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PMC:7402624 / 16801-18448 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T117 184-189 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T118 271-274 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T119 334-339 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T120 378-381 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T121 558-563 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T122 884-888 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T123 973-978 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T124 1207-1210 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T125 1255-1260 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T126 1511-1515 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T127 1615-1620 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
573 178-181 Gene denotes CD8 Gene:925
574 328-331 Gene denotes CD8 Gene:925
575 372-376 Gene denotes CD38 Gene:952
576 392-396 Gene denotes CD39 Gene:953
577 402-405 Gene denotes PD1 Gene:6622
578 506-510 Gene denotes CD95 Gene:355
579 552-555 Gene denotes CD8 Gene:925
580 683-688 Gene denotes T-bet Gene:30009
581 693-699 Gene denotes CX3CR1 Gene:1524
582 878-881 Gene denotes CD8 Gene:925
583 1070-1074 Gene denotes CD27 Gene:939
584 1075-1079 Gene denotes CCR7 Gene:1236
585 1119-1125 Gene denotes CX3CR1 Gene:1524
586 1148-1153 Gene denotes T-bet Gene:30009
587 1202-1206 Gene denotes CD27 Gene:100520023
588 1214-1218 Gene denotes CD38 Gene:100511702
589 1224-1228 Gene denotes PD-1 Gene:100513601
590 1376-1380 Gene denotes CD27 Gene:939
591 1381-1385 Gene denotes CCR7 Gene:1236
592 1505-1508 Gene denotes CD8 Gene:925
593 1609-1612 Gene denotes CD8 Gene:925
594 1363-1368 Gene denotes Eomes Gene:8320
595 223-231 Species denotes patients Tax:9606
596 295-303 Species denotes patients Tax:9606
597 777-785 Species denotes patients Tax:9606
598 914-926 Species denotes cluster (Fig Tax:100569
599 1042-1050 Species denotes patients Tax:9606
600 1538-1546 Species denotes patients Tax:9606
601 1638-1646 Species denotes patients Tax:9606
602 1425-1432 Species denotes Cluster Tax:100569
603 214-222 Disease denotes COVID-19 MESH:C000657245
604 286-294 Disease denotes COVID-19 MESH:C000657245
605 313-315 Disease denotes HD MESH:D006816
606 606-608 Disease denotes HD MESH:D006816
607 768-776 Disease denotes COVID-19 MESH:C000657245
608 1033-1041 Disease denotes COVID-19 MESH:C000657245
609 1288-1296 Disease denotes COVID-19 MESH:C000657245
610 1463-1465 Disease denotes HD MESH:D006816
611 1529-1537 Disease denotes COVID-19 MESH:C000657245

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T127 214-222 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T128 286-294 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T129 313-315 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T130 319-321 Disease denotes RD http://purl.obolibrary.org/obo/MONDO_0009973
T131 518-521 Disease denotes FAS http://purl.obolibrary.org/obo/MONDO_0016011
T132 569-571 Disease denotes RD http://purl.obolibrary.org/obo/MONDO_0009973
T133 606-608 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T134 768-776 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T135 1033-1041 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T136 1288-1296 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T137 1463-1465 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T138 1529-1537 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T273 73-75 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T274 107-108 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T275 178-181 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T276 182-189 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T277 243-244 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T278 319-321 http://purl.obolibrary.org/obo/CLO_0008770 denotes RD
T279 328-331 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T280 332-339 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T281 372-376 http://purl.obolibrary.org/obo/PR_000001408 denotes CD38
T282 457-467 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T283 552-555 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T284 556-563 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T285 569-571 http://purl.obolibrary.org/obo/CLO_0008770 denotes RD
T286 878-881 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T287 882-888 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T288 973-978 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T289 1063-1069 http://purl.obolibrary.org/obo/PR_000001015 denotes CD45RA
T290 1070-1074 http://purl.obolibrary.org/obo/PR_000001963 denotes CD27
T291 1075-1079 http://purl.obolibrary.org/obo/PR_000001203 denotes CCR7
T292 1202-1206 http://purl.obolibrary.org/obo/PR_000001963 denotes CD27
T293 1214-1218 http://purl.obolibrary.org/obo/PR_000001408 denotes CD38
T294 1230-1239 http://purl.obolibrary.org/obo/CLO_0001658 denotes activated
T295 1255-1260 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T296 1369-1375 http://purl.obolibrary.org/obo/PR_000001015 denotes CD45RA
T297 1376-1380 http://purl.obolibrary.org/obo/PR_000001963 denotes CD27
T298 1381-1385 http://purl.obolibrary.org/obo/PR_000001203 denotes CCR7
T299 1433-1435 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T300 1505-1508 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T301 1509-1515 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T302 1584-1593 http://purl.obolibrary.org/obo/CLO_0001658 denotes activated
T303 1609-1612 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T304 1613-1620 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T305 1624-1625 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T84 313-315 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T85 319-321 Chemical denotes RD http://purl.obolibrary.org/obo/CHEBI_73812
T86 382-384 Chemical denotes DR http://purl.obolibrary.org/obo/CHEBI_73445
T87 402-405 Chemical denotes PD1 http://purl.obolibrary.org/obo/CHEBI_138655
T88 518-521 Chemical denotes FAS http://purl.obolibrary.org/obo/CHEBI_76181
T89 569-571 Chemical denotes RD http://purl.obolibrary.org/obo/CHEBI_73812
T90 606-608 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T91 1211-1213 Chemical denotes DR http://purl.obolibrary.org/obo/CHEBI_73445
T92 1224-1226 Chemical denotes PD http://purl.obolibrary.org/obo/CHEBI_74756
T93 1463-1465 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T7 1387-1390 GlycoEpitope denotes EM1 http://www.glycoepitope.jp/epitopes/AN0701

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T107 0-106 Sentence denotes To gain more insights, we applied global high-dimensional mapping of the 27-parameter flow cytometry data.
T108 107-242 Sentence denotes A tSNE representation of the data highlighted key regions of non-naïve CD8 T cells found preferentially in COVID-19 patients (Fig. 2G).
T109 243-523 Sentence denotes A major region of this tSNE map present in COVID-19 patients, but not HD or RD, were CD8 T cells that enriched for expression of CD38, HLA-DR, KI67, CD39, and PD1 (Fig. 2G), highlighting the co-expression of these activation markers with other features including CD95 (i.e., FAS).
T110 524-710 Sentence denotes Notably, although non-naïve CD8 T cells from RD were highly similar to those from HD, subtle differences existed, including in the lower region highlighted by T-bet and CX3CR1 (Fig. 2G).
T111 711-932 Sentence denotes To further define and quantify these differences between COVID-19 patients and controls, we performed FlowSOM clustering (Fig. 2H) and compared expression of fourteen CD8 T cell markers to identify each cluster (Fig. 2I).
T112 933-1172 Sentence denotes This approach identified an increase in cells in several clusters including Clusters 1, 2, and 5 in COVID-19 patients, reflecting CD45RA+CD27−CCR7− TEMRA-like populations that expressed CX3CR1 and varying levels of T-bet (Fig. 2, I and J).
T113 1173-1337 Sentence denotes Clusters 12 and 14 contained CD27+HLA-DR+CD38+KI67+PD-1+ activated, proliferating cells and were more prevalent in COVID-19 disease (Fig. 2, I and J, and fig. S2F).
T114 1338-1498 Sentence denotes In contrast, the central Eomes+CD45RA−CD27+CCR7− EM1-like Cluster 6 and T-bethiCX3CR1+ Cluster 11 were decreased compared to HD (Fig. 2, I and J, and fig. S2F).
T115 1499-1647 Sentence denotes Thus, CD8 T cell responses in COVID-19 patients were characterized by populations of activated, proliferating CD8 T cells in a subgroup of patients.