PMC:7402624 / 50537-52517
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T430 | 285-290 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T431 | 364-369 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T432 | 381-383 | Body_part | denotes | PB | http://purl.org/sig/ont/fma/fma84371 |
| T433 | 461-466 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T434 | 500-504 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T435 | 557-562 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T436 | 701-705 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T437 | 863-867 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T438 | 1693-1698 | Body_part | denotes | serum | http://purl.org/sig/ont/fma/fma63083 |
| T439 | 1699-1707 | Body_part | denotes | cytokine | http://purl.org/sig/ont/fma/fma84050 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T22 | 1693-1698 | Body_part | denotes | serum | http://purl.obolibrary.org/obo/UBERON_0001977 |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 1677 | 279-282 | Gene | denotes | CD4 | Gene:920 |
| 1678 | 307-310 | Gene | denotes | CD8 | Gene:925 |
| 1679 | 358-361 | Gene | denotes | CD8 | Gene:925 |
| 1680 | 375-379 | Gene | denotes | Tbet | Gene:30009 |
| 1681 | 455-458 | Gene | denotes | CD8 | Gene:925 |
| 1682 | 494-497 | Gene | denotes | CD4 | Gene:920 |
| 1683 | 657-665 | Species | denotes | patients | Tax:9606 |
| 1684 | 772-780 | Species | denotes | patients | Tax:9606 |
| 1685 | 983-990 | Species | denotes | patient | Tax:9606 |
| 1686 | 1004-1013 | Species | denotes | SARS-CoV2 | Tax:2697049 |
| 1687 | 1042-1050 | Species | denotes | patients | Tax:9606 |
| 1688 | 1354-1362 | Species | denotes | patients | Tax:9606 |
| 1689 | 1452-1460 | Species | denotes | patients | Tax:9606 |
| 1690 | 1912-1919 | Species | denotes | patient | Tax:9606 |
| 1691 | 129-137 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 1692 | 158-160 | Disease | denotes | HD | MESH:D006816 |
| 1693 | 815-817 | Disease | denotes | HD | MESH:D006816 |
| 1694 | 1014-1023 | Disease | denotes | infection | MESH:D007239 |
| 1695 | 1251-1259 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 1696 | 1386-1394 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 1697 | 1497-1505 | Disease | denotes | COVID-19 | MESH:C000657245 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T345 | 129-137 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T346 | 158-160 | Disease | denotes | HD | http://purl.obolibrary.org/obo/MONDO_0007739 |
| T347 | 165-167 | Disease | denotes | RD | http://purl.obolibrary.org/obo/MONDO_0009973 |
| T348 | 381-383 | Disease | denotes | PB | http://purl.obolibrary.org/obo/MONDO_0019035 |
| T349 | 815-817 | Disease | denotes | HD | http://purl.obolibrary.org/obo/MONDO_0007739 |
| T350 | 822-824 | Disease | denotes | RD | http://purl.obolibrary.org/obo/MONDO_0009973 |
| T351 | 1004-1008 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T352 | 1014-1023 | Disease | denotes | infection | http://purl.obolibrary.org/obo/MONDO_0005550 |
| T353 | 1251-1259 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T354 | 1386-1394 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T355 | 1497-1505 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T782 | 63-70 | http://purl.obolibrary.org/obo/SO_0000418 | denotes | signals |
| T783 | 165-167 | http://purl.obolibrary.org/obo/CLO_0008770 | denotes | RD |
| T784 | 269-278 | http://purl.obolibrary.org/obo/CLO_0001658 | denotes | activated |
| T785 | 279-282 | http://purl.obolibrary.org/obo/PR_000001004 | denotes | CD4 |
| T786 | 283-290 | http://purl.obolibrary.org/obo/CL_0000084 | denotes | T cells |
| T787 | 307-310 | http://purl.obolibrary.org/obo/CLO_0053438 | denotes | CD8 |
| T788 | 322-332 | http://purl.obolibrary.org/obo/CLO_0001658 | denotes | activation |
| T789 | 358-361 | http://purl.obolibrary.org/obo/CLO_0053438 | denotes | CD8 |
| T790 | 362-369 | http://purl.obolibrary.org/obo/CL_0000084 | denotes | T cells |
| T791 | 455-458 | http://purl.obolibrary.org/obo/CLO_0053438 | denotes | CD8 |
| T792 | 459-466 | http://purl.obolibrary.org/obo/CL_0000084 | denotes | T cells |
| T793 | 494-497 | http://purl.obolibrary.org/obo/PR_000001004 | denotes | CD4 |
| T794 | 498-504 | http://purl.obolibrary.org/obo/CL_0000084 | denotes | T cell |
| T795 | 505-515 | http://purl.obolibrary.org/obo/CLO_0001658 | denotes | activation |
| T796 | 520-523 | http://purl.obolibrary.org/obo/CLO_0051582 | denotes | has |
| T797 | 555-562 | http://purl.obolibrary.org/obo/CL_0000236 | denotes | B cells |
| T798 | 645-646 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T799 | 679-689 | http://purl.obolibrary.org/obo/CLO_0001658 | denotes | activation |
| T800 | 699-705 | http://purl.obolibrary.org/obo/CL_0000236 | denotes | B cell |
| T801 | 822-824 | http://purl.obolibrary.org/obo/CLO_0008770 | denotes | RD |
| T802 | 834-843 | http://purl.obolibrary.org/obo/CLO_0001658 | denotes | activated |
| T803 | 855-856 | http://purl.obolibrary.org/obo/CLO_0001021 | denotes | B |
| T804 | 861-867 | http://purl.obolibrary.org/obo/CL_0000084 | denotes | T cell |
| T805 | 1061-1062 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T806 | 1214-1215 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T67025 | 158-160 | Chemical | denotes | HD | http://purl.obolibrary.org/obo/CHEBI_73925 |
| T78964 | 165-167 | Chemical | denotes | RD | http://purl.obolibrary.org/obo/CHEBI_73812 |
| T6 | 250-258 | Chemical | denotes | effector | http://purl.obolibrary.org/obo/CHEBI_35224 |
| T44700 | 381-383 | Chemical | denotes | PB | http://purl.obolibrary.org/obo/CHEBI_53319|http://purl.obolibrary.org/obo/CHEBI_60686 |
| T9 | 441-449 | Chemical | denotes | effector | http://purl.obolibrary.org/obo/CHEBI_35224 |
| T18190 | 581-583 | Chemical | denotes | S8 | http://purl.obolibrary.org/obo/CHEBI_29385 |
| T8435 | 815-817 | Chemical | denotes | HD | http://purl.obolibrary.org/obo/CHEBI_73925 |
| T70189 | 822-824 | Chemical | denotes | RD | http://purl.obolibrary.org/obo/CHEBI_73812 |
| T91436 | 1030-1035 | Chemical | denotes | group | http://purl.obolibrary.org/obo/CHEBI_24433 |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T93 | 498-515 | http://purl.obolibrary.org/obo/GO_0042110 | denotes | T cell activation |
| T94 | 500-515 | http://purl.obolibrary.org/obo/GO_0001775 | denotes | cell activation |
| T95 | 1228-1243 | http://purl.obolibrary.org/obo/GO_0006955 | denotes | immune response |
| T96 | 1592-1607 | http://purl.obolibrary.org/obo/GO_0006955 | denotes | immune response |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T291 | 0-168 | Sentence | denotes | More positive values in UMAP Components 1 or 2 captured mainly signals of change or differences in individual immune features in COVID-19 disease compared to HD and RD. |
| T292 | 169-585 | Sentence | denotes | UMAP Component 1 captured an immunotype (Immunotype 1) that was characterized by effector or highly activated CD4 T cells, low cTfh, some CD8 TEMRA-like activation, possibly hyperactivated CD8 T cells, and Tbet+ PB, whereas Component 2 or Immunotype 2 captured Tbetbright effector-like CD8 T cells, lacked some of the robust CD4 T cell activation but has some features of proliferating B cells (Fig. 6G and fig. S8). |
| T293 | 586-622 | Sentence | denotes | However, the data presented in Figs. |
| T294 | 623-716 | Sentence | denotes | 1 to 5 also suggested a subset of patients with minimal activation of T and B cell responses. |
| T295 | 717-912 | Sentence | denotes | To investigate this immune signature, we identified 20 patients who had responses more similar to HD and RD for five activated/responding B and T cell populations (Fig. 6J, middle, and fig. S10). |
| T296 | 913-1080 | Sentence | denotes | If the UMAP Components 1 and 2 captured two distinct “immunotypes” of patient responses to SARS-CoV2 infection, this group of 20 patients represent a third immunotype. |
| T297 | 1081-1403 | Sentence | denotes | Immunotype 3 was negatively associated with UMAP Components 1 and 2 and negatively associated with disease severity, suggesting that a less robust immune response during COVID-19 was associated with less severe pathology (Fig. 6K and fig. S10), despite the fact that these patients were hospitalized with COVID-19 disease. |
| T298 | 1404-1514 | Sentence | denotes | These data further emphasize the different ways patients can present and possibly succumb to COVID-19 disease. |
| T299 | 1515-1624 | Sentence | denotes | These patterns may be related to pre-existing conditions in combination with immune response characteristics. |
| T300 | 1625-1746 | Sentence | denotes | It is likely that additional immune features, such as comprehensive serum cytokine measurements, will improve this model. |
| T301 | 1747-1980 | Sentence | denotes | Nevertheless, the current computational approach integrating deep immune profiling with disease severity trajectory and other clinical information revealed distinct patient immunotypes linked to distinct clinical outcomes (fig. S11). |