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PMC:7402624 / 53777-55814 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T447 221-225 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T448 657-661 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T449 675-679 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T450 713-715 Body_part denotes PB http://purl.org/sig/ont/fma/fma84371
T451 902-906 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T452 1172-1177 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T453 1295-1300 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T454 1327-1329 Body_part denotes PB http://purl.org/sig/ont/fma/fma84371
T455 1366-1370 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T456 1400-1404 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T457 1426-1428 Body_part denotes PB http://purl.org/sig/ont/fma/fma84371
T458 1442-1447 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T459 1498-1508 Body_part denotes lymphocyte http://purl.org/sig/ont/fma/fma62863
T460 1613-1617 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T461 1673-1677 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1763 669-672 Gene denotes CD4 Gene:920
1764 1166-1169 Gene denotes CD4 Gene:920
1765 1289-1292 Gene denotes CD8 Gene:925
1766 1320-1325 Gene denotes T-bet Gene:30009
1767 1360-1363 Gene denotes CD8 Gene:925
1768 1394-1397 Gene denotes CD4 Gene:920
1769 1667-1670 Gene denotes CD4 Gene:920
1770 651-654 Gene denotes CD8 Gene:925
1771 69-77 Species denotes patients Tax:9606
1772 116-124 Species denotes patients Tax:9606
1773 415-424 Species denotes SARS-CoV2 Tax:2697049
1774 560-568 Species denotes patients Tax:9606
1775 625-633 Species denotes patients Tax:9606
1776 761-769 Species denotes patients Tax:9606
1777 862-870 Species denotes patients Tax:9606
1778 1089-1097 Species denotes patients Tax:9606
1779 1113-1121 Species denotes patients Tax:9606
1780 1997-2005 Species denotes patients Tax:9606
1781 2017-2026 Species denotes SARS-CoV2 Tax:2697049
1782 1575-1579 Chemical denotes UMAP
1783 47-55 Disease denotes COVID-19 MESH:C000657245
1784 107-115 Disease denotes COVID-19 MESH:C000657245
1785 287-296 Disease denotes infection MESH:D007239
1786 527-535 Disease denotes COVID-19 MESH:C000657245
1787 616-624 Disease denotes COVID-19 MESH:C000657245
1788 924-932 Disease denotes COVID-19 MESH:C000657245
1789 1080-1088 Disease denotes COVID-19 MESH:C000657245
1790 1521-1530 Disease denotes infection MESH:D007239
1791 2027-2036 Disease denotes infection MESH:D007239

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T365 47-55 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T366 107-115 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T367 287-296 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T368 415-419 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T369 527-535 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T370 616-624 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T371 713-715 Disease denotes PB http://purl.obolibrary.org/obo/MONDO_0019035
T372 924-932 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T373 1080-1088 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T374 1327-1329 Disease denotes PB http://purl.obolibrary.org/obo/MONDO_0019035
T375 1426-1428 Disease denotes PB http://purl.obolibrary.org/obo/MONDO_0019035
T376 1521-1530 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T377 2017-2021 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T378 2027-2036 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T817 90-91 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T818 213-214 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T819 219-225 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T820 505-506 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T821 651-654 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T822 655-661 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T823 669-672 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T824 673-679 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T825 680-690 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T826 734-735 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T827 894-895 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T828 900-906 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T829 1134-1144 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T830 1166-1169 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T831 1170-1177 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T832 1223-1233 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T833 1266-1275 http://purl.obolibrary.org/obo/CLO_0001658 denotes activated
T834 1289-1292 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T835 1293-1300 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T836 1305-1306 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T837 1360-1363 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T838 1364-1370 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T839 1394-1397 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T840 1398-1404 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T841 1440-1447 http://purl.obolibrary.org/obo/CL_0000236 denotes B cells
T842 1543-1544 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T843 1563-1573 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T844 1611-1617 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T845 1618-1628 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T846 1652-1653 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T847 1667-1670 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T848 1671-1677 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T849 1678-1688 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T35800 713-715 Chemical denotes PB http://purl.obolibrary.org/obo/CHEBI_53319|http://purl.obolibrary.org/obo/CHEBI_60686
T60468 1327-1329 Chemical denotes PB http://purl.obolibrary.org/obo/CHEBI_53319|http://purl.obolibrary.org/obo/CHEBI_60686
T13552 1346-1354 Chemical denotes effector http://purl.obolibrary.org/obo/CHEBI_35224
T70633 1426-1428 Chemical denotes PB http://purl.obolibrary.org/obo/CHEBI_53319|http://purl.obolibrary.org/obo/CHEBI_60686

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T101 19-34 http://purl.obolibrary.org/obo/GO_0006955 denotes immune response
T102 395-411 http://purl.obolibrary.org/obo/GO_0006955 denotes immune responses
T103 594-609 http://purl.obolibrary.org/obo/GO_0006955 denotes immune response
T104 673-690 http://purl.obolibrary.org/obo/GO_0042110 denotes T cell activation
T105 675-690 http://purl.obolibrary.org/obo/GO_0001775 denotes cell activation
T106 1433-1439 http://purl.obolibrary.org/obo/GO_0007613 denotes memory
T107 1611-1628 http://purl.obolibrary.org/obo/GO_0042110 denotes T cell activation
T108 1613-1628 http://purl.obolibrary.org/obo/GO_0001775 denotes cell activation
T109 1671-1688 http://purl.obolibrary.org/obo/GO_0042110 denotes T cell activation
T110 1673-1688 http://purl.obolibrary.org/obo/GO_0001775 denotes cell activation

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T312 0-125 Sentence denotes To interrogate the immune response patterns of COVID-19 hospitalized patients, we studied a cohort of ~125 COVID-19 patients.
T313 126-446 Sentence denotes We used high dimensional flow cytometry to perform deep immune profiling of individual B and T cell populations, with temporal analysis of immune changes during infection, and combined this profiling with extensive clinical data to understand the relationships between immune responses to SARS-CoV2 and disease severity.
T314 447-497 Sentence denotes Using this approach, we made several key findings.
T315 498-610 Sentence denotes First, a defining feature of COVID-19 disease in hospitalized patients was heterogeneity of the immune response.
T316 611-830 Sentence denotes Many COVID-19 patients displayed robust CD8 T cell and/or CD4 T cell activation and proliferation and PB responses, though a considerable subgroup of patients (~20%) had minimal detectable response compared to controls.
T317 831-1005 Sentence denotes Furthermore, even within those patients who mounted detectable B and T cell responses during COVID-19 disease, the immune characteristics of this response were heterogeneous.
T318 1006-1574 Sentence denotes By deep immune profiling, we identified three immunotypes in hospitalized COVID-19 patients including: (1) patients with robust activation and proliferation of CD4 T cells, relative lack of cTfh, together with modest activation of TEMRA-like as well as highly activated or exhausted CD8 T cells and a signature of T-bet+ PB; (2) Tbetbright effector-like CD8 T cell responses, less robust CD4 T cell responses, and Ki67+ PB and memory B cells; and (3) an immunotype largely lacking detectable lymphocyte response to infection, suggesting a failure of immune activation.
T319 1575-1733 Sentence denotes UMAP embedding further resolved the T cell activation immunotype, suggesting a link between CD4 T cell activation, Immunotype 1, and increased severity score.
T320 1734-1924 Sentence denotes Although differences in age and race existed between the cohorts and could impact some immune variables, the major UMAP relationships were preserved even when correcting for these variables.
T321 1925-2037 Sentence denotes Thus, these immunotypes may reflect fundamental differences in the ways patients respond to SARS-CoV2 infection.