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PMC:7402624 / 21674-23040 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T162 73-77 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T163 112-116 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T164 164-169 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T165 269-274 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T166 296-301 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T167 325-330 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T168 394-397 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T169 401-412 Body_part denotes CD38+ cells http://purl.org/sig/ont/fma/fma0326121
T170 407-412 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T171 506-509 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T172 513-524 Body_part denotes CD38+ cells http://purl.org/sig/ont/fma/fma0326121
T173 519-524 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T174 567-572 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T175 670-675 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T176 717-722 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T177 825-832 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T178 885-898 Body_part denotes cell clusters http://purl.org/sig/ont/fma/fma62807
T179 885-889 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T180 1042-1047 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T10 885-898 Body_part denotes cell clusters http://purl.obolibrary.org/obo/UBERON_0034922

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
773 67-70 Gene denotes CD4 Gene:920
774 106-109 Gene denotes CD4 Gene:920
775 290-293 Gene denotes CD4 Gene:920
776 319-322 Gene denotes CD8 Gene:925
777 401-405 Gene denotes CD38 Gene:952
778 513-517 Gene denotes CD38 Gene:952
779 540-543 Gene denotes CD4 Gene:920
780 561-564 Gene denotes CD8 Gene:925
781 664-667 Gene denotes CD4 Gene:920
782 711-714 Gene denotes CD4 Gene:920
783 879-882 Gene denotes CD4 Gene:920
784 1036-1039 Gene denotes CD4 Gene:920
785 365-373 Species denotes patients Tax:9606
786 607-615 Species denotes patients Tax:9606
787 749-757 Species denotes patients Tax:9606
788 1225-1232 Species denotes patient Tax:9606
789 1081-1088 Species denotes cluster Tax:100569
790 217-219 Disease denotes HD MESH:D006816
791 356-364 Disease denotes COVID-19 MESH:C000657245
792 460-462 Disease denotes HD MESH:D006816
793 598-606 Disease denotes COVID-19 MESH:C000657245
794 728-730 Disease denotes HD MESH:D006816
795 740-748 Disease denotes COVID-19 MESH:C000657245
796 1173-1175 Disease denotes HD MESH:D006816
797 1216-1224 Disease denotes COVID-19 MESH:C000657245

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T155 217-219 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T156 356-364 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T157 460-462 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T158 598-606 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T159 728-730 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T160 732-734 Disease denotes RD http://purl.obolibrary.org/obo/MONDO_0009973
T161 740-748 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T162 1173-1175 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T163 1202-1204 Disease denotes RD http://purl.obolibrary.org/obo/MONDO_0009973
T164 1216-1224 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T165 1295-1297 Disease denotes BH http://purl.obolibrary.org/obo/MONDO_0010873

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T391 1-2 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T392 67-70 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T393 71-77 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T394 88-89 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T395 106-109 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T396 110-116 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T397 164-169 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T398 269-274 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T399 284-301 http://purl.obolibrary.org/obo/CL_0000895 denotes naïve CD4 T cells
T400 319-322 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T401 323-330 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T402 401-405 http://purl.obolibrary.org/obo/PR_000001408 denotes CD38
T403 407-412 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T404 513-517 http://purl.obolibrary.org/obo/PR_000001408 denotes CD38
T405 519-524 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T406 540-543 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T407 561-564 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T408 565-572 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T409 658-675 http://purl.obolibrary.org/obo/CL_0000895 denotes naïve CD4 T cells
T410 705-722 http://purl.obolibrary.org/obo/CL_0000895 denotes naïve CD4 T cells
T411 732-734 http://purl.obolibrary.org/obo/CLO_0008770 denotes RD
T412 873-889 http://purl.obolibrary.org/obo/CL_0000895 denotes naïve CD4 T cell
T413 1030-1047 http://purl.obolibrary.org/obo/CL_0000895 denotes naïve CD4 T cells
T414 1112-1113 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T415 1202-1204 http://purl.obolibrary.org/obo/CLO_0008770 denotes RD
T416 1285-1289 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T116 217-219 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T117 398-400 Chemical denotes DR http://purl.obolibrary.org/obo/CHEBI_73445
T118 460-462 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T119 510-512 Chemical denotes DR http://purl.obolibrary.org/obo/CHEBI_73445
T120 728-730 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T121 732-734 Chemical denotes RD http://purl.obolibrary.org/obo/CHEBI_73812
T122 825-832 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T123 1166-1171 Chemical denotes donor http://purl.obolibrary.org/obo/CHEBI_17891
T124 1173-1175 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T125 1195-1200 Chemical denotes donor http://purl.obolibrary.org/obo/CHEBI_17891
T126 1202-1204 Chemical denotes RD http://purl.obolibrary.org/obo/CHEBI_73812

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T135 0-221 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 222-464 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 465-1089 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 1090-1239 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 1240-1366 Sentence denotes Significance determined by unpaired Wilcoxon test with BH correction: *p < 0.05, **p < 0.01, ***p < 0.001, and ****p < 0.0001.