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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T30868 104-108 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T64579 215-231 Body_part denotes epithelial cells http://purl.org/sig/ont/fma/fma66768
T18385 226-231 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T26459 331-336 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T74490 363-374 Body_part denotes pneumocytes http://purl.org/sig/ont/fma/fma62499
T57427 392-403 Body_part denotes pneumocytes http://purl.org/sig/ont/fma/fma62499
T45527 509-513 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T71902 593-604 Body_part denotes pneumocytes http://purl.org/sig/ont/fma/fma62499
T62436 716-727 Body_part denotes pneumocytes http://purl.org/sig/ont/fma/fma62499
T41832 742-747 Body_part denotes Cells http://purl.org/sig/ont/fma/fma68646
T321 758-762 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T76609 781-791 Body_part denotes pneumocyte http://purl.org/sig/ont/fma/fma62499
T23388 806-810 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T38118 854-859 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T76254 967-972 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T70818 983-988 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T15181 1053-1058 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T16876 1265-1269 Body_part denotes Lung http://purl.org/sig/ont/fma/fma7195
T10381 1336-1352 Body_part denotes epithelial cells http://purl.org/sig/ont/fma/fma66768
T43874 1347-1352 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T26007 1360-1365 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T98068 1388-1392 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T99509 1399-1405 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T29624 1442-1447 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T89353 1463-1468 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T39897 1494-1499 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T13798 1513-1518 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T19523 1531-1542 Body_part denotes pneumocytes http://purl.org/sig/ont/fma/fma62499
T40933 1560-1571 Body_part denotes pneumocytes http://purl.org/sig/ont/fma/fma62499
T71611 1633-1638 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T53856 1674-1679 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T6586 1683-1689 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T46157 1726-1730 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T54100 1736-1740 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T47693 1756-1761 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T49420 1771-1776 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T18542 1832-1837 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T45700 1849-1854 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T70996 2023-2038 Body_part denotes epithelial cell http://purl.org/sig/ont/fma/fma66768
T87517 2034-2038 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T76289 2098-2103 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T28685 2189-2194 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T55403 2235-2239 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T83597 2277-2282 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T11799 2340-2345 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T14134 2370-2381 Body_part denotes pneumocytes http://purl.org/sig/ont/fma/fma62499
T63492 2436-2447 Body_part denotes pneumocytes http://purl.org/sig/ont/fma/fma62499
T25039 2473-2478 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T14862 2573-2589 Body_part denotes epithelial cells http://purl.org/sig/ont/fma/fma66768
T38033 2584-2589 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T7095 2697-2702 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T34 104-108 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T35 509-513 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T36 1265-1269 Body_part denotes Lung http://purl.obolibrary.org/obo/UBERON_0002048
T37 1399-1405 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T38 1683-1689 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T39 1726-1730 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T106 283-287 Disease denotes STAR http://purl.obolibrary.org/obo/MONDO_0010408
T107 1191-1203 Disease denotes inflammation http://purl.obolibrary.org/obo/MONDO_0021166
T108 1243-1255 Disease denotes Tuberculosis http://purl.obolibrary.org/obo/MONDO_0018076

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T32896 12-13 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T62302 104-108 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T49811 104-108 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T83510 141-160 http://purl.obolibrary.org/obo/NCBITaxon_9541 denotes Macaca fascicularis
T95036 215-225 http://purl.obolibrary.org/obo/CL_0000066 denotes epithelial
T34107 226-231 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T2157 268-270 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T63441 331-336 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T39559 376-378 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T74853 509-513 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T2994 509-513 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T21425 561-565 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Test
T43594 742-747 http://purl.obolibrary.org/obo/GO_0005623 denotes Cells
T81133 758-762 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T47932 806-816 http://purl.obolibrary.org/obo/CL_0000000 denotes cell types
T61012 854-859 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T89605 947-952 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T35819 967-972 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T41200 983-988 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T11298 1053-1058 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T39187 1068-1075 http://purl.obolibrary.org/obo/UBERON_0001005 denotes airways
T12030 1079-1085 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T67132 1155-1156 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T26933 1236-1238 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T73657 1265-1269 http://purl.obolibrary.org/obo/UBERON_0002048 denotes Lung
T20633 1265-1269 http://www.ebi.ac.uk/efo/EFO_0000934 denotes Lung
T61293 1313-1314 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T38285 1336-1346 http://purl.obolibrary.org/obo/CL_0000066 denotes epithelial
T57087 1347-1352 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T71105 1360-1365 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T63382 1388-1397 http://purl.obolibrary.org/obo/CL_0000000 denotes cell type
T17198 1442-1447 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T82766 1463-1468 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T19623 1478-1480 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T37996 1494-1499 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T69593 1513-1518 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T27809 1548-1550 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T85798 1619-1620 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T80701 1633-1638 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T46135 1674-1679 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T9290 1726-1730 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T95835 1726-1730 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T64574 1736-1745 http://purl.obolibrary.org/obo/CL_0000000 denotes cell type
T34712 1756-1761 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T48746 1771-1776 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T82967 1832-1837 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T84738 1849-1854 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T48976 1953-1957 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Test
T44586 2008-2013 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T18907 2023-2033 http://purl.obolibrary.org/obo/CL_0000066 denotes epithelial
T89339 2034-2043 http://purl.obolibrary.org/obo/CL_0000000 denotes cell type
T66912 2098-2103 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T58845 2189-2194 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T54918 2235-2239 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T45497 2277-2282 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T61092 2292-2296 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T69561 2340-2345 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T90995 2473-2478 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T58071 2520-2525 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T53729 2573-2583 http://purl.obolibrary.org/obo/CL_0000066 denotes epithelial
T23060 2584-2589 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T54660 2611-2615 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T48816 2697-2702 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T68923 2718-2725 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animals

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T70 186-188 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T71 279-281 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T72 360-362 Chemical denotes II http://purl.obolibrary.org/obo/CHEBI_74067
T73 590-592 Chemical denotes II http://purl.obolibrary.org/obo/CHEBI_74067
T74 647-660 Chemical denotes antimicrobial http://purl.obolibrary.org/obo/CHEBI_33281
T75 713-715 Chemical denotes II http://purl.obolibrary.org/obo/CHEBI_74067
T76 1176-1179 Chemical denotes IFN http://purl.obolibrary.org/obo/CHEBI_52999
T77 1557-1559 Chemical denotes II http://purl.obolibrary.org/obo/CHEBI_74067
T78 1603-1605 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T79 1613-1615 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T80 1965-1967 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T81 2203-2208 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T82 2498-2500 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T83 2679-2681 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T85557 1191-1203 http://purl.obolibrary.org/obo/GO_0006954 denotes inflammation

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T105 0-297 Sentence denotes Next, using a previously unpublished scRNA-seq dataset consisting of granuloma and adjacent, uninvolved lung samples from Mtb-infected NHPs (Macaca fascicularis) collected with Seq-Well S3, we identified subsets of epithelial cells expressing ACE2 and TMPRSS2 (Figure S1 ; Table S3; STAR Methods).
T106 298-567 Sentence denotes The majority of ACE2 + TMPRSS2 + cells were, once again, type II pneumocytes (22%) and type I pneumocytes (9.7%) and were largely enriched within granulomatous regions compared with those in adjacent uninvolved lung (Figures S1B and S1C) (p = 0.006, Fisher Exact Test).
T107 568-741 Sentence denotes ACE2 + TMPRSS2 + type II pneumocytes expressed significantly higher amounts of antimicrobial effectors such as LCN2 compared with remaining type II pneumocytes (Figure S1D).
T108 742-1011 Sentence denotes Cells with club cell/secretory, type I pneumocyte, and ciliated cell types also contained some ACE2 + TMPRSS2 + cells, but we did not have sufficient power to detect significantly differentially expressed genes between these cells and other cells within those clusters.
T109 1012-1228 Sentence denotes Altogether, we identify ACE2 + TMPRSS2 + cells in lower airways of humans and NHPs with consistent cellular phenotypes and evidence supporting a potential role for IFN-associated inflammation in upregulation of ACE2.
T110 1229-1311 Sentence denotes Figure S1 NHP Tuberculosis Infected Lung and Granuloma, Related to Figures 1 and 2
T111 1312-1316 Sentence denotes (A).
T112 1317-1448 Sentence denotes UMAP projection of epithelial cells (1,099 cells) colored by annotated cell type, tissue source, and gating as ACE2+TMPRSS2+ cells.
T113 1449-1572 Sentence denotes ACE2+TMPRSS2+ cells comprise 11% of ciliated cells, 16% of club cells, 10% type I pneumocytes, and 22% type II pneumocytes.
T114 1573-1617 Sentence denotes Data generated using Seq-Well S3 (Table S3).
T115 1618-1622 Sentence denotes (B).
T116 1623-1746 Sentence denotes Number of cells (left) and % (right) ACE2+TMPRSS2+ cells by tissue source (granuloma versus uninvolved lung) and cell type.
T117 1747-1902 Sentence denotes Ciliated cells and club cells were omitted from this analysis as we detected too few cells (< 7 total cells) belonging to these clusters in the granulomas.
T118 1903-1969 Sentence denotes Statistical significance assessed by Fisher Exact Test (Table S3).
T119 1970-1974 Sentence denotes (C).
T120 1975-2065 Sentence denotes Dot plot of top cluster defining genes for each epithelial cell type and ACE2 and TMPRSS2.
T121 2066-2240 Sentence denotes Dot size represents fraction of cells expressing, and color intensity represents average log(normalized UMI + 1) among all cells in each group scaled between 0 and 1 by gene.
T122 2241-2394 Sentence denotes ACE2 expression is enriched in club cells (Bimodal test, Bonferroni-corrected p < 0.001), ciliated cells (p < 0.005), and type I pneumocytes (p < 0.001).
T123 2395-2502 Sentence denotes TMPRSS2 expression is enriched in type I pneumocytes (p < 0.001) and ciliated cells (p < 0.001) (Table S3).
T124 2503-2507 Sentence denotes (D).
T125 2508-2727 Sentence denotes Dot plot of genes differentially expressed between ACE2+TMPRSS2+ epithelial cells versus rest (Bimodal test, Bonferroni-corrected p < 0.01, log fold change > 0.5). (Table S3, c = number of cells, n = number of animals).

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T7 69-78 Phenotype denotes granuloma http://purl.obolibrary.org/obo/HP_0032252
T8 1274-1283 Phenotype denotes Granuloma http://purl.obolibrary.org/obo/HP_0032252
T9 1698-1707 Phenotype denotes granuloma http://purl.obolibrary.org/obo/HP_0032252
T10 1891-1901 Phenotype denotes granulomas http://purl.obolibrary.org/obo/HP_0032252

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
548 1239-1269 Disease denotes NHP Tuberculosis Infected Lung MESH:D012141
549 1274-1283 Disease denotes Granuloma MESH:D006099
554 1428-1432 Gene denotes ACE2 Gene:59272
555 1433-1440 Gene denotes TMPRSS2 Gene:7113
556 1449-1453 Gene denotes ACE2 Gene:59272
557 1454-1461 Gene denotes TMPRSS2 Gene:7113
562 1660-1664 Gene denotes ACE2 Gene:59272
563 1665-1672 Gene denotes TMPRSS2 Gene:7113
564 1698-1707 Disease denotes granuloma MESH:D006099
565 1891-1901 Disease denotes granulomas MESH:D006099
570 2048-2052 Gene denotes ACE2 Gene:59272
571 2057-2064 Gene denotes TMPRSS2 Gene:7113
572 2241-2245 Gene denotes ACE2 Gene:59272
573 2395-2402 Gene denotes TMPRSS2 Gene:7113
576 2559-2563 Gene denotes ACE2 Gene:59272
577 2564-2571 Gene denotes TMPRSS2 Gene:7113
597 243-247 Gene denotes ACE2 Gene:102130864
598 252-259 Gene denotes TMPRSS2 Gene:102137447
599 314-318 Gene denotes ACE2 Gene:102130864
600 321-328 Gene denotes TMPRSS2 Gene:102137447
601 568-572 Gene denotes ACE2 Gene:102130864
602 575-582 Gene denotes TMPRSS2 Gene:102137447
603 679-683 Gene denotes LCN2 Gene:3934
604 837-841 Gene denotes ACE2 Gene:102130864
605 844-851 Gene denotes TMPRSS2 Gene:102137447
606 1036-1040 Gene denotes ACE2 Gene:59272
607 1043-1050 Gene denotes TMPRSS2 Gene:7113
608 1176-1179 Gene denotes IFN Gene:3439
609 1223-1227 Gene denotes ACE2 Gene:59272
610 283-287 Gene denotes STAR Gene:102132972
611 141-160 Species denotes Macaca fascicularis Tax:9541
612 1079-1085 Species denotes humans Tax:9606
613 69-78 Disease denotes granuloma MESH:D006099
614 122-139 Disease denotes Mtb-infected NHPs MESH:D007239
615 1191-1203 Disease denotes inflammation MESH:D007249