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PMC:7252096 / 15195-16755 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T13117 7-11 Body_part denotes Lung http://purl.org/sig/ont/fma/fma7195
T97209 12-28 Body_part denotes Epithelial Cells http://purl.org/sig/ont/fma/fma66768
T58447 23-28 Body_part denotes Cells http://purl.org/sig/ont/fma/fma68646
T22748 43-46 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T72849 189-193 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T51464 194-200 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T32804 316-320 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T159 404-409 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T16248 436-439 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T57087 483-488 Body_part denotes Cells http://purl.org/sig/ont/fma/fma68646
T21872 533-537 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T163 692-695 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T38697 712-715 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T165 768-772 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T42440 858-863 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T17615 871-875 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T67803 900-904 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T7984 1011-1016 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T17779 1091-1095 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T52492 1143-1148 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T94798 1228-1239 Body_part denotes pneumocytes http://purl.org/sig/ont/fma/fma62499
T69556 1268-1279 Body_part denotes pneumocytes http://purl.org/sig/ont/fma/fma62499
T7255 1486-1489 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T30 7-11 Body_part denotes Lung http://purl.obolibrary.org/obo/UBERON_0002048
T31 189-193 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T32 194-200 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T92 77-89 Disease denotes tuberculosis http://purl.obolibrary.org/obo/MONDO_0018076
T93 433-435 Disease denotes TB http://purl.obolibrary.org/obo/MONDO_0018076
T94 448-450 Disease denotes TB http://purl.obolibrary.org/obo/MONDO_0018076
T95 548-552 Disease denotes STAR http://purl.obolibrary.org/obo/MONDO_0010408
T96 1494-1496 Disease denotes TB http://purl.obolibrary.org/obo/MONDO_0018076

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T86794 7-28 http://purl.obolibrary.org/obo/CL_0000082 denotes Lung Epithelial Cells
T51443 99-104 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Human
T63387 141-142 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T35956 183-188 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T32379 189-193 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T73304 189-193 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T7811 316-326 http://purl.obolibrary.org/obo/CL_0000000 denotes cell types
T89005 376-377 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T37671 404-409 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T53946 483-488 http://purl.obolibrary.org/obo/GO_0005623 denotes Cells
T21733 533-542 http://purl.obolibrary.org/obo/CL_0000000 denotes cell type
T96107 564-565 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T75647 590-591 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T62279 753-758 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T23408 768-777 http://purl.obolibrary.org/obo/CL_0000000 denotes cell type
T67693 858-863 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T25827 871-880 http://purl.obolibrary.org/obo/CL_0000000 denotes cell type
T4783 892-893 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T67532 900-904 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T46104 1011-1016 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T20388 1039-1048 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes are
T2783 1067-1069 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T54985 1067-1069 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T59240 1091-1101 http://purl.obolibrary.org/obo/CL_0000000 denotes cell types
T38339 1143-1148 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T65003 1205-1210 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T49895 1302-1307 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T27452 1313-1314 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T55966 1393-1403 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes; the
T60530 1436-1438 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T6253 1436-1438 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T52423 1470-1475 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T18839 1535-1539 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T75828 1557-1559 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T26490 1557-1559 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T59 112-114 Chemical denotes Co http://purl.obolibrary.org/obo/CHEBI_27638
T60 273-275 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T61 1067-1069 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T62 1436-1438 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T63 1557-1559 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T86 140-353 Sentence denotes (A) Schematic of protocol for isolation of human lung tissue from surgical excess, creation of scRNA-seq libraries by using Seq-Well S3, and computational analysis to identify cell types by using unbiased methods.
T87 354-482 Sentence denotes Shown on the right is a UMAP projection of 18,915 cells across 8 donors (n = 3 TB+HIV+; n = 3 TB+; n = 2 non-infected patients).
T88 483-562 Sentence denotes Cells represented by points, colored according to cell type (see STAR Methods).
T89 563-656 Sentence denotes (B) UMAP projection as in (A), points colored by detection of ACE2 (top) or TMPRSS2 (bottom).
T90 657-725 Sentence denotes Color coding is as follows: black, RNA positive; blue, RNA negative.
T91 726-1017 Sentence denotes (C) Dot plot of 2 defining genes for each cell type (FDR-adjusted p < 0.001), and ACE2 and TMPRSS2; dot size represents fraction of cells within cell type expressing a given gene, and color intensity represents binned count-based expression amount (log(scaled UMI+1)) among expressing cells.
T92 1018-1070 Sentence denotes All cluster-defining genes are provided in Table S2.
T93 1071-1149 Sentence denotes Red arrow indicates cell types with largest proportion of ACE2+TMPRSS2+ cells.
T94 1150-1280 Sentence denotes (D) Volcano plot identifying significantly upregulated genes in ACE2+TMPRSS2+ pneumocytes compared with all remaining pneumocytes.
T95 1281-1365 Sentence denotes Red points represent genes with a FDR-adjusted p < 0.05, and log2(fold change) >1.5.
T96 1366-1439 Sentence denotes Text highlighting specific genes; the full list is available in Table S2.
T97 1440-1541 Sentence denotes (E) Expression of ACE2 across human donors by HIV and TB status (p = 0.009 by likelihood-ratio test).
T98 1542-1560 Sentence denotes See also Table S2.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
430 123-127 Gene denotes ACE2 Gene:59272
431 99-104 Species denotes Human Tax:9606
432 43-57 Disease denotes HIV-1-Infected MESH:D015658
433 63-98 Disease denotes Mycobacterium-tuberculosis-Infected MESH:D014376
439 548-552 Gene denotes STAR Gene:6770
440 183-188 Species denotes human Tax:9606
441 472-480 Species denotes patients Tax:9606
442 436-439 Species denotes HIV Tax:12721
443 463-471 Disease denotes infected MESH:D007239
446 625-629 Gene denotes ACE2 Gene:59272
447 639-646 Gene denotes TMPRSS2 Gene:7113
452 808-812 Gene denotes ACE2 Gene:59272
453 817-824 Gene denotes TMPRSS2 Gene:7113
454 1129-1133 Gene denotes ACE2 Gene:59272
455 1134-1141 Gene denotes TMPRSS2 Gene:7113
458 1214-1218 Gene denotes ACE2 Gene:59272
459 1219-1226 Gene denotes TMPRSS2 Gene:7113
464 1458-1462 Gene denotes ACE2 Gene:59272
465 1470-1475 Species denotes human Tax:9606
466 1486-1489 Species denotes HIV Tax:12721
467 1494-1496 Chemical denotes TB MESH:D013725