> top > docs > PMC:7402624 > spans > 41271-52517 > annotations

PMC:7402624 / 41271-52517 JSONTXT

Annnotations TAB JSON ListView MergeView

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T380 72-76 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T381 524-528 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T382 670-675 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T383 708-713 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T384 841-845 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T385 852-856 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T386 957-960 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T387 976-981 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T388 1008-1011 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T389 1027-1032 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T390 2386-2393 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T391 3205-3209 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T392 3506-3510 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T393 3556-3560 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T394 3568-3572 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T395 3579-3583 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T396 3791-3796 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T397 3821-3825 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T398 4080-4084 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T399 4568-4572 Body_part denotes axis http://purl.org/sig/ont/fma/fma12520
T400 4657-4661 Body_part denotes axis http://purl.org/sig/ont/fma/fma12520
T401 5446-5451 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T402 5478-5483 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T403 5495-5497 Body_part denotes PB http://purl.org/sig/ont/fma/fma84371
T404 5561-5565 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T405 5673-5675 Body_part denotes PB http://purl.org/sig/ont/fma/fma84371
T406 5752-5757 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T407 5769-5771 Body_part denotes PB http://purl.org/sig/ont/fma/fma84371
T408 5806-5809 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T409 5843-5848 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T410 6052-6057 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T411 6131-6136 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T412 6221-6226 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T413 6439-6443 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T414 6570-6575 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T415 6661-6666 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T416 6847-6852 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T417 6935-6940 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T418 7017-7022 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T419 7086-7091 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T420 7164-7168 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T421 7337-7341 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T422 7413-7418 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T423 7456-7458 Body_part denotes PB http://purl.org/sig/ont/fma/fma84371
T424 7857-7860 Body_part denotes IgM http://purl.org/sig/ont/fma/fma62873
T425 7861-7869 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T426 8174-8179 Body_part denotes organ http://purl.org/sig/ont/fma/fma67498
T427 8212-8218 Body_part denotes kidney http://purl.org/sig/ont/fma/fma7203
T428 8434-8442 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T429 8690-8700 Body_part denotes eosinophil http://purl.org/sig/ont/fma/fma62861
T430 9551-9556 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T431 9630-9635 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T432 9647-9649 Body_part denotes PB http://purl.org/sig/ont/fma/fma84371
T433 9727-9732 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T434 9766-9770 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T435 9823-9828 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T436 9967-9971 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T437 10129-10133 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T438 10959-10964 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T439 10965-10973 Body_part denotes cytokine http://purl.org/sig/ont/fma/fma84050

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T17 344-349 Body_part denotes Scale http://purl.obolibrary.org/obo/UBERON_0002542
T18 1242-1247 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542
T19 2053-2058 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542
T20 8174-8179 Body_part denotes organ http://purl.obolibrary.org/obo/UBERON_0000062
T21 8212-8218 Body_part denotes kidney http://purl.obolibrary.org/obo/UBERON_0002113
T22 10959-10964 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
446 1706-1708 Disease denotes HD MESH:D006816
447 1737-1745 Disease denotes COVID-19 MESH:C000657245
1457 112-120 Disease denotes COVID-19 MESH:C000657245
1474 656-659 Gene denotes CD8 Gene:925
1475 664-667 Gene denotes CD4 Gene:920
1476 702-705 Gene denotes CD8 Gene:925
1477 964-968 Gene denotes CD38 Gene:952
1478 970-973 Gene denotes CD8 Gene:925
1479 1015-1019 Gene denotes CD38 Gene:952
1480 1021-1024 Gene denotes CD4 Gene:920
1481 255-263 Species denotes patients Tax:9606
1482 759-767 Species denotes patients Tax:9606
1483 1051-1059 Species denotes patients Tax:9606
1484 199-207 Disease denotes COVID-19 MESH:C000657245
1485 246-254 Disease denotes COVID-19 MESH:C000657245
1486 363-368 Disease denotes COVID MESH:C000657245
1487 372-377 Disease denotes death MESH:D003643
1488 383-388 Disease denotes COVID MESH:C000657245
1489 436-441 Disease denotes COVID MESH:C000657245
1492 1205-1212 Species denotes patient Tax:9606
1493 1196-1204 Disease denotes COVID-19 MESH:C000657245
1505 1569-1573 Chemical denotes UMAP
1506 1252-1260 Disease denotes COVID-19 MESH:C000657245
1507 1533-1542 Disease denotes mortality MESH:D003643
1521 3550-3553 Gene denotes CD8 Gene:925
1522 3562-3565 Gene denotes CD4 Gene:920
1523 2917-2924 Species denotes patient Tax:9606
1524 3403-3410 Species denotes patient Tax:9606
1525 3445-3453 Species denotes patients Tax:9606
1526 3632-3639 Species denotes patient Tax:9606
1527 3741-3749 Species denotes patients Tax:9606
1528 3860-3868 Species denotes patients Tax:9606
1529 3732-3740 Disease denotes COVID-19 MESH:C000657245
1541 3978-3986 Species denotes patients Tax:9606
1542 4498-4506 Species denotes patients Tax:9606
1543 4817-4824 Species denotes patient Tax:9606
1544 4846-4854 Species denotes patients Tax:9606
1545 5068-5076 Species denotes patients Tax:9606
1546 4292-4300 Disease denotes COVID-19 MESH:C000657245
1547 4483-4485 Disease denotes HD MESH:D006816
1548 4489-4497 Disease denotes COVID-19 MESH:C000657245
1549 4837-4845 Disease denotes COVID-19 MESH:C000657245
1550 5052-5054 Disease denotes HD MESH:D006816
1551 5059-5067 Disease denotes COVID-19 MESH:C000657245
1568 5432-5435 Gene denotes CD4 Gene:920
1569 5440-5443 Gene denotes CD8 Gene:925
1570 5666-5671 Gene denotes T-bet Gene:30009
1571 5736-5741 Gene denotes T-bet Gene:30009
1572 5762-5767 Gene denotes CD138 Gene:6382
1573 5813-5817 Gene denotes CD38 Gene:952
1574 5829-5832 Gene denotes CD4 Gene:920
1575 5837-5840 Gene denotes CD8 Gene:925
1576 6029-6034 Gene denotes T-bet Gene:30009
1577 6046-6049 Gene denotes CD8 Gene:925
1578 6108-6113 Gene denotes T-bet Gene:30009
1579 6125-6128 Gene denotes CD4 Gene:920
1580 6201-6206 Gene denotes Eomes Gene:8320
1581 6208-6211 Gene denotes CD8 Gene:925
1582 6215-6218 Gene denotes CD4 Gene:920
1583 5495-5497 Chemical denotes PB
1609 6564-6567 Gene denotes CD8 Gene:925
1610 6611-6616 Gene denotes T-bet Gene:30009
1611 6617-6623 Gene denotes CX3CR1 Gene:1524
1612 6836-6840 Gene denotes PD-1 Gene:100513601
1613 6841-6845 Gene denotes CD39 Gene:397298
1614 6929-6932 Gene denotes CD8 Gene:925
1615 7011-7014 Gene denotes CD4 Gene:920
1616 7080-7083 Gene denotes CD4 Gene:920
1617 7158-7161 Gene denotes CD4 Gene:920
1618 7200-7204 Gene denotes CD95 Gene:355
1619 7331-7334 Gene denotes CD4 Gene:920
1620 7443-7448 Gene denotes T-bet Gene:30009
1621 7449-7454 Gene denotes CD138 Gene:6382
1622 7526-7530 Gene denotes Tbet Gene:30009
1623 7531-7536 Gene denotes CD138 Gene:6382
1624 6477-6485 Species denotes patients Tax:9606
1625 6585-6592 Species denotes Cluster Tax:100569
1626 6790-6797 Species denotes Cluster Tax:100569
1627 7032-7039 Species denotes Cluster Tax:100569
1628 7214-7221 Species denotes Cluster Tax:100569
1629 7432-7439 Species denotes Cluster Tax:100569
1630 7460-7467 Species denotes Cluster Tax:100569
1631 7538-7545 Species denotes Cluster Tax:100569
1632 7382-7386 Chemical denotes cTfh
1633 6468-6476 Disease denotes COVID-19 MESH:C000657245
1645 8153-8157 Gene denotes IL-6 Gene:3569
1646 8870-8878 Species denotes patients Tax:9606
1647 8749-8759 Chemical denotes Remdesivir MESH:C000606551
1648 8116-8128 Disease denotes inflammation MESH:D007249
1649 8160-8172 Disease denotes co-infection MESH:D060085
1650 8174-8187 Disease denotes organ failure MESH:D009102
1651 8206-8226 Disease denotes acute kidney disease MESH:D058186
1652 8231-8250 Disease denotes renal insufficiency MESH:D051437
1653 8831-8840 Disease denotes mortality MESH:D003643
1654 8939-8947 Disease denotes COVID-19 MESH:C000657245
1655 9155-9163 Disease denotes COVID-19 MESH:C000657245
1677 9545-9548 Gene denotes CD4 Gene:920
1678 9573-9576 Gene denotes CD8 Gene:925
1679 9624-9627 Gene denotes CD8 Gene:925
1680 9641-9645 Gene denotes Tbet Gene:30009
1681 9721-9724 Gene denotes CD8 Gene:925
1682 9760-9763 Gene denotes CD4 Gene:920
1683 9923-9931 Species denotes patients Tax:9606
1684 10038-10046 Species denotes patients Tax:9606
1685 10249-10256 Species denotes patient Tax:9606
1686 10270-10279 Species denotes SARS-CoV2 Tax:2697049
1687 10308-10316 Species denotes patients Tax:9606
1688 10620-10628 Species denotes patients Tax:9606
1689 10718-10726 Species denotes patients Tax:9606
1690 11178-11185 Species denotes patient Tax:9606
1691 9395-9403 Disease denotes COVID-19 MESH:C000657245
1692 9424-9426 Disease denotes HD MESH:D006816
1693 10081-10083 Disease denotes HD MESH:D006816
1694 10280-10289 Disease denotes infection MESH:D007239
1695 10517-10525 Disease denotes COVID-19 MESH:C000657245
1696 10652-10660 Disease denotes COVID-19 MESH:C000657245
1697 10763-10771 Disease denotes COVID-19 MESH:C000657245

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T316 112-120 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T317 199-207 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T318 246-254 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T319 1196-1204 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T320 1252-1260 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T321 1376-1378 Disease denotes BH http://purl.obolibrary.org/obo/MONDO_0010873
T322 1706-1708 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T323 1728-1730 Disease denotes RD http://purl.obolibrary.org/obo/MONDO_0009973
T324 1737-1745 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T325 3732-3740 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T326 4292-4300 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T327 4483-4485 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T328 4489-4497 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T329 4837-4845 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T330 5018-5020 Disease denotes RD http://purl.obolibrary.org/obo/MONDO_0009973
T331 5052-5054 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T332 5059-5067 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T333 5495-5497 Disease denotes PB http://purl.obolibrary.org/obo/MONDO_0019035
T334 5673-5675 Disease denotes PB http://purl.obolibrary.org/obo/MONDO_0019035
T335 5769-5771 Disease denotes PB http://purl.obolibrary.org/obo/MONDO_0019035
T336 6468-6476 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T337 7456-7458 Disease denotes PB http://purl.obolibrary.org/obo/MONDO_0019035
T338 8116-8128 Disease denotes inflammation http://purl.obolibrary.org/obo/MONDO_0021166
T339 8163-8172 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T340 8212-8226 Disease denotes kidney disease http://purl.obolibrary.org/obo/MONDO_0001343|http://purl.obolibrary.org/obo/MONDO_0005240
T342 8231-8250 Disease denotes renal insufficiency http://purl.obolibrary.org/obo/MONDO_0001106
T343 8939-8947 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T344 9155-9163 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T345 9395-9403 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T346 9424-9426 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T347 9431-9433 Disease denotes RD http://purl.obolibrary.org/obo/MONDO_0009973
T348 9647-9649 Disease denotes PB http://purl.obolibrary.org/obo/MONDO_0019035
T349 10081-10083 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T350 10088-10090 Disease denotes RD http://purl.obolibrary.org/obo/MONDO_0009973
T351 10270-10274 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T352 10280-10289 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T353 10517-10525 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T354 10652-10660 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T355 10763-10771 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T688 64-65 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T689 70-76 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T690 522-528 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T691 656-659 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T692 664-667 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T693 668-675 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T694 682-683 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T695 702-705 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T696 706-713 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T697 839-845 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T698 850-856 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T699 935-936 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T700 964-968 http://purl.obolibrary.org/obo/PR_000001408 denotes CD38
T701 970-973 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T702 974-981 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T703 1015-1019 http://purl.obolibrary.org/obo/PR_000001408 denotes CD38
T704 1021-1024 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T705 1025-1032 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T706 1227-1228 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T707 1281-1282 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T708 1366-1370 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T709 1728-1730 http://purl.obolibrary.org/obo/CLO_0008770 denotes RD
T710 2223-2229 http://purl.obolibrary.org/obo/CLO_0054111 denotes 1 (C1)
T711 2247-2249 http://purl.obolibrary.org/obo/CLO_0002105 denotes C2
T712 2247-2249 http://purl.obolibrary.org/obo/CLO_0051742 denotes C2
T713 3203-3209 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T714 3504-3510 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T715 3550-3553 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T716 3554-3560 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T717 3562-3565 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T718 3566-3572 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T719 3577-3583 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T720 3611-3612 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T721 3789-3796 http://purl.obolibrary.org/obo/CL_0000236 denotes B cells
T722 3821-3831 http://purl.obolibrary.org/obo/CL_0000000 denotes cell types
T723 4037-4038 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T724 4078-4084 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T725 4244-4246 http://purl.obolibrary.org/obo/CLO_0008933 denotes S5
T726 4459-4460 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T727 4941-4942 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T728 5018-5020 http://purl.obolibrary.org/obo/CLO_0008770 denotes RD
T729 5346-5348 http://purl.obolibrary.org/obo/CLO_0008933 denotes S5
T730 5432-5435 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T731 5440-5443 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T732 5444-5451 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T733 5478-5483 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T734 5559-5565 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T735 5653-5654 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T736 5655-5661 http://purl.obolibrary.org/obo/SO_0000418 denotes signal
T737 5695-5697 http://purl.obolibrary.org/obo/CLO_0008933 denotes S5
T738 5750-5757 http://purl.obolibrary.org/obo/CL_0000236 denotes B cells
T739 5796-5805 http://purl.obolibrary.org/obo/CLO_0001658 denotes Activated
T740 5813-5817 http://purl.obolibrary.org/obo/PR_000001408 denotes CD38
T741 5829-5832 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T742 5837-5840 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T743 5841-5848 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T744 6007-6008 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T745 6046-6049 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T746 6050-6057 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T747 6119-6136 http://purl.obolibrary.org/obo/CL_0000895 denotes naïve CD4 T cells
T748 6189-6191 http://purl.obolibrary.org/obo/CLO_0008933 denotes S5
T749 6208-6211 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T750 6215-6218 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T751 6219-6226 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T752 6328-6330 http://purl.obolibrary.org/obo/CLO_0008933 denotes S5
T753 6439-6449 http://purl.obolibrary.org/obo/CL_0000000 denotes cell types
T754 6564-6567 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T755 6568-6575 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T756 6593-6595 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T757 6661-6666 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T758 6811-6820 http://purl.obolibrary.org/obo/CLO_0001658 denotes activated
T759 6847-6852 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T760 6929-6932 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T761 6933-6940 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T762 7011-7014 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T763 7015-7022 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T764 7055-7064 http://purl.obolibrary.org/obo/CLO_0001658 denotes activated
T765 7080-7083 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T766 7084-7091 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T767 7139-7140 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T768 7148-7157 http://purl.obolibrary.org/obo/CLO_0001658 denotes activated
T769 7158-7161 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T770 7162-7168 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T771 7331-7334 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T772 7335-7341 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T773 7411-7418 http://purl.obolibrary.org/obo/CL_0000236 denotes B cells
T774 7759-7761 http://purl.obolibrary.org/obo/CLO_0008935 denotes S9
T775 7763-7764 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T776 8174-8179 http://purl.obolibrary.org/obo/UBERON_0003103 denotes organ
T777 8212-8218 http://purl.obolibrary.org/obo/UBERON_0002113 denotes kidney
T778 8212-8218 http://www.ebi.ac.uk/efo/EFO_0000927 denotes kidney
T779 8212-8218 http://www.ebi.ac.uk/efo/EFO_0000929 denotes kidney
T780 9046-9047 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T781 9206-9207 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T782 9329-9336 http://purl.obolibrary.org/obo/SO_0000418 denotes signals
T783 9431-9433 http://purl.obolibrary.org/obo/CLO_0008770 denotes RD
T784 9535-9544 http://purl.obolibrary.org/obo/CLO_0001658 denotes activated
T785 9545-9548 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T786 9549-9556 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T787 9573-9576 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T788 9588-9598 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T789 9624-9627 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T790 9628-9635 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T791 9721-9724 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T792 9725-9732 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T793 9760-9763 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T794 9764-9770 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T795 9771-9781 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T796 9786-9789 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T797 9821-9828 http://purl.obolibrary.org/obo/CL_0000236 denotes B cells
T798 9911-9912 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T799 9945-9955 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T800 9965-9971 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T801 10088-10090 http://purl.obolibrary.org/obo/CLO_0008770 denotes RD
T802 10100-10109 http://purl.obolibrary.org/obo/CLO_0001658 denotes activated
T803 10121-10122 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T804 10127-10133 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T805 10327-10328 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T806 10480-10481 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T293 961-963 Chemical denotes DR http://purl.obolibrary.org/obo/CHEBI_73445
T294 1012-1014 Chemical denotes DR http://purl.obolibrary.org/obo/CHEBI_73445
T295 1499-1504 Chemical denotes donor http://purl.obolibrary.org/obo/CHEBI_17891
T296 1699-1704 Chemical denotes donor http://purl.obolibrary.org/obo/CHEBI_17891
T297 1706-1708 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T298 1721-1726 Chemical denotes donor http://purl.obolibrary.org/obo/CHEBI_17891
T299 1728-1730 Chemical denotes RD http://purl.obolibrary.org/obo/CHEBI_73812
T300 1874-1879 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T301 2247-2249 Chemical denotes C2 http://purl.obolibrary.org/obo/CHEBI_30083
T302 2386-2393 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T303 3284-3286 Chemical denotes 6C http://purl.obolibrary.org/obo/CHEBI_27594
T304 3529-3531 Chemical denotes 6C http://purl.obolibrary.org/obo/CHEBI_27594
T305 4244-4246 Chemical denotes S5 http://purl.obolibrary.org/obo/CHEBI_29386
T306 4483-4485 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T307 4825-4830 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T308 5018-5020 Chemical denotes RD http://purl.obolibrary.org/obo/CHEBI_73812
T309 5052-5054 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T310 5346-5348 Chemical denotes S5 http://purl.obolibrary.org/obo/CHEBI_29386
T311 5495-5497 Chemical denotes PB http://purl.obolibrary.org/obo/CHEBI_53319|http://purl.obolibrary.org/obo/CHEBI_60686
T313 5673-5675 Chemical denotes PB http://purl.obolibrary.org/obo/CHEBI_53319|http://purl.obolibrary.org/obo/CHEBI_60686
T315 5695-5697 Chemical denotes S5 http://purl.obolibrary.org/obo/CHEBI_29386
T316 5769-5771 Chemical denotes PB http://purl.obolibrary.org/obo/CHEBI_53319|http://purl.obolibrary.org/obo/CHEBI_60686
T318 5810-5812 Chemical denotes DR http://purl.obolibrary.org/obo/CHEBI_73445
T319 6003-6005 Chemical denotes S8 http://purl.obolibrary.org/obo/CHEBI_29385
T320 6189-6191 Chemical denotes S5 http://purl.obolibrary.org/obo/CHEBI_29386
T321 6328-6330 Chemical denotes S5 http://purl.obolibrary.org/obo/CHEBI_29386
T322 6647-6655 Chemical denotes effector http://purl.obolibrary.org/obo/CHEBI_35224
T323 6836-6838 Chemical denotes PD http://purl.obolibrary.org/obo/CHEBI_74756
T324 6898-6906 Chemical denotes effector http://purl.obolibrary.org/obo/CHEBI_35224
T325 7456-7458 Chemical denotes PB http://purl.obolibrary.org/obo/CHEBI_53319|http://purl.obolibrary.org/obo/CHEBI_60686
T33355 8153-8155 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T91403 8708-8713 Chemical denotes NSAID http://purl.obolibrary.org/obo/CHEBI_35475
T67025 9424-9426 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T78964 9431-9433 Chemical denotes RD http://purl.obolibrary.org/obo/CHEBI_73812
T6 9516-9524 Chemical denotes effector http://purl.obolibrary.org/obo/CHEBI_35224
T44700 9647-9649 Chemical denotes PB http://purl.obolibrary.org/obo/CHEBI_53319|http://purl.obolibrary.org/obo/CHEBI_60686
T9 9707-9715 Chemical denotes effector http://purl.obolibrary.org/obo/CHEBI_35224
T18190 9847-9849 Chemical denotes S8 http://purl.obolibrary.org/obo/CHEBI_29385
T8435 10081-10083 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T70189 10088-10090 Chemical denotes RD http://purl.obolibrary.org/obo/CHEBI_73812
T91436 10296-10301 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T89 178-194 http://purl.obolibrary.org/obo/GO_0006955 denotes immune responses
T90 5743-5749 http://purl.obolibrary.org/obo/GO_0007613 denotes memory
T91 8116-8128 http://purl.obolibrary.org/obo/GO_0006954 denotes inflammation
T92 8386-8397 http://purl.obolibrary.org/obo/GO_0050817 denotes coagulation
T93 9764-9781 http://purl.obolibrary.org/obo/GO_0042110 denotes T cell activation
T94 9766-9781 http://purl.obolibrary.org/obo/GO_0001775 denotes cell activation
T95 10494-10509 http://purl.obolibrary.org/obo/GO_0006955 denotes immune response
T96 10858-10873 http://purl.obolibrary.org/obo/GO_0006955 denotes immune response

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T13 8212-8226 Phenotype denotes kidney disease http://purl.obolibrary.org/obo/HP_0000112
T14 8231-8250 Phenotype denotes renal insufficiency http://purl.obolibrary.org/obo/HP_0000083

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T239 0-129 Sentence denotes Identifying “immunotypes” and relationships between circulating B and T cell responses with disease severity in COVID-19 patients
T240 130-486 Sentence denotes To further investigate the relationship between immune responses and COVID-19 disease trajectory, we stratified the COVID-19 patients (n = 125) into eight different categories according to the NIH Ordinal Severity Scale ranging from COVID 1 (death) and COVID 2 (requiring maximal clinical intervention) to COVID 8 (at home with no required care) (Fig. 6A).
T241 487-594 Sentence denotes We then asked how changes in T and B cell populations defined above on D0 were related to disease severity.
T242 595-747 Sentence denotes More severe disease was associated with lower frequencies of CD8 and CD4 T cells, with a greater effect on CD8 T cells in less severe disease (Fig. 6B).
T243 748-943 Sentence denotes Taking all patients together, there were no statistically significant changes in the major T cell and B cell subsets related to disease severity though some trends were present (fig. S7, A to C).
T244 944-1104 Sentence denotes In contrast, HLA-DR+CD38+ CD8 T cells as well as both KI67+ and HLA-DR+CD38+ CD4 T cells were increased in patients with more severe disease (fig. S7, D and E).
T245 1105-1225 Sentence denotes Fig. 6 High dimensional analysis of immune phenotypes with clinical data reveals distinct COVID-19 patient immunotypes.
T246 1226-1320 Sentence denotes (A) NIH ordinal scale for COVID-19 clinical severity. (B) Frequencies of major immune subsets.
T247 1321-1814 Sentence denotes Significance determined by unpaired Wilcoxon test with BH correction: *p < 0.05, **p < 0.01, ***p < 0.001, and ****p < 0.0001. (C) Heatmap of indicated immune parameters by row; donor type, disease severity, and mortality indicated across top. (D) UMAP projection of aggregated flow cytometry data. (E) Transformed UMAP projection; density contours drawn separately for healthy donor (HD), recovered donor (RD), and COVID-19 subjects (see Methods). (F) Bars represent mean of UMAP Component 1.
T248 1815-2013 Sentence denotes Dots represent individual subjects; bars shaded by subject group and/or severity score. (G) Density contour plots indicating variation of specified immune features across UMAP Component coordinates.
T249 2014-2135 Sentence denotes Relative expression (according to heat scale) shown for both individual patients (points) and overall density (contours).
T250 2136-2813 Sentence denotes Spearman’s Rank Correlation coefficient (ρ) and p-value for each feature vs. Component 1 (C1) and Component 2 (C2) shown. (H) (Left) Spearman correlation between UMAP Components 1 and 2 and FlowSOM clusters. (Right) Select FlowSOM clusters and their protein expression. (I) Spearman correlation between UMAP Components 1 and 2 and clinical metadata. (J) Heatmap of immune parameters used to define Immunotype 3 indicated by row; disease severity and mortality indicated across top. (K) (Left) Transformed UMAP projection; patient status for Immunotype 3 indicated by color. (Right) Spearman correlation between Immunotype 3 and disease severity, mortality, and UMAP Components.
T251 2814-2880 Sentence denotes There were two challenges with extracting meaning from these data.
T252 2881-3007 Sentence denotes First, there was considerable inter-patient heterogeneity for each of these immune features related to disease severity score.
T253 3008-3165 Sentence denotes Second, these binary comparisons (e.g., one immune subset versus one clinical feature) vastly underutilized the high dimensional information in this dataset.
T254 3166-3288 Sentence denotes Thus, we next visualized major T and B cell subpopulation data as it related to clinical disease severity score (Fig. 6C).
T255 3289-3411 Sentence denotes Data were clustered based on immune features and then overlaid with the disease severity score over time for each patient.
T256 3412-3533 Sentence denotes This analysis revealed groups of patients with similar composite immune signatures of T and B cell populations (Fig. 6C).
T257 3534-3681 Sentence denotes When individual CD8 T cell, CD4 T cell, or B cell populations were examined, a similar concept of patient subgroups emerged (fig. S7, F, G, and H).
T258 3682-3894 Sentence denotes These data suggested the idea of “immunotypes” of COVID-19 patients based on integrated responses of T and B cells, though some individual cell types and/or phenotypes separated patients more clearly than others.
T259 3895-4107 Sentence denotes These approaches provided insight into potential immune phenotypes associated with patients with severe disease, but suffered from the use of a small number of manually selected T or B cell subsets or phenotypes.
T260 4108-4435 Sentence denotes We therefore next employed Uniform Manifold Approximation and Projection (UMAP) to distill the ~200 flow cytometry features (see tables S5 and S6) representing the immune landscape of COVID-19 disease in two dimensional space, creating compact meta features (or Components) that could then be correlated with clinical outcomes.
T261 4436-4633 Sentence denotes This analysis revealed a clear trajectory from HD to COVID-19 patients (Fig. 6D), which we centered and aligned with the horizontal axis (“Component 1”) to facilitate downstream analysis (Fig. 6E).
T262 4634-4764 Sentence denotes An orthogonal vertical axis coordinate (“Component 2”) also existed that captured non-overlapping aspects of the immune landscape.
T263 4765-4887 Sentence denotes We next calculated the mean of Component 1 for each patient group, with COVID-19 patients separated by severity (Fig. 6E).
T264 4888-5002 Sentence denotes The contribution of Component 1 clearly increased in a stepwise manner with increasing disease severity (Fig. 6F).
T265 5003-5077 Sentence denotes Interestingly, RD were subtly positioned between HD and COVID-19 patients.
T266 5078-5244 Sentence denotes Component 1 remained an independent predictor of disease severity (P = 5.5 × 10−5) even after adjusting for the confounding demographic factors of age, sex, and race.
T267 5245-5357 Sentence denotes We next investigated how the UMAP Components were associated with individual immune features (tables S5 and S6).
T268 5358-5494 Sentence denotes UMAP Component 1 captured immune features, including the relative loss of CD4 and CD8 T cells and increase in nonB:nonT cells (Fig. 6G).
T269 5495-5541 Sentence denotes PB also associated with Component 1 (Fig. 6G).
T270 5542-5630 Sentence denotes Other individual B cell features were differentially captured by UMAP Component 1 and 2.
T271 5631-5795 Sentence denotes Component 1 contained a signal for T-bet+ PB populations (table S5) whereas Component 2 was enriched for T-bet+ memory B cells and CD138+ PB populations (table S6).
T272 5796-6015 Sentence denotes Activated HLA-DR+CD38+ and KI67+ CD4 and CD8 T cells had contributions to both Component 1 and Component 2, with these features residing in the upper right corner of the UMAP plot (Fig. 6, G and H, and fig. S8, A to D).
T273 6016-6200 Sentence denotes In contrast, T-bet+ non-naïve CD8 T cells were strongly associated with Component 2 whereas T-bet+ non-naïve CD4 T cells were also linked to Component 1 (Fig. 6G and tables S5 and S6).
T274 6201-6339 Sentence denotes Eomes+ CD8 or CD4 T cells were both associated with Component 2 and negatively associated with Component 1 (Fig. 6G and tables S5 and S6).
T275 6340-6397 Sentence denotes We next took advantage of the FlowSOM clustering in Figs.
T276 6398-6549 Sentence denotes 2 to 4 that identified individual immune cell types most perturbed in COVID-19 patients and linked these FlowSOM clusters to UMAP Components (Fig. 6H).
T277 6550-6768 Sentence denotes For non-naïve CD8 T cells, FlowSOM Cluster 11 that contained T-bet+CX3CR1+ but non-proliferating effector-like cells was positively correlated with UMAP Component 2 and negatively correlated with Component 1 (Fig. 6H).
T278 6769-7006 Sentence denotes In contrast, FlowSOM Cluster 14 contained activated, proliferating PD-1+CD39+ cells that might reflect either recently generated effector or possibly exhausted CD8 T cells (50) and was strongly associated with UMAP Component 1 (Fig. 6H).
T279 7007-7274 Sentence denotes For CD4 T cells, FlowSOM Cluster 14, containing activated, proliferating CD4 T cells, was captured by both UMAP Components, whereas a second activated CD4 T cell population that also expressed CD95 (FlowSOM Cluster 13) was only captured by UMAP Component 1 (Fig. 6H).
T280 7275-7397 Sentence denotes In addition, Component 1 was negatively correlated with CD4 T cell FlowSOM Clusters 2 and 3 that contained cTfh (Fig. 6H).
T281 7398-7601 Sentence denotes Finally, for B cells, the FlowSOM Cluster of T-bet+CD138+ PB (Cluster 5) was positively correlated with Component 1 whereas the Tbet-CD138+ Cluster 3 was negatively correlated with Component 1 (Fig. 6H).
T282 7602-7770 Sentence denotes Locations in the UMAP immune landscape were dynamic, changing from D0 to D7 for both Component 1 and Component 2 consistent with the data in Fig. 5 and fig. S9, A to F.
T283 7771-7888 Sentence denotes The most dynamic changes in Component 1 were associated with the largest increases in IgM antibody levels (fig. S9G).
T284 7889-8049 Sentence denotes Given the association of the UMAP Component 1 with disease severity, we next examined the connections between UMAP Components with individual clinical features.
T285 8050-8261 Sentence denotes UMAP Component 1 correlated with several clinical measurements of inflammation (e.g., ferritin, hsCRP, IL-6), co-infection, organ failure (APACHE III), and acute kidney disease and renal insufficiency (Fig. 6I).
T286 8262-8425 Sentence denotes It was interesting, however, that, although D-dimer was elevated, this feature did not correlate with UMAP Component 1, but coagulation complication did (Fig. 6I).
T287 8426-8545 Sentence denotes Several antibody features also correlated with Component 1 consistent with some of the immune features discussed above.
T288 8546-8770 Sentence denotes In contrast, Component 2 lacked positive correlation to many of these clinical features of disease and rather was negatively correlated only to eosinophil count, NSAID use, and subsequent treatment with Remdesivir (Fig. 6I).
T289 8771-8966 Sentence denotes UMAP Component 1, but not Component 2, also correlated with mortality, although there were clearly patients with high Component 2, but low Component 1 who succumbed to COVID-19 disease (Fig. 6E).
T290 8967-9265 Sentence denotes These data indicate that the immune features captured by UMAP Component 1 have a strong relationship to many features of disease severity, whereas other features of immune dynamics during COVID-19 disease captured by UMAP Component 2 have a distinct relationship with clinical disease presentation.
T291 9266-9434 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 9435-9851 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 9852-9888 Sentence denotes However, the data presented in Figs.
T294 9889-9982 Sentence denotes 1 to 5 also suggested a subset of patients with minimal activation of T and B cell responses.
T295 9983-10178 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 10179-10346 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 10347-10669 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 10670-10780 Sentence denotes These data further emphasize the different ways patients can present and possibly succumb to COVID-19 disease.
T299 10781-10890 Sentence denotes These patterns may be related to pre-existing conditions in combination with immune response characteristics.
T300 10891-11012 Sentence denotes It is likely that additional immune features, such as comprehensive serum cytokine measurements, will improve this model.
T301 11013-11246 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).

2_test

Id Subject Object Predicate Lexical cue
32669297-26485519-135105217 6942-6944 26485519 denotes 50