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PMC:7402624 / 21566-23040 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T160 14-18 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T161 94-98 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T162 181-185 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T163 220-224 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T164 272-277 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T165 377-382 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T166 404-409 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T167 433-438 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T168 502-505 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T169 509-520 Body_part denotes CD38+ cells http://purl.org/sig/ont/fma/fma0326121
T170 515-520 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T171 614-617 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T172 621-632 Body_part denotes CD38+ cells http://purl.org/sig/ont/fma/fma0326121
T173 627-632 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T174 675-680 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T175 778-783 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T176 825-830 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T177 933-940 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T178 993-1006 Body_part denotes cell clusters http://purl.org/sig/ont/fma/fma62807
T179 993-997 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T180 1150-1155 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T10 993-1006 Body_part denotes cell clusters http://purl.obolibrary.org/obo/UBERON_0034922

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
744 8-11 Gene denotes CD4 Gene:920
745 88-91 Gene denotes CD4 Gene:920
746 54-62 Species denotes patients Tax:9606
747 45-53 Disease denotes COVID-19 MESH:C000657245
773 175-178 Gene denotes CD4 Gene:920
774 214-217 Gene denotes CD4 Gene:920
775 398-401 Gene denotes CD4 Gene:920
776 427-430 Gene denotes CD8 Gene:925
777 509-513 Gene denotes CD38 Gene:952
778 621-625 Gene denotes CD38 Gene:952
779 648-651 Gene denotes CD4 Gene:920
780 669-672 Gene denotes CD8 Gene:925
781 772-775 Gene denotes CD4 Gene:920
782 819-822 Gene denotes CD4 Gene:920
783 987-990 Gene denotes CD4 Gene:920
784 1144-1147 Gene denotes CD4 Gene:920
785 473-481 Species denotes patients Tax:9606
786 715-723 Species denotes patients Tax:9606
787 857-865 Species denotes patients Tax:9606
788 1333-1340 Species denotes patient Tax:9606
789 1189-1196 Species denotes cluster Tax:100569
790 325-327 Disease denotes HD MESH:D006816
791 464-472 Disease denotes COVID-19 MESH:C000657245
792 568-570 Disease denotes HD MESH:D006816
793 706-714 Disease denotes COVID-19 MESH:C000657245
794 836-838 Disease denotes HD MESH:D006816
795 848-856 Disease denotes COVID-19 MESH:C000657245
796 1281-1283 Disease denotes HD MESH:D006816
797 1324-1332 Disease denotes COVID-19 MESH:C000657245

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T154 45-53 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T155 325-327 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T156 464-472 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T157 568-570 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T158 706-714 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T159 836-838 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T160 840-842 Disease denotes RD http://purl.obolibrary.org/obo/MONDO_0009973
T161 848-856 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T162 1281-1283 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T163 1310-1312 Disease denotes RD http://purl.obolibrary.org/obo/MONDO_0009973
T164 1324-1332 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T165 1403-1405 Disease denotes BH http://purl.obolibrary.org/obo/MONDO_0010873

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T385 8-11 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T386 12-18 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T387 19-29 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T388 33-34 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T389 88-91 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T390 92-98 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T391 109-110 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T392 175-178 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T393 179-185 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T394 196-197 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T395 214-217 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T396 218-224 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T397 272-277 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T398 377-382 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T399 392-409 http://purl.obolibrary.org/obo/CL_0000895 denotes naïve CD4 T cells
T400 427-430 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T401 431-438 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T402 509-513 http://purl.obolibrary.org/obo/PR_000001408 denotes CD38
T403 515-520 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T404 621-625 http://purl.obolibrary.org/obo/PR_000001408 denotes CD38
T405 627-632 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T406 648-651 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T407 669-672 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T408 673-680 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T409 766-783 http://purl.obolibrary.org/obo/CL_0000895 denotes naïve CD4 T cells
T410 813-830 http://purl.obolibrary.org/obo/CL_0000895 denotes naïve CD4 T cells
T411 840-842 http://purl.obolibrary.org/obo/CLO_0008770 denotes RD
T412 981-997 http://purl.obolibrary.org/obo/CL_0000895 denotes naïve CD4 T cell
T413 1138-1155 http://purl.obolibrary.org/obo/CL_0000895 denotes naïve CD4 T cells
T414 1220-1221 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T415 1310-1312 http://purl.obolibrary.org/obo/CLO_0008770 denotes RD
T416 1393-1397 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T116 325-327 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T117 506-508 Chemical denotes DR http://purl.obolibrary.org/obo/CHEBI_73445
T118 568-570 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T119 618-620 Chemical denotes DR http://purl.obolibrary.org/obo/CHEBI_73445
T120 836-838 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T121 840-842 Chemical denotes RD http://purl.obolibrary.org/obo/CHEBI_73812
T122 933-940 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T123 1274-1279 Chemical denotes donor http://purl.obolibrary.org/obo/CHEBI_17891
T124 1281-1283 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T125 1303-1308 Chemical denotes donor http://purl.obolibrary.org/obo/CHEBI_17891
T126 1310-1312 Chemical denotes RD http://purl.obolibrary.org/obo/CHEBI_73812

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T54 12-29 http://purl.obolibrary.org/obo/GO_0042110 denotes T cell activation
T55 14-29 http://purl.obolibrary.org/obo/GO_0001775 denotes cell activation

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T134 0-107 Sentence denotes Fig. 3 CD4 T cell activation in a subset of COVID-19 patients associates with distinct CD4 T cell subsets.
T135 108-329 Sentence denotes (A) Representative flow cytometry plots of the gating strategy for CD4 T cell subsets. (B) Frequencies of CD4 T cell subsets as indicated. (C) Frequencies of KI67+ cells; green line at upper decile of healthy donors (HD).
T136 330-572 Sentence denotes Representative flow cytometry plots. (D) KI67+ cells from non-naïve CD4 T cells versus non-naïve CD8 T cells, Spearman correlation of COVID-19 patients. (E) Frequencies of HLA-DR+CD38+ cells; green line at upper decile of healthy donors (HD).
T137 573-1197 Sentence denotes Representative flow cytometry plots. (F) HLA-DR+CD38+ cells from non-naïve CD4 versus non-naïve CD8 T cells, Spearman correlation of COVID-19 patients. (G) (Top) Global viSNE projection of non-naïve CD4 T cells for all subjects pooled, non-naïve CD4 T cells from HD, RD, and COVID-19 patients concatenated and overlaid. (Bottom) viSNE projections of indicated protein expression. (H) viSNE projection of non-naïve CD4 T cell clusters identified by FlowSOM clustering. (I) Mean fluorescence intensity (MFI) as indicated, column-scaled z-score. (J) Percentage of non-naïve CD4 T cells from each cohort in each FlowSOM cluster.
T138 1198-1347 Sentence denotes Boxes represent IQR. (B, C, E, J) Each dot represents an individual healthy donor (HD; green), recovered donor (RD; blue), or COVID-19 patient (red).
T139 1348-1474 Sentence denotes Significance determined by unpaired Wilcoxon test with BH correction: *p < 0.05, **p < 0.01, ***p < 0.001, and ****p < 0.0001.