PMC:7402624 / 28213-29831
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T235 | 43-45 | Body_part | denotes | PB | http://purl.org/sig/ont/fma/fma84371 |
| T236 | 48-52 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T237 | 121-123 | Body_part | denotes | PB | http://purl.org/sig/ont/fma/fma84371 |
| T238 | 226-231 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T239 | 318-322 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T240 | 366-371 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T241 | 415-417 | Body_part | denotes | PB | http://purl.org/sig/ont/fma/fma84371 |
| T242 | 471-473 | Body_part | denotes | PB | http://purl.org/sig/ont/fma/fma84371 |
| T243 | 493-496 | Body_part | denotes | IgG | http://purl.org/sig/ont/fma/fma62872 |
| T244 | 575-578 | Body_part | denotes | IgM | http://purl.org/sig/ont/fma/fma62873 |
| T245 | 587-590 | Body_part | denotes | IgG | http://purl.org/sig/ont/fma/fma62872 |
| T246 | 631-636 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T247 | 669-673 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T248 | 768-775 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T249 | 901-905 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T250 | 1033-1038 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T251 | 1117-1130 | Body_part | denotes | cell clusters | http://purl.org/sig/ont/fma/fma62807 |
| T252 | 1117-1121 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T253 | 1230-1235 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T13 | 1117-1130 | Body_part | denotes | cell clusters | http://purl.obolibrary.org/obo/UBERON_0034922 |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 1054 | 273-278 | Gene | denotes | CXCR5 | Gene:643 |
| 1055 | 302-307 | Gene | denotes | CXCR5 | Gene:643 |
| 1056 | 336-341 | Gene | denotes | CXCR5 | Gene:643 |
| 1057 | 360-363 | Gene | denotes | CD4 | Gene:920 |
| 1058 | 825-830 | Gene | denotes | Mover | Gene:127262 |
| 1059 | 1269-1276 | Species | denotes | cluster | Tax:100569 |
| 1060 | 483-492 | Species | denotes | SARS-CoV2 | Tax:2697049 |
| 1061 | 561-570 | Species | denotes | SARS-CoV2 | Tax:2697049 |
| 1062 | 376-380 | Chemical | denotes | cTfh | |
| 1063 | 415-417 | Chemical | denotes | PB | |
| 1064 | 432-436 | Chemical | denotes | cTfh | |
| 1065 | 155-157 | Disease | denotes | HD | MESH:D006816 |
| 1066 | 1352-1354 | Disease | denotes | HD | MESH:D006816 |
| 1067 | 1395-1403 | Disease | denotes | COVID-19 | MESH:C000657245 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T220 | 43-45 | Disease | denotes | PB | http://purl.obolibrary.org/obo/MONDO_0019035 |
| T221 | 121-123 | Disease | denotes | PB | http://purl.obolibrary.org/obo/MONDO_0019035 |
| T222 | 155-157 | Disease | denotes | HD | http://purl.obolibrary.org/obo/MONDO_0007739 |
| T223 | 415-417 | Disease | denotes | PB | http://purl.obolibrary.org/obo/MONDO_0019035 |
| T224 | 471-473 | Disease | denotes | PB | http://purl.obolibrary.org/obo/MONDO_0019035 |
| T225 | 483-487 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T226 | 561-565 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T227 | 1352-1354 | Disease | denotes | HD | http://purl.obolibrary.org/obo/MONDO_0007739 |
| T228 | 1381-1383 | Disease | denotes | RD | http://purl.obolibrary.org/obo/MONDO_0009973 |
| T229 | 1395-1403 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T230 | 1487-1489 | Disease | denotes | BH | http://purl.obolibrary.org/obo/MONDO_0010873 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T489 | 1-2 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T490 | 46-52 | http://purl.obolibrary.org/obo/CL_0000236 | denotes | B cell |
| T491 | 63-64 | http://purl.obolibrary.org/obo/CLO_0001021 | denotes | B |
| T492 | 155-162 | http://purl.obolibrary.org/obo/CLO_0050940 | denotes | HD. (C) |
| T493 | 224-231 | http://purl.obolibrary.org/obo/CL_0000236 | denotes | B cells |
| T494 | 316-322 | http://purl.obolibrary.org/obo/CL_0000236 | denotes | B cell |
| T495 | 354-371 | http://purl.obolibrary.org/obo/CL_0000895 | denotes | naïve CD4 T cells |
| T496 | 422-431 | http://purl.obolibrary.org/obo/CLO_0001658 | denotes | activated |
| T497 | 537-546 | http://purl.obolibrary.org/obo/CLO_0001658 | denotes | activated |
| T498 | 629-636 | http://purl.obolibrary.org/obo/CL_0000236 | denotes | B cells |
| T499 | 667-673 | http://purl.obolibrary.org/obo/CL_0000236 | denotes | B cell |
| T500 | 899-905 | http://purl.obolibrary.org/obo/CL_0000236 | denotes | B cell |
| T501 | 1031-1038 | http://purl.obolibrary.org/obo/CL_0000236 | denotes | B cells |
| T502 | 1115-1121 | http://purl.obolibrary.org/obo/CL_0000236 | denotes | B cell |
| T503 | 1228-1235 | http://purl.obolibrary.org/obo/CL_0000236 | denotes | B cells |
| T504 | 1300-1301 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T505 | 1381-1383 | http://purl.obolibrary.org/obo/CLO_0008770 | denotes | RD |
| T506 | 1421-1422 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T507 | 1477-1481 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | test |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T187 | 43-45 | Chemical | denotes | PB | http://purl.obolibrary.org/obo/CHEBI_53319|http://purl.obolibrary.org/obo/CHEBI_60686 |
| T189 | 121-123 | Chemical | denotes | PB | http://purl.obolibrary.org/obo/CHEBI_53319|http://purl.obolibrary.org/obo/CHEBI_60686 |
| T191 | 155-157 | Chemical | denotes | HD | http://purl.obolibrary.org/obo/CHEBI_73925 |
| T192 | 415-417 | Chemical | denotes | PB | http://purl.obolibrary.org/obo/CHEBI_53319|http://purl.obolibrary.org/obo/CHEBI_60686 |
| T194 | 471-473 | Chemical | denotes | PB | http://purl.obolibrary.org/obo/CHEBI_53319|http://purl.obolibrary.org/obo/CHEBI_60686 |
| T196 | 768-775 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T197 | 993-998 | Chemical | denotes | group | http://purl.obolibrary.org/obo/CHEBI_24433 |
| T198 | 1345-1350 | Chemical | denotes | donor | http://purl.obolibrary.org/obo/CHEBI_17891 |
| T199 | 1352-1354 | Chemical | denotes | HD | http://purl.obolibrary.org/obo/CHEBI_73925 |
| T200 | 1374-1379 | Chemical | denotes | donor | http://purl.obolibrary.org/obo/CHEBI_17891 |
| T201 | 1381-1383 | Chemical | denotes | RD | http://purl.obolibrary.org/obo/CHEBI_73812 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T172 | 0-1277 | 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 | 1278-1618 | 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. |