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PMC:7200337 / 31821-33675 JSONTXT

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2_test

Id Subject Object Predicate Lexical cue
32505227-16868248-46575314 658-662 16868248 denotes 2006
32505227-16525420-46575315 678-682 16525420 denotes 2006
T2441 658-662 16868248 denotes 2006
T35567 678-682 16525420 denotes 2006

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T320 64-69 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T321 77-82 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T322 124-132 Body_part denotes cytokine http://purl.org/sig/ont/fma/fma84050
T323 185-190 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T324 317-321 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T325 376-384 Body_part denotes cytokine http://purl.org/sig/ont/fma/fma84050
T326 492-501 Body_part denotes Cytokines http://purl.org/sig/ont/fma/fma84050
T327 540-544 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T328 562-567 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T329 628-639 Body_part denotes endothelium http://purl.org/sig/ont/fma/fma63916
T330 728-735 Body_part denotes spleens http://purl.org/sig/ont/fma/fma7196
T331 740-757 Body_part denotes hilar lymph nodes http://purl.org/sig/ont/fma/fma276990
T332 832-836 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T333 846-857 Body_part denotes lymphocytes http://purl.org/sig/ont/fma/fma62863
T334 1072-1083 Body_part denotes lymphocytes http://purl.org/sig/ont/fma/fma62863
T335 1125-1129 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T336 1213-1218 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T337 1219-1230 Body_part denotes compartment http://purl.org/sig/ont/fma/fma76577
T338 1340-1344 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T339 1516-1526 Body_part denotes lymphocyte http://purl.org/sig/ont/fma/fma62863
T340 1547-1552 Body_part denotes lungs http://purl.org/sig/ont/fma/fma68877
T341 1670-1682 Body_part denotes neutrophilic http://purl.org/sig/ont/fma/fma62860

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T38 77-82 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T39 185-190 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T40 562-567 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T41 603-609 Body_part denotes organs http://purl.obolibrary.org/obo/UBERON_0000062
T42 628-639 Body_part denotes endothelium http://purl.obolibrary.org/obo/UBERON_0001986
T43 728-735 Body_part denotes spleens http://purl.obolibrary.org/obo/UBERON_0002106
T44 746-757 Body_part denotes lymph nodes http://purl.obolibrary.org/obo/UBERON_0000029
T45 746-751 Body_part denotes lymph http://purl.obolibrary.org/obo/UBERON_0002391
T46 1213-1218 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T213 149-160 Disease denotes lymphopenia http://purl.obolibrary.org/obo/MONDO_0003783
T214 791-799 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T215 1154-1163 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T216 1292-1300 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T217 1463-1467 Disease denotes ARDS http://purl.obolibrary.org/obo/MONDO_0006502
T218 1478-1486 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T219 1489-1498 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T220 1641-1649 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T221 1821-1832 Disease denotes lymphopenia http://purl.obolibrary.org/obo/MONDO_0003783
T222 1836-1844 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T366 62-69 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T367 77-82 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T368 77-82 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T369 315-321 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T370 538-544 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T371 562-567 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T372 562-567 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T373 594-609 http://purl.obolibrary.org/obo/UBERON_0004177 denotes lymphoid organs
T374 628-639 http://purl.obolibrary.org/obo/UBERON_0001986 denotes endothelium
T375 728-735 http://purl.obolibrary.org/obo/UBERON_0002106 denotes spleens
T376 746-757 http://purl.obolibrary.org/obo/UBERON_0000029 denotes lymph nodes
T377 832-836 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T378 1123-1129 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T379 1213-1218 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T380 1213-1218 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T381 1334-1337 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T382 1338-1344 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T383 1436-1437 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T384 1547-1552 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lungs

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T145 191-193 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T147 197-199 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T149 892-894 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T151 987-989 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T153 1001-1011 Chemical denotes antagonist http://purl.obolibrary.org/obo/CHEBI_48706
T154 1012-1023 Chemical denotes tocilizumab http://purl.obolibrary.org/obo/CHEBI_64360
T155 1278-1281 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T21 44-69 Phenotype denotes reduced number of T cells http://purl.obolibrary.org/obo/HP_0005403
T22 149-160 Phenotype denotes lymphopenia http://purl.obolibrary.org/obo/HP_0001888
T23 1821-1832 Phenotype denotes lymphopenia http://purl.obolibrary.org/obo/HP_0001888

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T128 581-590 http://purl.obolibrary.org/obo/GO_0051235 denotes retention
T129 832-842 http://purl.obolibrary.org/obo/GO_0008219 denotes cell death

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1061 191-195 Gene denotes IL-6 Gene:3569
1062 197-202 Gene denotes IL-10 Gene:3586
1063 208-213 Gene denotes TNF-α Gene:7124
1064 520-525 Gene denotes TNF-α Gene:7124
1065 892-896 Gene denotes IL-6 Gene:3569
1066 912-916 Gene denotes FasL Gene:356
1067 1334-1337 Gene denotes CD8 Gene:925
1068 1755-1757 Gene denotes to Gene:6999
1069 1460-1462 Gene denotes to Gene:6999
1070 1142-1144 Gene denotes to Gene:6999
1071 1034-1036 Gene denotes to Gene:6999
1072 788-790 Gene denotes to Gene:6999
1073 625-627 Gene denotes to Gene:6999
1074 293-295 Gene denotes to Gene:6999
1075 167-169 Gene denotes to Gene:6999
1076 37-39 Gene denotes to Gene:6999
1077 273-281 Species denotes patients Tax:9606
1078 765-773 Species denotes patients Tax:9606
1079 1301-1309 Species denotes patients Tax:9606
1080 1438-1445 Species denotes patient Tax:9606
1081 1650-1658 Species denotes patients Tax:9606
1082 1845-1853 Species denotes patients Tax:9606
1083 1012-1023 Chemical denotes tocilizumab MESH:C502936
1084 149-160 Disease denotes lymphopenia MESH:D008231
1085 791-799 Disease denotes COVID-19 MESH:C000657245
1086 837-842 Disease denotes death MESH:D003643
1087 1154-1163 Disease denotes infection MESH:D007239
1088 1292-1300 Disease denotes COVID-19 MESH:C000657245
1089 1463-1467 Disease denotes ARDS MESH:D012128
1090 1483-1498 Disease denotes CoV-2 infection MESH:C000657245
1091 1641-1649 Disease denotes COVID-19 MESH:C000657245
1092 1821-1832 Disease denotes lymphopenia MESH:D008231
1093 1836-1844 Disease denotes COVID-19 MESH:C000657245

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T179 0-140 Sentence denotes Several mechanisms likely contribute to the reduced number of T cells in the blood, including effects from the inflammatory cytokine milieu.
T180 141-491 Sentence denotes Indeed, lymphopenia seems to correlate with serum IL-6, IL-10, and TNF-α (Diao et al., 2020, Wan et al., 2020a), while convalescent patients were found to have restored bulk T cell frequencies paired with overall lower proinflammatory cytokine levels (Chen et al., 2020f, Diao et al., 2020, Liu et al., 2020a, Liu et al., 2020b, Zheng et al., 2020b).
T181 492-684 Sentence denotes Cytokines such as IFN-I and TNF-α may inhibit T cell recirculation in blood by promoting retention in lymphoid organs and attachment to endothelium (Kamphuis et al., 2006, Shiow et al., 2006).
T182 685-951 Sentence denotes However, in an autopsy study examining the spleens and hilar lymph nodes of six patients who succumbed to COVID-19, Chen et al. observed extensive cell death of lymphocytes and suggested potential roles for IL-6 as well as Fas-FasL interactions (Chen et al., 2020h).
T183 952-1122 Sentence denotes In support of this hypothesis, the IL-6 receptor antagonist tocilizumab was found to increase the number of circulating lymphocytes (Giamarellos-Bourboulis et al., 2020).
T184 1123-1398 Sentence denotes T cell recruitment to sites of infection may also reduce their presence in the peripheral blood compartment. scRNA-seq analysis of bronchoalveolar lavage (BAL) fluid of COVID-19 patients revealed an increase in CD8 T cell infiltrate with clonal expansion (Liao et al., 2020).
T185 1399-1572 Sentence denotes Likewise, post-mortem examination of a patient who succumbed to ARDS following SARS-CoV-2 infection showed extensive lymphocyte infiltration in the lungs (Xu et al., 2020c).
T186 1573-1717 Sentence denotes However, another study that examined post-mortem biopsies from four COVID-19 patients only found neutrophilic infiltration (Tian et al., 2020a).
T187 1718-1854 Sentence denotes Further studies are therefore needed to better determine the cause and impact of the commonly observed lymphopenia in COVID-19 patients.