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PMC:7200337 / 15504-18766 JSONTXT

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2_test

Id Subject Object Predicate Lexical cue
32505227-19851468-46575254 345-349 19851468 denotes 2009
32505227-23015710-46575255 497-501 23015710 denotes 2012
32505227-26867177-46575256 809-813 26867177 denotes 2016
32505227-16985170-46575257 1021-1025 16985170 denotes 2007
32505227-22345460-46575259 1719-1723 22345460 denotes 2012
T96613 345-349 19851468 denotes 2009
T13230 497-501 23015710 denotes 2012
T82690 809-813 26867177 denotes 2016
T43572 1021-1025 16985170 denotes 2007
T36838 1719-1723 22345460 denotes 2012

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T80 72-84 Body_part denotes myeloid cell http://purl.org/sig/ont/fma/fma70339
T81 80-84 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T82 315-319 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T83 390-401 Body_part denotes macrophages http://purl.org/sig/ont/fma/fma63261
T84 623-632 Body_part denotes monocytes http://purl.org/sig/ont/fma/fma62864
T85 633-644 Body_part denotes macrophages http://purl.org/sig/ont/fma/fma63261
T86 653-657 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T87 658-666 Body_part denotes cytokine http://purl.org/sig/ont/fma/fma84050
T88 671-680 Body_part denotes chemokine http://purl.org/sig/ont/fma/fma241981
T89 739-743 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T90 1168-1176 Body_part denotes alveolar http://purl.org/sig/ont/fma/fma264783
T91 1222-1233 Body_part denotes lymphocytes http://purl.org/sig/ont/fma/fma62863
T92 1238-1247 Body_part denotes monocytes http://purl.org/sig/ont/fma/fma62864
T93 1268-1279 Body_part denotes macrophages http://purl.org/sig/ont/fma/fma63261
T94 1287-1295 Body_part denotes alveolar http://purl.org/sig/ont/fma/fma264783
T95 1493-1509 Body_part denotes immunoglobulin G http://purl.org/sig/ont/fma/fma62872
T96 1511-1514 Body_part denotes IgG http://purl.org/sig/ont/fma/fma62872
T97 1547-1551 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T98 1584-1604 Body_part denotes alveolar macrophages http://purl.org/sig/ont/fma/fma83023
T99 1678-1686 Body_part denotes monocyte http://purl.org/sig/ont/fma/fma62864
T100 1777-1785 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T101 1900-1912 Body_part denotes Myeloid Cell http://purl.org/sig/ont/fma/fma70339
T102 1908-1912 Body_part denotes Cell http://purl.org/sig/ont/fma/fma68646
T103 1936-1943 Body_part denotes NK Cell http://purl.org/sig/ont/fma/fma63147
T104 1939-1943 Body_part denotes Cell http://purl.org/sig/ont/fma/fma68646
T105 2053-2057 Body_part denotes IL-1 http://purl.org/sig/ont/fma/fma86583
T106 2098-2107 Body_part denotes epithelia http://purl.org/sig/ont/fma/fma9639
T107 2165-2176 Body_part denotes macrophages http://purl.org/sig/ont/fma/fma63261
T108 2207-2216 Body_part denotes monocytes http://purl.org/sig/ont/fma/fma62864
T109 2229-2241 Body_part denotes granulocytes http://purl.org/sig/ont/fma/fma62854
T110 2246-2257 Body_part denotes lymphocytes http://purl.org/sig/ont/fma/fma62863
T111 2313-2322 Body_part denotes monocytes http://purl.org/sig/ont/fma/fma62864
T112 2382-2390 Body_part denotes monocyte http://purl.org/sig/ont/fma/fma62864
T113 2399-2410 Body_part denotes macrophages http://purl.org/sig/ont/fma/fma63261
T114 2557-2569 Body_part denotes neutrophilic http://purl.org/sig/ont/fma/fma62860
T115 2636-2649 Body_part denotes myeloid cells http://purl.org/sig/ont/fma/fma70339
T116 2644-2649 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T117 2727-2735 Body_part denotes Monocyte http://purl.org/sig/ont/fma/fma62864
T118 2770-2778 Body_part denotes NK cells http://purl.org/sig/ont/fma/fma63147
T119 2773-2778 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T120 2784-2789 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T121 2853-2861 Body_part denotes NK cells http://purl.org/sig/ont/fma/fma63147
T122 2856-2861 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T123 2918-2923 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T124 2941-2950 Body_part denotes monocytes http://purl.org/sig/ont/fma/fma62864
T125 3088-3097 Body_part denotes monocytes http://purl.org/sig/ont/fma/fma62864
T126 3105-3116 Body_part denotes macrophages http://purl.org/sig/ont/fma/fma63261
T127 3126-3137 Body_part denotes eosinophils http://purl.org/sig/ont/fma/fma62861
T128 3147-3158 Body_part denotes neutrophils http://purl.org/sig/ont/fma/fma62860
T129 3169-3179 Body_part denotes neutrophil http://purl.org/sig/ont/fma/fma62860
T130 3199-3203 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T8 653-657 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T9 1547-1551 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T10 2098-2107 Body_part denotes epithelia http://purl.obolibrary.org/obo/UBERON_0000483
T11 2784-2789 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T101 14-22 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T102 100-108 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T103 174-182 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T104 209-217 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T105 220-229 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T106 269-271 Disease denotes AM http://purl.obolibrary.org/obo/MONDO_0020320
T107 422-438 Disease denotes hypersensitivity http://purl.obolibrary.org/obo/MONDO_0000605|http://purl.obolibrary.org/obo/MONDO_0005271
T109 458-462 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T110 540-548 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T111 867-875 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T112 1052-1060 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T113 1190-1199 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T114 1440-1448 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T115 1541-1558 Disease denotes acute lung injury http://purl.obolibrary.org/obo/MONDO_0006502|http://purl.obolibrary.org/obo/MONDO_0015796
T117 1552-1558 Disease denotes injury http://purl.obolibrary.org/obo/MONDO_0021178
T118 1868-1876 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T119 1879-1888 Disease denotes Infection http://purl.obolibrary.org/obo/MONDO_0005550
T120 1984-1992 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T121 2505-2508 Disease denotes CRS http://purl.obolibrary.org/obo/MONDO_0007399|http://purl.obolibrary.org/obo/MONDO_0017361
T123 2611-2619 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T124 2904-2908 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T125 3217-3261 Disease denotes secondary hemophagocytic lymphohistiocytosis http://purl.obolibrary.org/obo/MONDO_0015542
T126 3227-3261 Disease denotes hemophagocytic lymphohistiocytosis http://purl.obolibrary.org/obo/MONDO_0015540

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T82044 80-84 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T94640 233-238 http://purl.obolibrary.org/obo/CLO_0007836 denotes mouse
T89368 313-319 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T84481 320-330 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T74943 415-421 http://purl.obolibrary.org/obo/UBERON_0001005 denotes airway
T54060 596-605 http://purl.obolibrary.org/obo/SO_0000418 denotes signaling
T5697 623-632 http://purl.obolibrary.org/obo/CL_0000576 denotes monocytes
T18605 653-657 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T63442 653-657 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T57672 737-743 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T38000 1117-1126 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humanized
T70288 1238-1247 http://purl.obolibrary.org/obo/CL_0000576 denotes monocytes
T68687 1392-1397 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T44500 1398-1405 http://purl.obolibrary.org/obo/NCBITaxon_9443 denotes primate
T8952 1472-1477 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T25639 1547-1551 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T77587 1547-1551 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T2661 1678-1686 http://purl.obolibrary.org/obo/CL_0000576 denotes monocyte
T26384 1700-1704 http://purl.obolibrary.org/obo/CLO_0053704 denotes IL-8
T13152 1908-1912 http://purl.obolibrary.org/obo/GO_0005623 denotes Cell
T45733 1913-1923 http://purl.obolibrary.org/obo/CLO_0001658 denotes Activation
T38010 1936-1943 http://purl.obolibrary.org/obo/CL_0000623 denotes NK Cell
T11301 2207-2216 http://purl.obolibrary.org/obo/CL_0000576 denotes monocytes
T3621 2299-2300 http://purl.obolibrary.org/obo/CLO_0001020 denotes ɑ
T320 2313-2322 http://purl.obolibrary.org/obo/CL_0000576 denotes monocytes
T78868 2382-2390 http://purl.obolibrary.org/obo/CL_0000576 denotes monocyte
T1737 2644-2649 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T84467 2727-2735 http://purl.obolibrary.org/obo/CL_0000576 denotes Monocyte
T47301 2753-2755 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T48426 2770-2778 http://purl.obolibrary.org/obo/CL_0000623 denotes NK cells
T52652 2784-2789 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T31933 2784-2789 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T14324 2853-2861 http://purl.obolibrary.org/obo/CL_0000623 denotes NK cells
T89373 2918-2923 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T45576 2941-2950 http://purl.obolibrary.org/obo/CL_0000576 denotes monocytes
T99791 3088-3097 http://purl.obolibrary.org/obo/CL_0000576 denotes monocytes
T48410 3199-3203 http://purl.obolibrary.org/obo/GO_0005623 denotes cell

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T71 720-727 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T72 1700-1702 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T74 2047-2049 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T76 2053-2055 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T78 2286-2288 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T80 2744-2749 Chemical denotes CXCL9 http://purl.obolibrary.org/obo/CHEBI_138154
T81 2825-2834 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T82 3034-3046 Chemical denotes nitric oxide http://purl.obolibrary.org/obo/CHEBI_16480
T83 3041-3046 Chemical denotes oxide http://purl.obolibrary.org/obo/CHEBI_25741|http://purl.obolibrary.org/obo/CHEBI_29356

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T13 422-438 Phenotype denotes hypersensitivity http://purl.obolibrary.org/obo/HP_0041092
T14 1190-1199 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T15 1541-1558 Phenotype denotes acute lung injury http://www.orpha.net/ORDO/Orphanet_178320

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T71 183-195 http://purl.obolibrary.org/obo/GO_0009405 denotes pathogenesis
T72 313-330 http://purl.obolibrary.org/obo/GO_0042110 denotes T cell activation
T73 315-330 http://purl.obolibrary.org/obo/GO_0001775 denotes cell activation
T74 422-438 http://purl.obolibrary.org/obo/GO_0002524 denotes hypersensitivity
T75 596-605 http://purl.obolibrary.org/obo/GO_0023052 denotes signaling
T76 889-901 http://purl.obolibrary.org/obo/GO_0009405 denotes pathogenesis
T77 1908-1923 http://purl.obolibrary.org/obo/GO_0001775 denotes Cell Activation
T78 2524-2545 http://purl.obolibrary.org/obo/GO_0006954 denotes inflammatory response
T79 3199-3209 http://purl.obolibrary.org/obo/GO_0008219 denotes cell death

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
493 1868-1888 Disease denotes SARS-CoV-2 Infection MESH:C000657245
496 2032-2045 Species denotes coronaviruses Tax:11118
497 1984-1992 Disease denotes COVID-19 MESH:C000657245
508 2047-2051 Gene denotes IL-6 Gene:3569
509 2053-2058 Gene denotes IL-1β Gene:3552
510 2286-2290 Gene denotes IL-6 Gene:3569
511 2295-2300 Gene denotes TNF-ɑ Gene:7124
512 2744-2755 Gene denotes CXCL9/10/11 Gene:4283
513 2079-2087 Disease denotes infected MESH:D007239
514 2423-2436 Disease denotes dysfunctional MESH:D009461
515 2557-2597 Disease denotes neutrophilic NETosis and microthrombosis MESH:C564275
516 2611-2619 Disease denotes COVID-19 MESH:C000657245
517 2904-2917 Disease denotes SARS-infected MESH:D045169
526 3000-3004 Gene denotes Arg1 Gene:383
527 3006-3016 Gene denotes arginase 1 Gene:383
528 3018-3022 Gene denotes iNOS Gene:4843
529 3099-3103 Gene denotes Macs Gene:4082
530 2983-2985 Gene denotes to Gene:6999
531 3160-3167 Disease denotes NETosis
532 3204-3209 Disease denotes death MESH:D003643
533 3217-3261 Disease denotes secondary hemophagocytic lymphohistiocytosis MESH:D051359
568 371-376 Gene denotes FIZZ1 Gene:84666
569 1127-1132 Gene denotes hACE2 Gene:59272
570 1691-1695 Gene denotes CCL2 Gene:6347
571 1700-1704 Gene denotes IL-8 Gene:3576
572 1842-1844 Gene denotes to Gene:6999
573 1807-1809 Gene denotes to Gene:6999
574 1764-1766 Gene denotes to Gene:6999
575 1563-1565 Gene denotes to Gene:6999
576 950-952 Gene denotes to Gene:6999
577 157-159 Gene denotes to Gene:6999
578 42-44 Gene denotes to Gene:6999
579 23-31 Species denotes patients Tax:9606
580 100-108 Species denotes SARS-CoV Tax:694009
581 115-123 Species denotes MERS-CoV Tax:1335626
582 233-238 Species denotes mouse Tax:10090
583 533-539 Species denotes murine Tax:10090
584 540-548 Species denotes SARS-CoV Tax:694009
585 867-877 Species denotes SARS-CoV-2 Tax:2697049
586 968-974 Species denotes murine Tax:10090
587 975-978 Species denotes CoV Tax:11118
588 1052-1062 Species denotes SARS-CoV-2 Tax:2697049
589 1133-1137 Species denotes mice Tax:10090
590 1343-1350 Species denotes patient Tax:9606
591 1392-1397 Species denotes human Tax:9606
592 1424-1431 Species denotes patient Tax:9606
593 1440-1448 Species denotes SARS-CoV Tax:694009
594 14-22 Disease denotes COVID-19 MESH:C000657245
595 72-96 Disease denotes myeloid cell dysfunction MESH:D023981
596 174-182 Disease denotes COVID-19 MESH:C000657245
597 209-229 Disease denotes SARS-CoV-1 infection MESH:C000657245
598 422-438 Disease denotes hypersensitivity MESH:D004342
599 474-482 Disease denotes fibrosis MESH:D005355
600 1190-1199 Disease denotes pneumonia MESH:D011014
601 1547-1558 Disease denotes lung injury MESH:D055370

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T88 0-208 Sentence denotes While data on COVID-19 patients continues to rapidly emerge, studies of myeloid cell dysfunction in SARS-CoV-1 and MERS-CoV can provide an important roadmap to understanding COVID-19 pathogenesis (Figure 2 ).
T89 209-351 Sentence denotes SARS-CoV-1 infection in mouse models results in an aberrant AM phenotype that limits DC trafficking and T cell activation (Zhao et al., 2009).
T90 352-503 Sentence denotes Additionally, YM1+ FIZZ1+ alternative macrophages can increase airway hypersensitivity, thus exacerbating SARS-associated fibrosis (Page et al., 2012).
T91 504-815 Sentence denotes Further, as described above, murine SARS-CoV-1 studies have demonstrated that delayed IFN-I signaling and inflammatory monocytes-macrophages promote lung cytokine and chemokine levels, vascular leakage, and impaired antigen-specific T cell responses, culminating in lethal disease (Channappanavar et al., 2016).
T92 816-1027 Sentence denotes The role played by prominent IFN-producing pDCs in SARS-CoV-2 control or pathogenesis warrants investigation, as they have been shown to be critical in murine CoV (MHV) control (Cervantes-Barragan et al., 2007).
T93 1028-1379 Sentence denotes Longitudinal studies in SARS-CoV-2 models are awaited, but initial phenotypic studies in humanized hACE2 mice have shown the characteristic alveolar interstitial pneumonia, with infiltration of lymphocytes and monocytes and accumulation of macrophages in the alveolar lumen (Bao et al., 2020a), which recapitulates patient findings (Xu et al., 2020c).
T94 1380-1743 Sentence denotes Lastly, non-human primate (NHP) studies and patient data on SARS-CoV-1 have also shown that virus spike-specific immunoglobulin G (IgG) responses can exacerbate acute lung injury due to repolarization of alveolar macrophages into proinflammatory phenotypes and enhanced recruitment of inflammatory monocyte via CCL2 and IL-8 (Clay et al., 2012, Liu et al., 2019).
T95 1744-1858 Sentence denotes However, the extent to which the antibody response contributes to disease pathophysiology remains to be confirmed.
T96 1859-1952 Sentence denotes Figure 2 SARS-CoV-2 Infection Results in Myeloid Cell Activation and Changes NK Cell Function
T97 1953-2046 Sentence denotes Based on data from preliminary COVID-19 studies and earlier studies in related coronaviruses.
T98 2047-2275 Sentence denotes IL-6, IL-1β, and IFN-I/III from infected pulmonary epithelia can induce inflammatory programs in resident (alternate) macrophages while recruiting inflammatory monocytes, as well as granulocytes and lymphocytes from circulation.
T99 2276-2368 Sentence denotes Sustained IL-6 and TNF-ɑ by incoming monocytes can drive several hyperinflammation cascades.
T100 2369-2491 Sentence denotes Inflammatory monocyte-derived macrophages can amplify dysfunctional responses in various ways (listed in top-left corner).
T101 2492-2629 Sentence denotes The systemic CRS- and sHLH-like inflammatory response can induce neutrophilic NETosis and microthrombosis, aggravating COVID-19 severity.
T102 2630-2726 Sentence denotes Other myeloid cells, such as pDCs, are purported to have an IFN-dependent role in viral control.
T103 2727-2790 Sentence denotes Monocyte-derived CXCL9/10/11 might recruit NK cells from blood.
T104 2791-2951 Sentence denotes Preliminary data suggest that the antiviral function of these NK cells might be regulated through crosstalk with SARS-infected cells and inflammatory monocytes.
T105 2952-2999 Sentence denotes Dashed lines indicate pathways to be confirmed.
T106 3000-3262 Sentence denotes Arg1, arginase 1; iNOS, inducible-nitric oxide synthase; Inflamm., inflammatory; Mono., monocytes; Macs, macrophages; Eosino, eosinophils; Neutro, neutrophils; NETosis, neutrophil extracellular trap cell death; SHLH, secondary hemophagocytic lymphohistiocytosis.