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PMC:7402624 / 28090-29831 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T232 37-41 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T233 69-80 Body_part denotes plasmablast http://purl.org/sig/ont/fma/fma84371
T234 105-109 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T235 166-168 Body_part denotes PB http://purl.org/sig/ont/fma/fma84371
T236 171-175 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T237 244-246 Body_part denotes PB http://purl.org/sig/ont/fma/fma84371
T238 349-354 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T239 441-445 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T240 489-494 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T241 538-540 Body_part denotes PB http://purl.org/sig/ont/fma/fma84371
T242 594-596 Body_part denotes PB http://purl.org/sig/ont/fma/fma84371
T243 616-619 Body_part denotes IgG http://purl.org/sig/ont/fma/fma62872
T244 698-701 Body_part denotes IgM http://purl.org/sig/ont/fma/fma62873
T245 710-713 Body_part denotes IgG http://purl.org/sig/ont/fma/fma62872
T246 754-759 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T247 792-796 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T248 891-898 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T249 1024-1028 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T250 1156-1161 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T251 1240-1253 Body_part denotes cell clusters http://purl.org/sig/ont/fma/fma62807
T252 1240-1244 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T253 1353-1358 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T13 1240-1253 Body_part denotes cell clusters http://purl.obolibrary.org/obo/UBERON_0034922

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1038 27-34 Species denotes patient Tax:9606
1039 18-26 Disease denotes COVID-19 MESH:C000657245
1054 396-401 Gene denotes CXCR5 Gene:643
1055 425-430 Gene denotes CXCR5 Gene:643
1056 459-464 Gene denotes CXCR5 Gene:643
1057 483-486 Gene denotes CD4 Gene:920
1058 948-953 Gene denotes Mover Gene:127262
1059 1392-1399 Species denotes cluster Tax:100569
1060 606-615 Species denotes SARS-CoV2 Tax:2697049
1061 684-693 Species denotes SARS-CoV2 Tax:2697049
1062 499-503 Chemical denotes cTfh
1063 538-540 Chemical denotes PB
1064 555-559 Chemical denotes cTfh
1065 278-280 Disease denotes HD MESH:D006816
1066 1475-1477 Disease denotes HD MESH:D006816
1067 1518-1526 Disease denotes COVID-19 MESH:C000657245

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T219 18-26 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T220 166-168 Disease denotes PB http://purl.obolibrary.org/obo/MONDO_0019035
T221 244-246 Disease denotes PB http://purl.obolibrary.org/obo/MONDO_0019035
T222 278-280 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T223 538-540 Disease denotes PB http://purl.obolibrary.org/obo/MONDO_0019035
T224 594-596 Disease denotes PB http://purl.obolibrary.org/obo/MONDO_0019035
T225 606-610 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T226 684-688 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T227 1475-1477 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T228 1504-1506 Disease denotes RD http://purl.obolibrary.org/obo/MONDO_0009973
T229 1518-1526 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T230 1610-1612 Disease denotes BH http://purl.obolibrary.org/obo/MONDO_0010873

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T487 35-41 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T488 103-109 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T489 124-125 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T490 169-175 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T491 186-187 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T492 278-285 http://purl.obolibrary.org/obo/CLO_0050940 denotes HD. (C)
T493 347-354 http://purl.obolibrary.org/obo/CL_0000236 denotes B cells
T494 439-445 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T495 477-494 http://purl.obolibrary.org/obo/CL_0000895 denotes naïve CD4 T cells
T496 545-554 http://purl.obolibrary.org/obo/CLO_0001658 denotes activated
T497 660-669 http://purl.obolibrary.org/obo/CLO_0001658 denotes activated
T498 752-759 http://purl.obolibrary.org/obo/CL_0000236 denotes B cells
T499 790-796 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T500 1022-1028 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T501 1154-1161 http://purl.obolibrary.org/obo/CL_0000236 denotes B cells
T502 1238-1244 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T503 1351-1358 http://purl.obolibrary.org/obo/CL_0000236 denotes B cells
T504 1423-1424 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T505 1504-1506 http://purl.obolibrary.org/obo/CLO_0008770 denotes RD
T506 1544-1545 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T507 1600-1604 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T187 166-168 Chemical denotes PB http://purl.obolibrary.org/obo/CHEBI_53319|http://purl.obolibrary.org/obo/CHEBI_60686
T189 244-246 Chemical denotes PB http://purl.obolibrary.org/obo/CHEBI_53319|http://purl.obolibrary.org/obo/CHEBI_60686
T191 278-280 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T192 538-540 Chemical denotes PB http://purl.obolibrary.org/obo/CHEBI_53319|http://purl.obolibrary.org/obo/CHEBI_60686
T194 594-596 Chemical denotes PB http://purl.obolibrary.org/obo/CHEBI_53319|http://purl.obolibrary.org/obo/CHEBI_60686
T196 891-898 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T197 1116-1121 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T198 1468-1473 Chemical denotes donor http://purl.obolibrary.org/obo/CHEBI_17891
T199 1475-1477 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T200 1497-1502 Chemical denotes donor http://purl.obolibrary.org/obo/CHEBI_17891
T201 1504-1506 Chemical denotes RD http://purl.obolibrary.org/obo/CHEBI_73812

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T172 123-1400 Sentence denotes (A) Gating strategy and frequencies of non-PB B cell subsets. (B) Representative flow cytometry plots and frequencies of PB; green line at upper decile of HD. (C) Representative flow cytometry plots and frequencies of KI67+ B cells. (D) (Left) Representative histograms of CXCR5 expression and (right) CXCR5 GMFI of B cell subsets. (E) CXCR5 GMFI of non-naïve CD4 T cells and cTfh. (F) Spearman correlation between PB and activated cTfh. (G) Spearman correlation between PB and anti-SARS-CoV2 IgG. (H and I) Spearman correlation between activated cTfh and anti-SARS-CoV2 (H) IgM and (I) IgG. (J) (Top) Global viSNE projection of B cells for all subjects pooled, with B cell populations of each cohort concatenated and overlaid. (Bottom) viSNE projections of indicated protein expression. (K) Hierarchical clustering of Earth Mover’s Distance (EMD) using Pearson correlation, calculated pairwise for B cell populations for all subjects; row-scaled z-score. (L) Percentage of cohort in each EMD group. (M) Global viSNE projection of B cells for all subjects pooled, with EMD groups 1-3 concatenated and overlaid. (N) B cell clusters identified by FlowSOM clustering. (O) MFI as indicated; column-scaled z-score. (P) Percentage of B cells from each cohort in each FlowSOM cluster.
T173 1401-1741 Sentence denotes Boxes represent IQR. (A to F, P) Dots represent individual healthy donor (HD; green), recovered donor (RD; blue), or COVID-19 (red) subjects. (A to E, P) Significance determined by unpaired Wilcoxon test with BH correction: *p < 0.05, **p < 0.01, ***p < 0.001, and ****p < 0.0001. (GtoI) Black horizontal line represents positive threshold.