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PMC:7402624 / 28082-29831 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T232 45-49 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T233 77-88 Body_part denotes plasmablast http://purl.org/sig/ont/fma/fma84371
T234 113-117 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T235 174-176 Body_part denotes PB http://purl.org/sig/ont/fma/fma84371
T236 179-183 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T237 252-254 Body_part denotes PB http://purl.org/sig/ont/fma/fma84371
T238 357-362 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T239 449-453 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T240 497-502 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T241 546-548 Body_part denotes PB http://purl.org/sig/ont/fma/fma84371
T242 602-604 Body_part denotes PB http://purl.org/sig/ont/fma/fma84371
T243 624-627 Body_part denotes IgG http://purl.org/sig/ont/fma/fma62872
T244 706-709 Body_part denotes IgM http://purl.org/sig/ont/fma/fma62873
T245 718-721 Body_part denotes IgG http://purl.org/sig/ont/fma/fma62872
T246 762-767 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T247 800-804 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T248 899-906 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T249 1032-1036 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T250 1164-1169 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T251 1248-1261 Body_part denotes cell clusters http://purl.org/sig/ont/fma/fma62807
T252 1248-1252 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T253 1361-1366 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T13 1248-1261 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 35-42 Species denotes patient Tax:9606
1039 26-34 Disease denotes COVID-19 MESH:C000657245
1054 404-409 Gene denotes CXCR5 Gene:643
1055 433-438 Gene denotes CXCR5 Gene:643
1056 467-472 Gene denotes CXCR5 Gene:643
1057 491-494 Gene denotes CD4 Gene:920
1058 956-961 Gene denotes Mover Gene:127262
1059 1400-1407 Species denotes cluster Tax:100569
1060 614-623 Species denotes SARS-CoV2 Tax:2697049
1061 692-701 Species denotes SARS-CoV2 Tax:2697049
1062 507-511 Chemical denotes cTfh
1063 546-548 Chemical denotes PB
1064 563-567 Chemical denotes cTfh
1065 286-288 Disease denotes HD MESH:D006816
1066 1483-1485 Disease denotes HD MESH:D006816
1067 1526-1534 Disease denotes COVID-19 MESH:C000657245

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T219 26-34 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T220 174-176 Disease denotes PB http://purl.obolibrary.org/obo/MONDO_0019035
T221 252-254 Disease denotes PB http://purl.obolibrary.org/obo/MONDO_0019035
T222 286-288 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T223 546-548 Disease denotes PB http://purl.obolibrary.org/obo/MONDO_0019035
T224 602-604 Disease denotes PB http://purl.obolibrary.org/obo/MONDO_0019035
T225 614-618 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T226 692-696 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T227 1483-1485 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T228 1512-1514 Disease denotes RD http://purl.obolibrary.org/obo/MONDO_0009973
T229 1526-1534 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T230 1618-1620 Disease denotes BH http://purl.obolibrary.org/obo/MONDO_0010873

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T487 43-49 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T488 111-117 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T489 132-133 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T490 177-183 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T491 194-195 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T492 286-293 http://purl.obolibrary.org/obo/CLO_0050940 denotes HD. (C)
T493 355-362 http://purl.obolibrary.org/obo/CL_0000236 denotes B cells
T494 447-453 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T495 485-502 http://purl.obolibrary.org/obo/CL_0000895 denotes naïve CD4 T cells
T496 553-562 http://purl.obolibrary.org/obo/CLO_0001658 denotes activated
T497 668-677 http://purl.obolibrary.org/obo/CLO_0001658 denotes activated
T498 760-767 http://purl.obolibrary.org/obo/CL_0000236 denotes B cells
T499 798-804 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T500 1030-1036 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T501 1162-1169 http://purl.obolibrary.org/obo/CL_0000236 denotes B cells
T502 1246-1252 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T503 1359-1366 http://purl.obolibrary.org/obo/CL_0000236 denotes B cells
T504 1431-1432 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T505 1512-1514 http://purl.obolibrary.org/obo/CLO_0008770 denotes RD
T506 1552-1553 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T507 1608-1612 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T187 174-176 Chemical denotes PB http://purl.obolibrary.org/obo/CHEBI_53319|http://purl.obolibrary.org/obo/CHEBI_60686
T189 252-254 Chemical denotes PB http://purl.obolibrary.org/obo/CHEBI_53319|http://purl.obolibrary.org/obo/CHEBI_60686
T191 286-288 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T192 546-548 Chemical denotes PB http://purl.obolibrary.org/obo/CHEBI_53319|http://purl.obolibrary.org/obo/CHEBI_60686
T194 602-604 Chemical denotes PB http://purl.obolibrary.org/obo/CHEBI_53319|http://purl.obolibrary.org/obo/CHEBI_60686
T196 899-906 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T197 1124-1129 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T198 1476-1481 Chemical denotes donor http://purl.obolibrary.org/obo/CHEBI_17891
T199 1483-1485 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T200 1505-1510 Chemical denotes donor http://purl.obolibrary.org/obo/CHEBI_17891
T201 1512-1514 Chemical denotes RD http://purl.obolibrary.org/obo/CHEBI_73812

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T171 0-130 Sentence denotes Fig. 4 Deep profiling of COVID-19 patient B cell populations reveals robust plasmablast populations and other B cell alterations.
T172 131-1408 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 1409-1749 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.