PMC:7172841 / 92-1279
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T1 | 388-398 | Body_part | denotes | macrophage | http://purl.org/sig/ont/fma/fma63261 |
| T2 | 443-452 | Body_part | denotes | leukocyte | http://purl.org/sig/ont/fma/fma62852 |
| T3 | 472-475 | Body_part | denotes | HLA | http://purl.org/sig/ont/fma/fma84795 |
| T4 | 532-543 | Body_part | denotes | lymphocytes | http://purl.org/sig/ont/fma/fma62863 |
| T5 | 550-561 | Body_part | denotes | lymphocytes | http://purl.org/sig/ont/fma/fma62863 |
| T6 | 587-592 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T7 | 630-643 | Body_part | denotes | interleukin-6 | http://purl.org/sig/ont/fma/fma264829 |
| T8 | 677-686 | Body_part | denotes | monocytes | http://purl.org/sig/ont/fma/fma62864 |
| T9 | 776-782 | Body_part | denotes | plasma | http://purl.org/sig/ont/fma/fma62970 |
| T10 | 793-796 | Body_part | denotes | HLA | http://purl.org/sig/ont/fma/fma84795 |
| T11 | 964-975 | Body_part | denotes | lymphocytes | http://purl.org/sig/ont/fma/fma62863 |
| T12 | 1083-1086 | Body_part | denotes | HLA | http://purl.org/sig/ont/fma/fma84795 |
| T13 | 1144-1152 | Body_part | denotes | cytokine | http://purl.org/sig/ont/fma/fma84050 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T3 | 29-37 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T4 | 185-204 | Disease | denotes | respiratory failure | http://purl.obolibrary.org/obo/MONDO_0021113 |
| T5 | 214-222 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T6 | 256-274 | Disease | denotes | immune dysfunction | http://purl.obolibrary.org/obo/MONDO_0005046 |
| T7 | 310-318 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T8 | 388-418 | Disease | denotes | macrophage activation syndrome | http://purl.obolibrary.org/obo/MONDO_0015545 |
| T9 | 420-423 | Disease | denotes | MAS | http://purl.obolibrary.org/obo/MONDO_0015545 |
| T10 | 594-599 | Disease | denotes | Tumor | http://purl.obolibrary.org/obo/MONDO_0005070 |
| T11 | 726-742 | Disease | denotes | bacterial sepsis | http://purl.obolibrary.org/obo/MONDO_0005229 |
| T12 | 746-755 | Disease | denotes | influenza | http://purl.obolibrary.org/obo/MONDO_0005812 |
| T13 | 757-765 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T14 | 757-761 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T15 | 1036-1044 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T16 | 1105-1116 | Disease | denotes | lymphopenia | http://purl.obolibrary.org/obo/MONDO_0003783 |
| T17 | 1174-1186 | Disease | denotes | inflammation | http://purl.obolibrary.org/obo/MONDO_0021166 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T1 | 236-237 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T2 | 399-409 | http://purl.obolibrary.org/obo/CLO_0001658 | denotes | activation |
| T3 | 437-442 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T4 | 528-531 | http://purl.obolibrary.org/obo/PR_000001004 | denotes | CD4 |
| T5 | 545-549 | http://purl.obolibrary.org/obo/CLO_0053432 | denotes | CD19 |
| T6 | 582-592 | http://purl.obolibrary.org/obo/CL_0000623 | denotes | (NK) cells |
| T7 | 630-643 | http://purl.obolibrary.org/obo/PR_000001393 | denotes | interleukin-6 |
| T8 | 677-686 | http://purl.obolibrary.org/obo/CL_0000576 | denotes | monocytes |
| T9 | 702-703 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T10 | 776-782 | http://purl.obolibrary.org/obo/UBERON_0001969 | denotes | plasma |
| T11 | 881-886 | http://purl.obolibrary.org/obo/CLO_0007225 | denotes | label |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T1 | 453-460 | Chemical | denotes | antigen | http://purl.obolibrary.org/obo/CHEBI_59132 |
| T2 | 476-478 | Chemical | denotes | DR | http://purl.obolibrary.org/obo/CHEBI_73445 |
| T3 | 645-647 | Chemical | denotes | IL | http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072 |
| T5 | 797-799 | Chemical | denotes | DR | http://purl.obolibrary.org/obo/CHEBI_73445 |
| T6 | 851-853 | Chemical | denotes | IL | http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072 |
| T8 | 881-886 | Chemical | denotes | label | http://purl.obolibrary.org/obo/CHEBI_35209 |
| T9 | 1065-1067 | Chemical | denotes | IL | http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072 |
| T11 | 1087-1089 | Chemical | denotes | DR | http://purl.obolibrary.org/obo/CHEBI_73445 |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T1 | 79-91 | http://purl.obolibrary.org/obo/GO_0009405 | denotes | pathogenesis |
| T2 | 287-303 | http://purl.obolibrary.org/obo/GO_0006955 | denotes | immune responses |
| T3 | 388-409 | http://purl.obolibrary.org/obo/GO_0042116 | denotes | macrophage activation |
| T4 | 600-608 | http://purl.obolibrary.org/obo/GO_0070265 | denotes | necrosis |
| T5 | 600-608 | http://purl.obolibrary.org/obo/GO_0019835 | denotes | necrosis |
| T6 | 600-608 | http://purl.obolibrary.org/obo/GO_0008219 | denotes | necrosis |
| T7 | 600-608 | http://purl.obolibrary.org/obo/GO_0001906 | denotes | necrosis |
| T8 | 644-661 | http://purl.obolibrary.org/obo/GO_0032635 | denotes | (IL-6) production |
| T9 | 1144-1163 | http://purl.obolibrary.org/obo/GO_0001816 | denotes | cytokine production |
| T10 | 1174-1186 | http://purl.obolibrary.org/obo/GO_0006954 | denotes | inflammation |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T3 | 0-7 | Sentence | denotes | Summary |
| T4 | 8-92 | Sentence | denotes | Proper management of COVID-19 mandates better understanding of disease pathogenesis. |
| T5 | 93-275 | Sentence | denotes | The sudden clinical deterioration 7–8 days after initial symptom onset suggests that severe respiratory failure (SRF) in COVID-19 is driven by a unique pattern of immune dysfunction. |
| T6 | 276-348 | Sentence | denotes | We studied immune responses of 54 COVID-19 patients, 28 of whom had SRF. |
| T7 | 349-593 | Sentence | denotes | All patients with SRF displayed either macrophage activation syndrome (MAS) or very low human leukocyte antigen D related (HLA-DR) expression accompanied by profound depletion of CD4 lymphocytes, CD19 lymphocytes, and natural killer (NK) cells. |
| T8 | 594-756 | Sentence | denotes | Tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) production by circulating monocytes was sustained, a pattern distinct from bacterial sepsis or influenza. |
| T9 | 757-976 | Sentence | denotes | SARS-CoV-2 patient plasma inhibited HLA-DR expression, and this was partially restored by the IL-6 blocker Tocilizumab; off-label Tocilizumab treatment of patients was accompanied by increase in circulating lymphocytes. |
| T10 | 977-1187 | Sentence | denotes | Thus, the unique pattern of immune dysregulation in severe COVID-19 is characterized by IL-6-mediated low HLA-DR expression and lymphopenia, associated with sustained cytokine production and hyper-inflammation. |
LitCovid-PD-HP
| Id | Subject | Object | Predicate | Lexical cue | hp_id |
|---|---|---|---|---|---|
| T3 | 185-204 | Phenotype | denotes | respiratory failure | http://purl.obolibrary.org/obo/HP_0002878 |
| T4 | 594-599 | Phenotype | denotes | Tumor | http://purl.obolibrary.org/obo/HP_0002664 |
| T5 | 736-742 | Phenotype | denotes | sepsis | http://purl.obolibrary.org/obo/HP_0100806 |
| T6 | 1005-1025 | Phenotype | denotes | immune dysregulation | http://purl.obolibrary.org/obo/HP_0002958 |
| T7 | 1105-1116 | Phenotype | denotes | lymphopenia | http://purl.obolibrary.org/obo/HP_0001888 |
LitCovid-PMC-OGER-BB
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T3 | 29-37 | SP_7 | denotes | COVID-19 |
| T4 | 185-196 | UBERON:0001004 | denotes | respiratory |
| T5 | 214-222 | SP_7 | denotes | COVID-19 |
| T6 | 256-262 | UBERON:0002405 | denotes | immune |
| T7 | 287-293 | UBERON:0002405;GO:0006955 | denotes | immune |
| T8 | 294-303 | GO:0006955 | denotes | responses |
| T9 | 310-318 | SP_7 | denotes | COVID-19 |
| T10 | 388-398 | CL:0000235;GO:0042116 | denotes | macrophage |
| T11 | 399-409 | GO:0042116 | denotes | activation |
| T12 | 437-442 | SP_6;NCBITaxon:9606 | denotes | human |
| T13 | 443-452 | CL:0000738 | denotes | leukocyte |
| T14 | 453-460 | CHEBI:59132;CHEBI:59132 | denotes | antigen |
| T15 | 472-475 | PR:000029150 | denotes | HLA |
| T16 | 480-490 | GO:0010467 | denotes | expression |
| T17 | 528-531 | PR:000001004 | denotes | CD4 |
| T18 | 532-543 | CL:0000542 | denotes | lymphocytes |
| T19 | 545-549 | PR:000001002 | denotes | CD19 |
| T20 | 550-561 | CL:0000542 | denotes | lymphocytes |
| T21 | 567-581 | CL:0000623 | denotes | natural killer |
| T22 | 594-617 | PR:000000134 | denotes | Tumor necrosis factor-α |
| T23 | 619-624 | PR:000000134 | denotes | TNF-α |
| T24 | 630-643 | PR:000001393 | denotes | interleukin-6 |
| T25 | 645-649 | PR:000001393 | denotes | IL-6 |
| T26 | 665-676 | CL:0000080 | denotes | circulating |
| T27 | 677-686 | CL:0000576 | denotes | monocytes |
| T28 | 726-735 | NCBITaxon:2 | denotes | bacterial |
| T29 | 757-767 | SP_7 | denotes | SARS-CoV-2 |
| T30 | 776-782 | UBERON:0001969 | denotes | plasma |
| T31 | 793-796 | PR:000029150 | denotes | HLA |
| T32 | 800-810 | GO:0010467 | denotes | expression |
| T33 | 851-855 | PR:000001393 | denotes | IL-6 |
| T34 | 864-875 | DG_35 | denotes | Tocilizumab |
| T35 | 887-898 | DG_35 | denotes | Tocilizumab |
| T36 | 952-963 | CL:0000080 | denotes | circulating |
| T37 | 964-975 | CL:0000542 | denotes | lymphocytes |
| T38 | 1005-1011 | UBERON:0002405 | denotes | immune |
| T39 | 1012-1025 | GO:0065007 | denotes | dysregulation |
| T40 | 1036-1044 | SP_7 | denotes | COVID-19 |
| T41 | 1065-1069 | PR:000001393 | denotes | IL-6 |
| T42 | 1083-1086 | PR:000029150 | denotes | HLA |
| T43 | 1090-1100 | GO:0010467 | denotes | expression |
| T24276 | 29-37 | SP_7 | denotes | COVID-19 |
| T25589 | 185-196 | UBERON:0001004 | denotes | respiratory |
| T59726 | 214-222 | SP_7 | denotes | COVID-19 |
| T67700 | 256-262 | UBERON:0002405 | denotes | immune |
| T7839 | 287-293 | UBERON:0002405;GO:0006955 | denotes | immune |
| T23482 | 294-303 | GO:0006955 | denotes | responses |
| T94326 | 310-318 | SP_7 | denotes | COVID-19 |
| T55692 | 388-398 | CL:0000235;GO:0042116 | denotes | macrophage |
| T76896 | 399-409 | GO:0042116 | denotes | activation |
| T56154 | 437-442 | SP_6;NCBITaxon:9606 | denotes | human |
| T45303 | 443-452 | CL:0000738 | denotes | leukocyte |
| T92944 | 453-460 | CHEBI:59132;CHEBI:59132 | denotes | antigen |
| T58214 | 472-475 | PR:000029150 | denotes | HLA |
| T41859 | 480-490 | GO:0010467 | denotes | expression |
| T17537 | 528-531 | PR:000001004 | denotes | CD4 |
| T14494 | 532-543 | CL:0000542 | denotes | lymphocytes |
| T5373 | 545-549 | PR:000001002 | denotes | CD19 |
| T95317 | 550-561 | CL:0000542 | denotes | lymphocytes |
| T66709 | 567-581 | CL:0000623 | denotes | natural killer |
| T65169 | 594-617 | PR:000000134 | denotes | Tumor necrosis factor-α |
| T5325 | 619-624 | PR:000000134 | denotes | TNF-α |
| T73676 | 630-643 | PR:000001393 | denotes | interleukin-6 |
| T94520 | 645-649 | PR:000001393 | denotes | IL-6 |
| T7633 | 665-676 | CL:0000080 | denotes | circulating |
| T99503 | 677-686 | CL:0000576 | denotes | monocytes |
| T38740 | 726-735 | NCBITaxon:2 | denotes | bacterial |
| T85947 | 757-767 | SP_7 | denotes | SARS-CoV-2 |
| T29939 | 776-782 | UBERON:0001969 | denotes | plasma |
| T8998 | 793-796 | PR:000029150 | denotes | HLA |
| T62491 | 800-810 | GO:0010467 | denotes | expression |
| T78149 | 851-855 | PR:000001393 | denotes | IL-6 |
| T18501 | 864-875 | DG_35 | denotes | Tocilizumab |
| T10312 | 887-898 | DG_35 | denotes | Tocilizumab |
| T74668 | 952-963 | CL:0000080 | denotes | circulating |
| T90672 | 964-975 | CL:0000542 | denotes | lymphocytes |
| T2958 | 1005-1011 | UBERON:0002405 | denotes | immune |
| T86620 | 1012-1025 | GO:0065007 | denotes | dysregulation |
| T3195 | 1036-1044 | SP_7 | denotes | COVID-19 |
| T88472 | 1065-1069 | PR:000001393 | denotes | IL-6 |
| T6458 | 1083-1086 | PR:000029150 | denotes | HLA |
| T72315 | 1090-1100 | GO:0010467 | denotes | expression |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 36 | 528-531 | Gene | denotes | CD4 | Gene:920 |
| 37 | 545-549 | Gene | denotes | CD19 | Gene:930 |
| 38 | 594-617 | Gene | denotes | Tumor necrosis factor-α | Gene:7124 |
| 39 | 619-624 | Gene | denotes | TNF-α | Gene:7124 |
| 40 | 630-643 | Gene | denotes | interleukin-6 | Gene:3569 |
| 41 | 645-649 | Gene | denotes | IL-6 | Gene:3569 |
| 42 | 851-855 | Gene | denotes | IL-6 | Gene:3569 |
| 43 | 1065-1069 | Gene | denotes | IL-6 | Gene:3569 |
| 44 | 319-327 | Species | denotes | patients | Tax:9606 |
| 45 | 353-361 | Species | denotes | patients | Tax:9606 |
| 46 | 757-767 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 47 | 768-775 | Species | denotes | patient | Tax:9606 |
| 48 | 912-920 | Species | denotes | patients | Tax:9606 |
| 49 | 746-755 | Species | denotes | influenza | Tax:11309 |
| 50 | 437-442 | Species | denotes | human | Tax:9606 |
| 51 | 864-875 | Chemical | denotes | Tocilizumab | MESH:C502936 |
| 52 | 887-898 | Chemical | denotes | Tocilizumab | MESH:C502936 |
| 53 | 29-37 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 54 | 185-204 | Disease | denotes | respiratory failure | MESH:D012131 |
| 55 | 206-209 | Disease | denotes | SRF | |
| 56 | 214-222 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 57 | 256-274 | Disease | denotes | immune dysfunction | MESH:D007154 |
| 58 | 310-318 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 59 | 344-347 | Disease | denotes | SRF | |
| 60 | 367-370 | Disease | denotes | SRF | |
| 61 | 388-418 | Disease | denotes | macrophage activation syndrome | MESH:D055501 |
| 62 | 736-742 | Disease | denotes | sepsis | MESH:D018805 |
| 63 | 1036-1044 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 64 | 1105-1116 | Disease | denotes | lymphopenia | MESH:D008231 |
| 65 | 1168-1186 | Disease | denotes | hyper-inflammation | MESH:D007249 |