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PMC:7354481 / 25703-29756 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T155 121-127 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T156 284-288 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T157 666-673 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T158 782-790 Body_part denotes cytokine http://purl.org/sig/ont/fma/fma84050
T159 791-799 Body_part denotes cytokine http://purl.org/sig/ont/fma/fma84050
T160 1082-1089 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T161 1358-1366 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T162 1974-1982 Body_part denotes cytokine http://purl.org/sig/ont/fma/fma84050
T163 2027-2035 Body_part denotes cytokine http://purl.org/sig/ont/fma/fma84050
T164 2036-2044 Body_part denotes cytokine http://purl.org/sig/ont/fma/fma84050
T165 2188-2196 Body_part denotes cytokine http://purl.org/sig/ont/fma/fma84050
T166 2319-2323 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T167 2324-2330 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T168 2407-2416 Body_part denotes chemokine http://purl.org/sig/ont/fma/fma241981
T169 2543-2553 Body_part denotes neutrophil http://purl.org/sig/ont/fma/fma62860
T170 2637-2641 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T171 2642-2648 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T172 2762-2772 Body_part denotes neutrophil http://purl.org/sig/ont/fma/fma62860
T173 2907-2911 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T174 2986-2993 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T175 3103-3112 Body_part denotes ribosomal http://purl.org/sig/ont/fma/fma66867
T176 3184-3188 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T177 3232-3236 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T178 3300-3304 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T179 3526-3532 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T180 3578-3586 Body_part denotes cytokine http://purl.org/sig/ont/fma/fma84050
T181 3691-3696 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T182 3718-3724 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T183 3750-3754 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T184 3831-3838 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T19 2319-2323 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T20 2324-2330 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T21 2637-2641 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T22 2642-2648 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T23 3184-3188 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T24 3300-3304 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T25 3718-3724 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T96 110-118 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T97 398-409 Disease denotes myocarditis http://purl.obolibrary.org/obo/MONDO_0004496
T98 655-663 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T99 906-914 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T100 1043-1051 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T101 1329-1337 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T102 1520-1528 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T103 1960-1968 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T104 2299-2307 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T105 2811-2819 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T106 2955-2958 Disease denotes SRP http://purl.obolibrary.org/obo/MONDO_0019691
T107 3166-3174 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T108 3280-3288 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T109 3631-3640 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T110 3820-3828 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T111 3949-3967 Disease denotes pulmonary fibrosis http://purl.obolibrary.org/obo/MONDO_0002771

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T251 72-77 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T252 185-188 http://purl.obolibrary.org/obo/PR_000001932 denotes Hsa
T253 237-238 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T254 282-288 http://purl.obolibrary.org/obo/CL_0000084 denotes T-cell
T255 321-323 http://purl.obolibrary.org/obo/CLO_0053799 denotes 45
T256 475-476 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T257 549-552 http://purl.obolibrary.org/obo/PR_000001932 denotes hsa
T258 563-565 http://purl.obolibrary.org/obo/CLO_0053799 denotes 45
T259 733-743 http://purl.obolibrary.org/obo/SO_0000418 denotes signalling
T260 961-966 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T261 1026-1033 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T262 1121-1129 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T263 1216-1218 http://purl.obolibrary.org/obo/CL_0000453 denotes LC
T264 1219-1221 http://purl.obolibrary.org/obo/CLO_0007874 denotes MS
T265 1222-1224 http://purl.obolibrary.org/obo/CLO_0007874 denotes MS
T266 1348-1350 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T267 1355-1357 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T268 1355-1357 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T269 1486-1488 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T270 2148-2153 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T271 2319-2323 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T272 2319-2323 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T273 2463-2473 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T274 2637-2641 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T275 2637-2641 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T276 2665-2667 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T277 2665-2667 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T278 2907-2911 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T279 3007-3015 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T280 3058-3071 http://purl.obolibrary.org/obo/PR_000005794 denotes ceruloplasmin
T281 3113-3125 http://purl.obolibrary.org/obo/OBI_0000245 denotes organization
T282 3184-3188 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T283 3184-3188 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T284 3232-3236 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T285 3300-3304 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T286 3300-3304 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T287 3576-3577 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T288 3597-3598 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T289 3642-3644 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48
T290 3691-3696 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T291 3750-3754 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T292 3793-3796 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T293 3872-3882 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T294 3888-3899 http://purl.obolibrary.org/obo/PR_000012867 denotes plasminogen
T295 3900-3909 http://purl.obolibrary.org/obo/CLO_0001658 denotes activator
T296 4002-4007 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T297 4049-4051 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T60 311-319 Chemical denotes antigens http://purl.obolibrary.org/obo/CHEBI_59132
T61 728-732 Chemical denotes beta http://purl.obolibrary.org/obo/CHEBI_10545
T62 756-764 Chemical denotes O-glycan http://purl.obolibrary.org/obo/CHEBI_59521
T63 1082-1089 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T64 1216-1218 Chemical denotes LC http://purl.obolibrary.org/obo/CHEBI_73582
T65 1219-1221 Chemical denotes MS http://purl.obolibrary.org/obo/CHEBI_73613
T66 1222-1224 Chemical denotes MS http://purl.obolibrary.org/obo/CHEBI_73613
T67 1355-1357 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T68 1358-1366 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T69 1583-1592 Chemical denotes N-glycans http://purl.obolibrary.org/obo/CHEBI_59520
T70 1585-1592 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T71 1619-1628 Chemical denotes O-glycans http://purl.obolibrary.org/obo/CHEBI_59521
T72 1621-1628 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T73 1826-1835 Chemical denotes biomarker http://purl.obolibrary.org/obo/CHEBI_59163
T74 2665-2667 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T75 2986-2993 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T76 3083-3090 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T77 3831-3838 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T78 3910-3919 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T24 239-245 Phenotype denotes sepsis http://purl.obolibrary.org/obo/HP_0100806
T25 398-409 Phenotype denotes myocarditis http://purl.obolibrary.org/obo/HP_0012819
T26 1974-1988 Phenotype denotes cytokine storm http://purl.obolibrary.org/obo/HP_0033041
T27 3949-3967 Phenotype denotes pulmonary fibrosis http://purl.obolibrary.org/obo/HP_0002206

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T70 469-473 http://purl.obolibrary.org/obo/GO_0004707 denotes MAPK
T71 733-743 http://purl.obolibrary.org/obo/GO_0023052 denotes signalling
T72 758-777 http://purl.obolibrary.org/obo/GO_0000271 denotes glycan biosynthesis
T73 765-777 http://purl.obolibrary.org/obo/GO_0009058 denotes biosynthesis
T74 1061-1076 http://purl.obolibrary.org/obo/GO_0006493 denotes O-glycosylation
T75 1063-1076 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation
T76 1121-1136 http://purl.obolibrary.org/obo/GO_0061025 denotes membrane fusion
T77 1173-1189 http://purl.obolibrary.org/obo/GO_0006955 denotes immune responses
T78 1416-1431 http://purl.obolibrary.org/obo/GO_0006493 denotes O-glycosylation
T79 1418-1431 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation
T80 1752-1767 http://purl.obolibrary.org/obo/GO_0006487 denotes N-glycosylation
T81 1754-1767 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation
T82 2458-2462 http://purl.obolibrary.org/obo/GO_0005007 denotes FGFR
T83 2543-2567 http://purl.obolibrary.org/obo/GO_0043312 denotes neutrophil degranulation
T84 2773-2784 http://purl.obolibrary.org/obo/GO_0009056 denotes degradation
T85 2972-2985 http://purl.obolibrary.org/obo/GO_0006412 denotes translational
T86 2986-3015 http://purl.obolibrary.org/obo/GO_0006612 denotes protein targeting to membrane
T87 2986-3003 http://purl.obolibrary.org/obo/GO_0006605 denotes protein targeting
T88 3031-3044 http://purl.obolibrary.org/obo/GO_0006412 denotes translational
T89 3083-3101 http://purl.obolibrary.org/obo/GO_0019882 denotes antigen processing
T90 3135-3147 http://purl.obolibrary.org/obo/GO_0036503 denotes ERAD pathway
T91 3135-3139 http://purl.obolibrary.org/obo/GO_0030433 denotes ERAD
T92 3232-3247 http://purl.obolibrary.org/obo/GO_0010467 denotes gene expression
T93 3666-3682 http://purl.obolibrary.org/obo/GO_0006955 denotes immune responses
T94 3718-3736 http://purl.obolibrary.org/obo/GO_0048771 denotes tissue remodelling
T95 3765-3774 http://purl.obolibrary.org/obo/GO_0097194 denotes apoptosis
T96 3765-3774 http://purl.obolibrary.org/obo/GO_0006915 denotes apoptosis
T97 3888-3909 http://purl.obolibrary.org/obo/GO_0031639 denotes plasminogen activator
T98 4019-4028 http://purl.obolibrary.org/obo/GO_0009058 denotes formation

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T176 0-184 Sentence denotes There is preliminary data about the existence of sequence similarity of human miRs in the spike region of the SARS-CoV-2 genome for both forward and reverse complementary strands [44].
T177 185-325 Sentence denotes Hsa-miR-8055, which was also previously shown to be a sepsis marker, was found to be involved in T-cell responses to specific antigens [45].
T178 326-567 Sentence denotes One of the differentially expressed circRNAs in children with fulminant myocarditis, Circ_0071542, was suggested to regulate the expression of MAPK, a well-characterized target in the development of disease through binding hsa-miR-8055 [45].
T179 568-821 Sentence denotes In our current study, we found that the miR-8066 sequence is present in four different SARS-CoV-2 genomes and shows strong association in KEGG pathways for TGF-beta signalling, mucin type O-glycan biosynthesis and cytokine-cytokine receptor interaction.
T180 822-983 Sentence denotes These targeted pathways are known, critical mediators for the clinical outcomes for SARS-CoV-2-infected patients and give us insight about virus pathophysiology.
T181 984-1195 Sentence denotes It is well established that for enveloped viruses, such as SARS-CoV-2, N- or O-glycosylation of S protein determines the viral entry and membrane fusion with functional elicitation of host immune responses [46].
T182 1196-1367 Sentence denotes The high-resolution LC-MS/MS experiment was performed to detect site-specific quantitative N-linked and O-linked glycan profiling on SARS-CoV-2 subunit S1 and S2 proteins.
T183 1368-1531 Sentence denotes The glycan profiling showed that two unexpected O-glycosylation sites on the receptor-binding domain (RBD) of subunit S1 increased the pathogenicity of SARS-CoV-2.
T184 1532-1725 Sentence denotes Therefore, our understanding of complex sialylated N-glycans and sialylated mucin type O-glycans on the functional RBD domain may help to evaluate better therapeutic or vaccine strategies [47].
T185 1726-1865 Sentence denotes Moreover, miR-8066 alters N-glycosylation patterns according to the microT-CDS pathway and may have biomarker potential for this mechanism.
T186 1866-2062 Sentence denotes In addition, miR-8066 is found to be associated with one of the critical clinical problems of COVID-19, the cytokine storm, owing to its potential effect on the cytokine-cytokine receptor pathway.
T187 2063-2226 Sentence denotes It is well established that miR-8066 affects PRLR, CXCL6, IL6, IL17 and ACVR1 target genes, which are crucial members of the cytokine regulatory network (Table 2).
T188 2227-2669 Sentence denotes According to previous NGS platform results obtained from healthy versus SARS-CoV-2-infected lung tissue biopsies (Bioproject PRJNA615032), the most highly upregulated pathways are chemokine binding receptors (p value 7.94 × 10−4), FGFR activation pathways (p value 0.002) and its downstream pathway (p value 0.001), neutrophil degranulation (p value 0.003), and IL10 (p value 0.005), when compared with normal lung tissue biopsies (Table S2).
T189 2670-2870 Sentence denotes On the contrary, according to the REACTOME pathway analysis of Bioproject PRJNA615032 data, neutrophil degradation was also downregulated in SARS-CoV-2-infected biopsy specimens (p value 1.74 × 10−6).
T190 2871-3206 Sentence denotes Briefly, the downregulation of host cell responses’ related pathway members such as SRP-dependent co-translational protein targeting to membrane, L13a-mediated translational silencing of ceruloplasmin expression antigen processing, ribosomal organization, and the ERAD pathway, were observed in COVID-19-positive lung biopsy specimens.
T191 3207-3413 Sentence denotes All of these preliminary gene expression differences, between normal and SARS-CoV-2-infected lung biopsies, are associated with detected miR pathways and highlight common clinical presentations of patients.
T192 3414-3646 Sentence denotes Each of these biological mechanisms, according to potential disease progression-related alterations in the host genome, is highly associated with TGF-β, which is a cytokine affecting a number of host responses during infection [48].
T193 3647-3789 Sentence denotes TGF-β mediates the immune responses of host cells, as well as altering tissue remodelling by affecting cell survival, apoptosis and migration.
T194 3790-4053 Sentence denotes It has been demonstrated that SARS-CoV N protein potentiate Smad-3 mediated TGF-β activation, and plasminogen activator inhibitor-1 (PAI-1), leading to severe pulmonary fibrosis and inactivation of pro-apoptotic genes by complex formation of Smad3 and Smad4 [48].

2_test

Id Subject Object Predicate Lexical cue
32512929-22753494-144200727 180-182 22753494 denotes 44
32512929-31198064-144200728 1191-1193 31198064 denotes 46
32512929-19534833-144200729 1721-1723 19534833 denotes 47

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
507 185-197 Gene denotes Hsa-miR-8055 Gene:102465861
508 549-561 Gene denotes hsa-miR-8055 Gene:102465861
509 608-616 Gene denotes miR-8066 Gene:102465868
510 724-732 Gene denotes TGF-beta Gene:7039
511 745-750 Gene denotes mucin Gene:100508689
512 1608-1613 Gene denotes mucin Gene:100508689
513 1736-1744 Gene denotes miR-8066 Gene:102465868
514 1879-1887 Gene denotes miR-8066 Gene:102465868
515 2091-2099 Gene denotes miR-8066 Gene:102465868
516 2108-2112 Gene denotes PRLR Gene:5618
517 2114-2119 Gene denotes CXCL6 Gene:6372
518 2121-2124 Gene denotes IL6 Gene:3569
519 2126-2130 Gene denotes IL17 Gene:3605
520 2135-2140 Gene denotes ACVR1 Gene:90
521 2589-2593 Gene denotes IL10 Gene:3586
522 3017-3021 Gene denotes L13a Gene:28998
523 3058-3071 Gene denotes ceruloplasmin Gene:1356
524 3560-3565 Gene denotes TGF-β Gene:7039
525 3647-3652 Gene denotes TGF-β Gene:7039
526 3850-3856 Gene denotes Smad-3 Gene:4088
527 3866-3871 Gene denotes TGF-β Gene:7039
528 3888-3921 Gene denotes plasminogen activator inhibitor-1 Gene:5054
529 3923-3928 Gene denotes PAI-1 Gene:5054
530 4032-4037 Gene denotes Smad3 Gene:4088
531 4042-4047 Gene denotes Smad4 Gene:4089
532 90-95 Gene denotes spike Gene:43740568
533 72-77 Species denotes human Tax:9606
534 110-120 Species denotes SARS-CoV-2 Tax:2697049
535 374-382 Species denotes children Tax:9606
536 655-665 Species denotes SARS-CoV-2 Tax:2697049
537 926-934 Species denotes patients Tax:9606
538 1043-1053 Species denotes SARS-CoV-2 Tax:2697049
539 1329-1339 Species denotes SARS-CoV-2 Tax:2697049
540 1520-1530 Species denotes SARS-CoV-2 Tax:2697049
541 3404-3412 Species denotes patients Tax:9606
542 3820-3828 Species denotes SARS-CoV Tax:694009
543 756-764 Chemical denotes O-glycan
544 1287-1295 Chemical denotes N-linked
545 1300-1315 Chemical denotes O-linked glycan
546 1372-1378 Chemical denotes glycan MESH:D011134
547 1583-1592 Chemical denotes N-glycans
548 1619-1628 Chemical denotes O-glycans
549 1801-1804 Chemical denotes CDS MESH:D002104
550 239-245 Disease denotes sepsis MESH:D018805
551 398-409 Disease denotes myocarditis MESH:D009205
552 906-925 Disease denotes SARS-CoV-2-infected MESH:C000657245
553 1960-1968 Disease denotes COVID-19 MESH:C000657245
554 2299-2318 Disease denotes SARS-CoV-2-infected MESH:C000657245
555 2811-2830 Disease denotes SARS-CoV-2-infected MESH:C000657245
556 3166-3174 Disease denotes COVID-19 MESH:C000657245
557 3280-3299 Disease denotes SARS-CoV-2-infected MESH:C000657245
558 3631-3640 Disease denotes infection MESH:D007239
559 3949-3967 Disease denotes pulmonary fibrosis MESH:D011658