.obolibrary.org/obo/GO_0050819 denotes anticoagulant activity

MyTest

Id Subject Object Predicate Lexical cue
33004529-15550023-29393015 186-188 15550023 denotes 54
33004529-16215381-29393015 186-188 16215381 denotes 54
33004529-9198130-29393016 517-519 9198130 denotes 57
33004529-9198130-29393017 639-641 9198130 denotes 57
33004529-14592828-29393018 643-645 14592828 denotes 58
33004529-3102560-29393019 822-824 3102560 denotes 59
33004529-8555486-29393019 822-824 8555486 denotes 59
33004529-11401891-29393019 822-824 11401891 denotes 59
33004529-19740417-29393020 1159-1161 19740417 denotes 46
33004529-19740417-29393021 1216-1218 19740417 denotes 46
33004529-15891319-29393022 1767-1769 15891319 denotes 22
33004529-17278083-29393023 1932-1934 17278083 denotes 62
33004529-23433188-29393024 2041-2043 23433188 denotes 63
33004529-24632673-29393025 2045-2047 24632673 denotes 64
33004529-18565951-29393026 2154-2156 18565951 denotes 65
33004529-16192478-29393027 2211-2213 16192478 denotes 66
33004529-23826709-29393028 2818-2820 23826709 denotes 68
33004529-17893198-29393029 3223-3225 17893198 denotes 69
33004529-17893198-29393030 3339-3341 17893198 denotes 69
33004529-32302438-29393031 3428-3430 32302438 denotes 70

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T66 178-184 Phenotype denotes sepsis http://purl.obolibrary.org/obo/HP_0100806
T67 798-804 Phenotype denotes sepsis http://purl.obolibrary.org/obo/HP_0100806
T68 968-978 Phenotype denotes pneumoniae http://purl.obolibrary.org/obo/HP_0002090
T69 1678-1684 Phenotype denotes sepsis http://purl.obolibrary.org/obo/HP_0100806
T70 1746-1765 Phenotype denotes respiratory failure http://purl.obolibrary.org/obo/HP_0002878
T71 1914-1919 Phenotype denotes shock http://purl.obolibrary.org/obo/HP_0031273
T72 2178-2184 Phenotype denotes sepsis http://purl.obolibrary.org/obo/HP_0100806
T73 2399-2405 Phenotype denotes sepsis http://purl.obolibrary.org/obo/HP_0100806
T74 2416-2421 Phenotype denotes shock http://purl.obolibrary.org/obo/HP_0031273
T75 2453-2458 Phenotype denotes Shock http://purl.obolibrary.org/obo/HP_0031273
T76 2543-2548 Phenotype denotes shock http://purl.obolibrary.org/obo/HP_0031273
T77 2917-2926 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T78 3324-3330 Phenotype denotes sepsis http://purl.obolibrary.org/obo/HP_0100806
T79 3542-3547 Phenotype denotes shock http://purl.obolibrary.org/obo/HP_0031273

2_test

Id Subject Object Predicate Lexical cue
33004529-15550023-29393015 186-188 15550023 denotes 54
33004529-16215381-29393015 186-188 16215381 denotes 54
33004529-9198130-29393016 517-519 9198130 denotes 57
33004529-9198130-29393017 639-641 9198130 denotes 57
33004529-14592828-29393018 643-645 14592828 denotes 58
33004529-3102560-29393019 822-824 3102560 denotes 59
33004529-8555486-29393019 822-824 8555486 denotes 59
33004529-11401891-29393019 822-824 11401891 denotes 59
33004529-19740417-29393020 1159-1161 19740417 denotes 46
33004529-19740417-29393021 1216-1218 19740417 denotes 46
33004529-15891319-29393022 1767-1769 15891319 denotes 22
33004529-17278083-29393023 1932-1934 17278083 denotes 62
33004529-23433188-29393024 2041-2043 23433188 denotes 63
33004529-24632673-29393025 2045-2047 24632673 denotes 64
33004529-18565951-29393026 2154-2156 18565951 denotes 65
33004529-16192478-29393027 2211-2213 16192478 denotes 66
33004529-23826709-29393028 2818-2820 23826709 denotes 68
33004529-17893198-29393029 3223-3225 17893198 denotes 69
33004529-17893198-29393030 3339-3341 17893198 denotes 69
33004529-32302438-29393031 3428-3430 32302438 denotes 70

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T92 0-19 Sentence denotes Activated protein C
T93 20-193 Sentence denotes APC plays a critical role in terminating coagulation by proteolytically inactivating factors Va and VIIIa, and has been widely investigated in the context of sepsis [54–56].
T94 194-356 Sentence denotes Once the coagulation cascade is activated, thrombin binds to thrombomodulin and, facilitated by the endothelial protein C receptor (EPCR), protein C is activated.
T95 357-574 Sentence denotes APC then binds to the EPCR and, together with its co-factor protein S, forms the EPCR-APC-protein S complex that binds and degrades factor Va and factor VIIIa [57], providing negative feedback for thrombin generation.
T96 575-647 Sentence denotes APC also exerts pro-fibrinolytic and anti-inflammatory effects [57, 58].
T97 648-829 Sentence denotes Preclinical studies support a beneficial effect of APC administration, showing that rhAPC attenuates tissue injury and improves survival in models of sepsis and lung injury [59–61].
T98 830-1220 Sentence denotes For example, in murine models of indirect lung injury (intravenous injection of lipopolysaccharide) and direct lung injury (Streptococcus pneumoniae infection), nebulised rhAPC specifically reduced local bronchoalveolar thrombin and fibrin generation without affecting intravascular thrombin generation or fibrinolytic activity [46] and without adversely affecting bacterial clearance [46].
T99 1221-1393 Sentence denotes This provides proof-of-principle that targeting the alveolar epithelium locally with nebulised rhAPC can attenuate coagulation activation without compromising host defence.
T100 1394-1500 Sentence denotes In clinical studies, systemic, rather than nebulised, delivery of APC has had initially promising results.
T101 1501-1771 Sentence denotes In the original landmark PROWESS study, intravenous infusion of rhAPC (drotrecogin alpha (activated) (DrotAA)) significantly reduced 28-day all-cause mortality in patients with sepsis (secondary to CAP) by 28% and reduced the resolution time of respiratory failure [22].
T102 1772-1936 Sentence denotes This resulted in the Infectious Diseases Society of America/American Thoracic Society recommending APC for the treatment of refractory septic shock due to CAP [62].
T103 1937-2215 Sentence denotes Although APC reduced coagulation activation and lung injury scores in a study of 27 patients with ARDS [63, 64], in a subsequent randomised controlled trial APC did not improve the clinical outcomes of ARDS patients [65] or of patients with sepsis and low of risk of death [66].
T104 2216-2427 Sentence denotes Furthermore, a meta-analysis of five studies involving 5101 participants concluded that APC was associated with higher risk of bleeding and should not be used in patients with severe sepsis or septic shock [67].
T105 2428-2621 Sentence denotes Importantly, the PROWESS-Shock study [55] failed to demonstrate an improvement in survival in patients with septic shock and eventually led to the withdrawal of DrotAA (Xigris) from the market.
T106 2622-2927 Sentence denotes However, the significant differences in patient characteristics between the PROWESS trials has led to the recommendation that a trial of DrotAA should be repeated using an optimised study design [68], and this could include a trial in a less heterogeneous high-risk population, such as COVID-19 pneumonia.
T107 2928-3113 Sentence denotes The preclinical and clinical data suggest nebulised rhAPC may not carry the same bleeding liability as intravenous administration and may be an appropriate route of drug administration.
T108 3114-3343 Sentence denotes Alternatively, the bleeding risk could be mitigated using an rhAPC variant with <10% anticoagulant activity [69], which in preclinical studies was as effective as wild-type APC in improving survival of mice in sepsis models [69].
T109 3344-3634 Sentence denotes In a small study of 11 COVID-19 patients, most had increased endogenous APC levels [70]; however, four patients had lower APC levels and in this subgroup of patients, particularly those with septic shock or at high risk of death, administration of rhAPC might warrant further investigation.