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PMC:7402624 / 21574-23040 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T160 6-10 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T161 86-90 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T162 173-177 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T163 212-216 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T164 264-269 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T165 369-374 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T166 396-401 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T167 425-430 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T168 494-497 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T169 501-512 Body_part denotes CD38+ cells http://purl.org/sig/ont/fma/fma0326121
T170 507-512 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T171 606-609 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T172 613-624 Body_part denotes CD38+ cells http://purl.org/sig/ont/fma/fma0326121
T173 619-624 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T174 667-672 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T175 770-775 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T176 817-822 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T177 925-932 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T178 985-998 Body_part denotes cell clusters http://purl.org/sig/ont/fma/fma62807
T179 985-989 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T180 1142-1147 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T10 985-998 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 0-3 Gene denotes CD4 Gene:920
745 80-83 Gene denotes CD4 Gene:920
746 46-54 Species denotes patients Tax:9606
747 37-45 Disease denotes COVID-19 MESH:C000657245
773 167-170 Gene denotes CD4 Gene:920
774 206-209 Gene denotes CD4 Gene:920
775 390-393 Gene denotes CD4 Gene:920
776 419-422 Gene denotes CD8 Gene:925
777 501-505 Gene denotes CD38 Gene:952
778 613-617 Gene denotes CD38 Gene:952
779 640-643 Gene denotes CD4 Gene:920
780 661-664 Gene denotes CD8 Gene:925
781 764-767 Gene denotes CD4 Gene:920
782 811-814 Gene denotes CD4 Gene:920
783 979-982 Gene denotes CD4 Gene:920
784 1136-1139 Gene denotes CD4 Gene:920
785 465-473 Species denotes patients Tax:9606
786 707-715 Species denotes patients Tax:9606
787 849-857 Species denotes patients Tax:9606
788 1325-1332 Species denotes patient Tax:9606
789 1181-1188 Species denotes cluster Tax:100569
790 317-319 Disease denotes HD MESH:D006816
791 456-464 Disease denotes COVID-19 MESH:C000657245
792 560-562 Disease denotes HD MESH:D006816
793 698-706 Disease denotes COVID-19 MESH:C000657245
794 828-830 Disease denotes HD MESH:D006816
795 840-848 Disease denotes COVID-19 MESH:C000657245
796 1273-1275 Disease denotes HD MESH:D006816
797 1316-1324 Disease denotes COVID-19 MESH:C000657245

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T154 37-45 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T155 317-319 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T156 456-464 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T157 560-562 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T158 698-706 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T159 828-830 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T160 832-834 Disease denotes RD http://purl.obolibrary.org/obo/MONDO_0009973
T161 840-848 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T162 1273-1275 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T163 1302-1304 Disease denotes RD http://purl.obolibrary.org/obo/MONDO_0009973
T164 1316-1324 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T165 1395-1397 Disease denotes BH http://purl.obolibrary.org/obo/MONDO_0010873

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T385 0-3 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T386 4-10 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T387 11-21 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T388 25-26 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T389 80-83 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T390 84-90 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T391 101-102 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T392 167-170 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T393 171-177 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T394 188-189 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T395 206-209 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T396 210-216 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T397 264-269 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T398 369-374 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T399 384-401 http://purl.obolibrary.org/obo/CL_0000895 denotes naïve CD4 T cells
T400 419-422 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T401 423-430 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T402 501-505 http://purl.obolibrary.org/obo/PR_000001408 denotes CD38
T403 507-512 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T404 613-617 http://purl.obolibrary.org/obo/PR_000001408 denotes CD38
T405 619-624 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T406 640-643 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T407 661-664 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T408 665-672 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T409 758-775 http://purl.obolibrary.org/obo/CL_0000895 denotes naïve CD4 T cells
T410 805-822 http://purl.obolibrary.org/obo/CL_0000895 denotes naïve CD4 T cells
T411 832-834 http://purl.obolibrary.org/obo/CLO_0008770 denotes RD
T412 973-989 http://purl.obolibrary.org/obo/CL_0000895 denotes naïve CD4 T cell
T413 1130-1147 http://purl.obolibrary.org/obo/CL_0000895 denotes naïve CD4 T cells
T414 1212-1213 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T415 1302-1304 http://purl.obolibrary.org/obo/CLO_0008770 denotes RD
T416 1385-1389 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T116 317-319 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T117 498-500 Chemical denotes DR http://purl.obolibrary.org/obo/CHEBI_73445
T118 560-562 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T119 610-612 Chemical denotes DR http://purl.obolibrary.org/obo/CHEBI_73445
T120 828-830 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T121 832-834 Chemical denotes RD http://purl.obolibrary.org/obo/CHEBI_73812
T122 925-932 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T123 1266-1271 Chemical denotes donor http://purl.obolibrary.org/obo/CHEBI_17891
T124 1273-1275 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T125 1295-1300 Chemical denotes donor http://purl.obolibrary.org/obo/CHEBI_17891
T126 1302-1304 Chemical denotes RD http://purl.obolibrary.org/obo/CHEBI_73812

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T54 4-21 http://purl.obolibrary.org/obo/GO_0042110 denotes T cell activation
T55 6-21 http://purl.obolibrary.org/obo/GO_0001775 denotes cell activation

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T135 100-321 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 322-564 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 565-1189 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 1190-1339 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 1340-1466 Sentence denotes Significance determined by unpaired Wilcoxon test with BH correction: *p < 0.05, **p < 0.01, ***p < 0.001, and ****p < 0.0001.