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PMC:7402624 / 14885-16800 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T92 73-78 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T93 140-143 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T94 208-211 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T95 237-242 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T96 338-343 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T97 419-424 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T98 487-491 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T99 645-650 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T100 695-698 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T101 782-786 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T102 863-866 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T103 877-882 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T104 942-947 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T105 986-989 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T106 1000-1005 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T107 1049-1052 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T108 1078-1083 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T109 1297-1301 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T110 1482-1487 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T111 1545-1549 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T112 1623-1626 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T113 1637-1642 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T114 1718-1722 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T115 1865-1869 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T116 1888-1893 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T8 1888-1893 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
492 67-70 Gene denotes CD8 Gene:925
493 131-135 Gene denotes CD38 Gene:952
494 215-219 Gene denotes CD38 Gene:952
495 231-234 Gene denotes CD8 Gene:925
496 332-335 Gene denotes CD8 Gene:925
497 413-416 Gene denotes CD8 Gene:925
498 706-710 Gene denotes CD38 Gene:952
499 776-779 Gene denotes CD8 Gene:925
500 858-862 Gene denotes CD38 Gene:952
501 871-874 Gene denotes CD8 Gene:925
502 936-939 Gene denotes CD8 Gene:925
503 981-985 Gene denotes CD38 Gene:952
504 994-997 Gene denotes CD8 Gene:925
505 1044-1048 Gene denotes CD38 Gene:952
506 1072-1075 Gene denotes CD8 Gene:925
507 1291-1294 Gene denotes CD8 Gene:925
508 1476-1479 Gene denotes CD8 Gene:925
509 1504-1508 Gene denotes IL-6 Gene:3569
510 1539-1542 Gene denotes CD8 Gene:925
511 1618-1622 Gene denotes CD38 Gene:952
512 1631-1634 Gene denotes CD8 Gene:925
513 1712-1715 Gene denotes CD8 Gene:925
514 1859-1862 Gene denotes CD8 Gene:925
515 639-642 Gene denotes CD8 Gene:925
516 255-263 Species denotes patients Tax:9606
517 316-324 Species denotes patients Tax:9606
518 1110-1118 Species denotes patients Tax:9606
519 1322-1330 Species denotes patients Tax:9606
520 1581-1589 Species denotes patients Tax:9606
521 1791-1799 Species denotes patients Tax:9606
522 1827-1835 Species denotes patients Tax:9606
523 1243-1251 Chemical denotes steroids MESH:D013256
524 11-27 Disease denotes viral infections MESH:D001102
525 246-254 Disease denotes COVID-19 MESH:C000657245
526 276-278 Disease denotes HD MESH:D006816
527 307-315 Disease denotes COVID-19 MESH:C000657245
528 371-373 Disease denotes HD MESH:D006816
529 1101-1109 Disease denotes COVID-19 MESH:C000657245
530 1139-1148 Disease denotes infection MESH:D007239
531 1313-1321 Disease denotes COVID-19 MESH:C000657245
532 1668-1670 Disease denotes HD MESH:D006816
533 1782-1790 Disease denotes COVID-19 MESH:C000657245

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T115 11-27 Disease denotes viral infections http://purl.obolibrary.org/obo/MONDO_0005108
T116 246-254 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T117 276-278 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T118 282-284 Disease denotes RD http://purl.obolibrary.org/obo/MONDO_0009973
T119 307-315 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T120 371-373 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T121 378-380 Disease denotes RD http://purl.obolibrary.org/obo/MONDO_0009973
T122 1101-1109 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T123 1139-1148 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T124 1313-1321 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T125 1668-1670 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T126 1782-1790 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T215 53-63 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T216 67-70 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T217 71-78 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T218 131-135 http://purl.obolibrary.org/obo/PR_000001408 denotes CD38
T219 148-150 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T220 152-154 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T221 167-168 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T222 215-219 http://purl.obolibrary.org/obo/PR_000001408 denotes CD38
T223 231-234 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T224 235-242 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T225 282-284 http://purl.obolibrary.org/obo/CLO_0008770 denotes RD
T226 332-335 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T227 336-343 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T228 378-380 http://purl.obolibrary.org/obo/CLO_0008770 denotes RD
T229 413-416 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T230 417-424 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T231 485-491 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T232 492-502 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T233 536-546 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T234 610-620 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T235 624-629 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T236 639-642 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T237 643-650 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T238 657-667 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T239 706-710 http://purl.obolibrary.org/obo/PR_000001408 denotes CD38
T240 776-779 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T241 780-786 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T242 858-862 http://purl.obolibrary.org/obo/PR_000001408 denotes CD38
T243 871-874 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T244 875-882 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T245 936-939 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T246 940-947 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T247 981-985 http://purl.obolibrary.org/obo/PR_000001408 denotes CD38
T248 994-997 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T249 998-1005 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T250 1044-1048 http://purl.obolibrary.org/obo/PR_000001408 denotes CD38
T251 1072-1075 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T252 1076-1083 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T253 1291-1294 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T254 1295-1301 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T255 1476-1479 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T256 1480-1487 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T257 1539-1542 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T258 1543-1549 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T259 1550-1560 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T260 1618-1622 http://purl.obolibrary.org/obo/PR_000001408 denotes CD38
T261 1631-1634 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T262 1635-1642 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T263 1712-1715 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T264 1716-1722 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T265 1723-1733 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T266 1738-1739 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T267 1801-1802 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T268 1859-1862 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T269 1863-1869 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T270 1870-1880 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T271 1888-1893 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T272 1888-1893 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T68 144-146 Chemical denotes DR http://purl.obolibrary.org/obo/CHEBI_73445
T69 212-214 Chemical denotes DR http://purl.obolibrary.org/obo/CHEBI_73445
T70 276-278 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T71 282-284 Chemical denotes RD http://purl.obolibrary.org/obo/CHEBI_73812
T72 371-373 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T73 378-380 Chemical denotes RD http://purl.obolibrary.org/obo/CHEBI_73812
T74 595-602 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T75 699-701 Chemical denotes DR http://purl.obolibrary.org/obo/CHEBI_73445
T76 867-869 Chemical denotes DR http://purl.obolibrary.org/obo/CHEBI_73445
T77 990-992 Chemical denotes DR http://purl.obolibrary.org/obo/CHEBI_73445
T78 1053-1055 Chemical denotes DR http://purl.obolibrary.org/obo/CHEBI_73445
T79 1243-1251 Chemical denotes steroids http://purl.obolibrary.org/obo/CHEBI_35341
T80 1504-1506 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T82 1627-1629 Chemical denotes DR http://purl.obolibrary.org/obo/CHEBI_73445
T83 1668-1670 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T36 11-27 http://purl.obolibrary.org/obo/GO_0016032 denotes viral infections
T37 485-502 http://purl.obolibrary.org/obo/GO_0042110 denotes T cell activation
T38 487-502 http://purl.obolibrary.org/obo/GO_0001775 denotes cell activation
T39 1543-1560 http://purl.obolibrary.org/obo/GO_0042110 denotes T cell activation
T40 1545-1560 http://purl.obolibrary.org/obo/GO_0001775 denotes cell activation
T41 1716-1733 http://purl.obolibrary.org/obo/GO_0042110 denotes T cell activation
T42 1718-1733 http://purl.obolibrary.org/obo/GO_0001775 denotes cell activation
T43 1863-1880 http://purl.obolibrary.org/obo/GO_0042110 denotes T cell activation
T44 1865-1880 http://purl.obolibrary.org/obo/GO_0001775 denotes cell activation

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T6 443-446 GlycoEpitope denotes EM1 http://www.glycoepitope.jp/epitopes/AN0701

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T96 0-156 Sentence denotes Most acute viral infections induce proliferation and activation of CD8 T cells detectable by increases in KI67 or co-expression of CD38 and HLA-DR (34, 35).
T97 157-303 Sentence denotes There was a significant increase in KI67+ and also HLA-DR+CD38+ non-naïve CD8 T cells in COVID-19 patients compared to HD or RD (Fig. 2, E and F).
T98 304-458 Sentence denotes In COVID-19 patients, KI67+ CD8 T cells were increased compared to HD and RD across all subsets of non-naïve CD8 T cells, including CM and EM1 (fig. S2B).
T99 459-651 Sentence denotes These data indicate broad T cell activation, potentially driven by bystander activation and/or homeostatic proliferation in addition to antigen-driven activation of virus-specific CD8 T cells.
T100 652-818 Sentence denotes This activation phenotype was confirmed by HLA-DR and CD38 co-expression that was significantly increased for all non-naïve CD8 T cell subsets (Fig. 2F and fig. S2C).
T101 819-912 Sentence denotes However, the magnitude of the KI67+ or CD38+HLA-DR+ CD8 T cells varied widely in this cohort.
T102 913-1017 Sentence denotes The frequency of KI67+ CD8 T cells correlated with the frequency of CD38+HLA-DR+ CD8 T cells (fig. S2D).
T103 1018-1263 Sentence denotes However, the frequency of CD38+HLA-DR+, but not KI67+ CD8 T cells, was elevated in COVID-19 patients who had concomitant infection with another microbe but was not impacted by pre-existing immunosuppression or treatment with steroids (fig. S2E).
T104 1264-1529 Sentence denotes Moreover, these changes in CD8 T cell subsets in COVID-19 patients did not show clear correlations with individual metrics of clinical disease such as hsCRP or D-dimer (fig. S2E), although the frequency of KI67+ CD8 T cells associated with IL-6 and ferritin levels.
T105 1530-1689 Sentence denotes Although CD8 T cell activation was common, ~20% of patients had no increase in KI67+ or CD38+HLA-DR+ CD8 T cells above the level found in HD (Fig. 2, E and F).
T106 1690-1915 Sentence denotes Thus, although robust CD8 T cell activation was a clear characteristic of many hospitalized COVID-19 patients, a substantial fraction of patients had little evidence of CD8 T cell activation in the blood compared to controls.

2_test

Id Subject Object Predicate Lexical cue
32669297-27031961-135105198 148-150 27031961 denotes 34
32669297-26362266-135105199 152-154 26362266 denotes 35