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PMC:7402624 / 47611-49159 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T413 99-103 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T414 230-235 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T415 321-326 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T416 507-512 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T417 595-600 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T418 677-682 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T419 746-751 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T420 824-828 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T421 997-1001 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T422 1073-1078 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T423 1116-1118 Body_part denotes PB http://purl.org/sig/ont/fma/fma84371
T424 1517-1520 Body_part denotes IgM http://purl.org/sig/ont/fma/fma62873
T425 1521-1529 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1609 224-227 Gene denotes CD8 Gene:925
1610 271-276 Gene denotes T-bet Gene:30009
1611 277-283 Gene denotes CX3CR1 Gene:1524
1612 496-500 Gene denotes PD-1 Gene:100513601
1613 501-505 Gene denotes CD39 Gene:397298
1614 589-592 Gene denotes CD8 Gene:925
1615 671-674 Gene denotes CD4 Gene:920
1616 740-743 Gene denotes CD4 Gene:920
1617 818-821 Gene denotes CD4 Gene:920
1618 860-864 Gene denotes CD95 Gene:355
1619 991-994 Gene denotes CD4 Gene:920
1620 1103-1108 Gene denotes T-bet Gene:30009
1621 1109-1114 Gene denotes CD138 Gene:6382
1622 1186-1190 Gene denotes Tbet Gene:30009
1623 1191-1196 Gene denotes CD138 Gene:6382
1624 137-145 Species denotes patients Tax:9606
1625 245-252 Species denotes Cluster Tax:100569
1626 450-457 Species denotes Cluster Tax:100569
1627 692-699 Species denotes Cluster Tax:100569
1628 874-881 Species denotes Cluster Tax:100569
1629 1092-1099 Species denotes Cluster Tax:100569
1630 1120-1127 Species denotes Cluster Tax:100569
1631 1198-1205 Species denotes Cluster Tax:100569
1632 1042-1046 Chemical denotes cTfh
1633 128-136 Disease denotes COVID-19 MESH:C000657245

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T336 128-136 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T337 1116-1118 Disease denotes PB http://purl.obolibrary.org/obo/MONDO_0019035

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T753 99-109 http://purl.obolibrary.org/obo/CL_0000000 denotes cell types
T754 224-227 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T755 228-235 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T756 253-255 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T757 321-326 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T758 471-480 http://purl.obolibrary.org/obo/CLO_0001658 denotes activated
T759 507-512 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T760 589-592 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T761 593-600 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T762 671-674 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T763 675-682 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T764 715-724 http://purl.obolibrary.org/obo/CLO_0001658 denotes activated
T765 740-743 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T766 744-751 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T767 799-800 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T768 808-817 http://purl.obolibrary.org/obo/CLO_0001658 denotes activated
T769 818-821 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T770 822-828 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T771 991-994 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T772 995-1001 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T773 1071-1078 http://purl.obolibrary.org/obo/CL_0000236 denotes B cells
T774 1419-1421 http://purl.obolibrary.org/obo/CLO_0008935 denotes S9
T775 1423-1424 http://purl.obolibrary.org/obo/CLO_0001020 denotes A

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T322 307-315 Chemical denotes effector http://purl.obolibrary.org/obo/CHEBI_35224
T323 496-498 Chemical denotes PD http://purl.obolibrary.org/obo/CHEBI_74756
T324 558-566 Chemical denotes effector http://purl.obolibrary.org/obo/CHEBI_35224
T325 1116-1118 Chemical denotes PB http://purl.obolibrary.org/obo/CHEBI_53319|http://purl.obolibrary.org/obo/CHEBI_60686

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T275 0-57 Sentence denotes We next took advantage of the FlowSOM clustering in Figs.
T276 58-209 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 210-428 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 429-666 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 667-934 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 935-1057 Sentence denotes In addition, Component 1 was negatively correlated with CD4 T cell FlowSOM Clusters 2 and 3 that contained cTfh (Fig. 6H).
T281 1058-1261 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 1262-1430 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 1431-1548 Sentence denotes The most dynamic changes in Component 1 were associated with the largest increases in IgM antibody levels (fig. S9G).

2_test

Id Subject Object Predicate Lexical cue
32669297-26485519-135105217 602-604 26485519 denotes 50