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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T603 16-32 Body_part denotes Nasal Epithelium http://purl.org/sig/ont/fma/fma63140
T604 22-32 Body_part denotes Epithelium http://purl.org/sig/ont/fma/fma9639
T605 239-255 Body_part denotes nasal epithelium http://purl.org/sig/ont/fma/fma63140
T606 245-255 Body_part denotes epithelium http://purl.org/sig/ont/fma/fma9639
T607 362-366 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T608 436-441 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T609 449-453 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T610 564-569 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T611 636-640 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T612 680-685 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T613 804-820 Body_part denotes Epithelial Cells http://purl.org/sig/ont/fma/fma66768
T614 815-820 Body_part denotes Cells http://purl.org/sig/ont/fma/fma68646
T615 826-831 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T616 916-932 Body_part denotes Epithelial Cells http://purl.org/sig/ont/fma/fma66768
T617 927-932 Body_part denotes Cells http://purl.org/sig/ont/fma/fma68646
T618 986-989 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T619 1006-1009 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T620 1074-1089 Body_part denotes Epithelial Cell http://purl.org/sig/ont/fma/fma66768
T621 1085-1089 Body_part denotes Cell http://purl.org/sig/ont/fma/fma68646
T622 1118-1123 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T623 1268-1273 Body_part denotes Cells http://purl.org/sig/ont/fma/fma68646
T624 1285-1289 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T625 1356-1361 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T626 1391-1406 Body_part denotes epithelial cell http://purl.org/sig/ont/fma/fma66768
T627 1402-1406 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T628 1551-1562 Body_part denotes pneumocytes http://purl.org/sig/ont/fma/fma62499
T629 1703-1708 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T630 1755-1760 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T631 1792-1795 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T632 1797-1802 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T633 1867-1872 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T634 1892-1897 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T635 1917-1920 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T636 1965-1969 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T637 2096-2103 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T638 2127-2138 Body_part denotes pneumocytes http://purl.org/sig/ont/fma/fma62499
T639 2172-2176 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T640 2692-2697 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T641 2739-2744 Body_part denotes Cells http://purl.org/sig/ont/fma/fma68646
T642 2855-2862 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T95 16-32 Body_part denotes Nasal Epithelium http://purl.obolibrary.org/obo/UBERON_0005384
T96 22-32 Body_part denotes Epithelium http://purl.obolibrary.org/obo/UBERON_0000483
T97 239-255 Body_part denotes nasal epithelium http://purl.obolibrary.org/obo/UBERON_0005384
T98 245-255 Body_part denotes epithelium http://purl.obolibrary.org/obo/UBERON_0000483
T99 1285-1289 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T100 1965-1969 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T101 2172-2176 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T174 1573-1582 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T175 1712-1721 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T176 2005-2014 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T177 2048-2057 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T178 2363-2372 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T179 2515-2524 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T180 2731-2737 Disease denotes asthma http://purl.obolibrary.org/obo/MONDO_0004979

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T842 7-9 http://purl.obolibrary.org/obo/CLO_0008933 denotes S5
T843 10-15 http://purl.obolibrary.org/obo/CLO_0007836 denotes Mouse
T844 22-32 http://purl.obolibrary.org/obo/UBERON_0000483 denotes Epithelium
T845 86-87 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T846 211-218 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animals
T847 245-255 http://purl.obolibrary.org/obo/UBERON_0000483 denotes epithelium
T848 320-321 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T849 347-352 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T850 362-371 http://purl.obolibrary.org/obo/CL_0000000 denotes cell type
T851 436-441 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T852 449-458 http://purl.obolibrary.org/obo/CL_0000000 denotes cell type
T853 564-569 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T854 592-601 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes are
T855 636-646 http://purl.obolibrary.org/obo/CL_0000000 denotes cell types
T856 680-685 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T857 757-762 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T858 804-814 http://purl.obolibrary.org/obo/CL_0000066 denotes Epithelial
T859 815-820 http://purl.obolibrary.org/obo/GO_0005623 denotes Cells
T860 822-825 http://purl.obolibrary.org/obo/CLO_0001007 denotes 380
T861 826-831 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T862 870-875 http://purl.obolibrary.org/obo/CLO_0007836 denotes mouse
T863 916-926 http://purl.obolibrary.org/obo/CL_0000066 denotes Epithelial
T864 927-932 http://purl.obolibrary.org/obo/GO_0005623 denotes Cells
T865 1074-1084 http://purl.obolibrary.org/obo/CL_0000066 denotes Epithelial
T866 1085-1089 http://purl.obolibrary.org/obo/GO_0005623 denotes Cell
T867 1118-1123 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T868 1268-1273 http://purl.obolibrary.org/obo/GO_0005623 denotes Cells
T869 1285-1289 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T870 1285-1289 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T871 1356-1361 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T872 1391-1401 http://purl.obolibrary.org/obo/CL_0000066 denotes epithelial
T873 1402-1411 http://purl.obolibrary.org/obo/CL_0000000 denotes cell type
T874 1480-1484 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T875 1675-1679 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T876 1703-1708 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T877 1755-1760 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T878 1779-1784 http://purl.obolibrary.org/obo/CLO_0007836 denotes mouse
T879 1797-1802 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T880 1808-1813 http://purl.obolibrary.org/obo/CLO_0007836 denotes mouse
T881 1867-1872 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T882 1892-1897 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T883 1959-1964 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T884 1965-1969 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T885 1965-1969 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T886 2015-2016 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T887 2017-2022 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T888 2107-2108 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T889 2172-2176 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T890 2172-2176 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T891 2435-2439 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T892 2587-2591 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T893 2692-2697 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T894 2713-2718 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T895 2739-2744 http://purl.obolibrary.org/obo/GO_0005623 denotes Cells
T896 2819-2820 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T897 2871-2874 http://purl.obolibrary.org/obo/CLO_0008693 denotes R&D
T898 2871-2874 http://purl.obolibrary.org/obo/CLO_0008770 denotes R&D

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T250 7-9 Chemical denotes S5 http://purl.obolibrary.org/obo/CHEBI_29386
T251 138-141 Chemical denotes IFN http://purl.obolibrary.org/obo/CHEBI_52999
T252 168-179 Chemical denotes application http://purl.obolibrary.org/obo/CHEBI_33232
T253 191-196 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T254 315-317 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T255 620-622 Chemical denotes S8 http://purl.obolibrary.org/obo/CHEBI_29385
T256 882-885 Chemical denotes IFN http://purl.obolibrary.org/obo/CHEBI_52999
T257 1152-1154 Chemical denotes WT http://purl.obolibrary.org/obo/CHEBI_141450
T258 1160-1163 Chemical denotes IFN http://purl.obolibrary.org/obo/CHEBI_52999
T259 1184-1187 Chemical denotes IFN http://purl.obolibrary.org/obo/CHEBI_52999
T260 1238-1243 Chemical denotes gamma http://purl.obolibrary.org/obo/CHEBI_30212
T261 1424-1426 Chemical denotes WT http://purl.obolibrary.org/obo/CHEBI_141450
T262 1548-1550 Chemical denotes II http://purl.obolibrary.org/obo/CHEBI_74067
T263 1593-1595 Chemical denotes WT http://purl.obolibrary.org/obo/CHEBI_141450
T264 1824-1826 Chemical denotes WT http://purl.obolibrary.org/obo/CHEBI_141450
T265 1828-1831 Chemical denotes IFN http://purl.obolibrary.org/obo/CHEBI_52999
T266 2085-2095 Chemical denotes surfactant http://purl.obolibrary.org/obo/CHEBI_35195
T267 2096-2103 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T268 2124-2126 Chemical denotes II http://purl.obolibrary.org/obo/CHEBI_74067
T269 2268-2271 Chemical denotes TPM http://purl.obolibrary.org/obo/CHEBI_63631
T24696 2755-2760 Chemical denotes donor http://purl.obolibrary.org/obo/CHEBI_17891
T22482 2855-2862 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T93675 2952-2957 Chemical denotes donor http://purl.obolibrary.org/obo/CHEBI_17891

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T299 0-84 Sentence denotes Figure S5 Mouse Nasal Epithelium Following Interferon-α Exposure Related to Figure 6
T300 85-89 Sentence denotes (A).
T301 90-198 Sentence denotes Schematic: mice were exposed to 10,000 units of IFN-α or saline by intranasal application (n = 2 per group).
T302 199-318 Sentence denotes After 12 h, animals were sacrificed and nasal epithelium was dissected and dissociated for scRNA-seq using Seq-Well S3.
T303 319-323 Sentence denotes (B).
T304 324-403 Sentence denotes Dot plot of 2 defining genes for each cell type, with Ace2, Tmprss2, and Cdhr3.
T305 404-570 Sentence denotes Dot size represents fraction of cells within cell type expressing, and color intensity binned count-based expression level (log(scaled UMI+1)) among expressing cells.
T306 571-623 Sentence denotes All cluster defining genes are provided in Table S8.
T307 624-686 Sentence denotes Red arrows: cell types with largest proportion of Ace2+ cells.
T308 687-784 Sentence denotes Dendrogram (left) by person correlation over differentially expressed genes with Ward clustering.
T309 785-789 Sentence denotes (C).
T310 790-847 Sentence denotes UMAP of Basal Epithelial Cells (380 cells) across 4 mice.
T311 848-854 Sentence denotes Black:
T312 855-896 Sentence denotes Saline-treated mouse; red: IFN-α treated.
T313 897-901 Sentence denotes (D).
T314 902-978 Sentence denotes UMAP of Basal Epithelial Cells as in C, points colored by detection of Ace2.
T315 979-1125 Sentence denotes Black: RNA positive, blue: RNA negative (6.6% Ace2+, Bonferroni-adjusted p = 1.1E-10 for Basal Epithelial Cell expression versus all other cells).
T316 1126-1130 Sentence denotes (E).
T317 1131-1267 Sentence denotes Schematic: wildtype (WT) and IFNγ-receptor knockout (IFNγR−/−) mice were infected intranasally with murine gamma-herpesvirus-68 (MHV68).
T318 1268-1363 Sentence denotes Cells from whole lung were digested for scRNA-seq using Drop-seq (yielding 5,558 Epcam+ cells).
T319 1364-1368 Sentence denotes (F).
T320 1369-1433 Sentence denotes Expression of Ace2 by epithelial cell type, wild type (WT) mice.
T321 1434-1512 Sentence denotes Statistical significance by Wilcoxon rank sum test with Bonferroni correction.
T322 1513-1517 Sentence denotes (G).
T323 1518-1601 Sentence denotes Expression of Ace2 among type II pneumocytes binned by infection status in WT mice.
T324 1602-1680 Sentence denotes All pairwise comparisons non-significant (p > 0.05) by Wilcoxon rank sum test.
T325 1681-1685 Sentence denotes (H).
T326 1686-1839 Sentence denotes Percent of Ace2+ cells by infection condition (uninfected, bystander cells in MHV68-infected mouse, MHV68 RNA+ cells) and mouse genotype (WT, IFNγR −/−).
T327 1840-1851 Sentence denotes Black bars:
T328 1852-1885 Sentence denotes Ace2+ positive cells; white bars:
T329 1886-1898 Sentence denotes Ace2- cells.
T330 1899-1903 Sentence denotes (I).
T331 1904-2058 Sentence denotes Schematic of RNA-Seq data from (Matos et al., 2019) of human lung explants (n = 5 donors) exposed to influenza A virus (IAV, H3N2) at 24 h post infection.
T332 2059-2063 Sentence denotes (J).
T333 2064-2186 Sentence denotes Expression of SFTPC (surfactant protein C, a marker of type II pneumocytes) versus ACE2 among mock-infected lung explants.
T334 2187-2267 Sentence denotes Statistical significance assessed by Pearson’s correlation, r = 0.93, p = 0.021.
T335 2268-2297 Sentence denotes TPM: transcripts per million.
T336 2298-2302 Sentence denotes (K).
T337 2303-2382 Sentence denotes SFTPC expression among matched donors following mock or IAV infection for 24 h.
T338 2383-2450 Sentence denotes Statistical significance assessed by ratio paired t test, p = 0.86.
T339 2451-2455 Sentence denotes (L).
T340 2456-2534 Sentence denotes ACE2 expression among matched donors following mock or IAV infection for 24 h.
T341 2535-2604 Sentence denotes Statistical significance assessed by ratio paired t test, p = 0.0054.
T342 2605-2609 Sentence denotes (M).
T343 2610-2738 Sentence denotes Western blot of fully-differentiated air-liquid interface cultures from bronchial cells derived from 4 human donors with asthma.
T344 2739-2849 Sentence denotes Cells from each donor were treated with 10 ng/mL IFNγ for 24 h, and compared to a matched untreated condition.
T345 2850-2876 Sentence denotes ACE2 protein: AF933 (R&D).
T346 2877-2991 Sentence denotes Fold changes quantified for IFNγ treated versus untreated for each patient donor following normalization to GAPDH.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T14 2731-2737 Phenotype denotes asthma http://purl.obolibrary.org/obo/HP_0002099

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1295 10-15 Species denotes Mouse Tax:10090
1298 138-143 Gene denotes IFN-α Gene:111654
1299 101-105 Species denotes mice Tax:10090
1304 378-382 Gene denotes Ace2 Gene:59272
1305 384-391 Gene denotes Tmprss2 Gene:7113
1306 397-402 Gene denotes Cdhr3 Gene:222256
1307 674-678 Gene denotes Ace2 Gene:59272
1311 882-887 Gene denotes IFN-α Gene:111654
1312 842-846 Species denotes mice Tax:10090
1313 870-875 Species denotes mouse Tax:10090
1316 973-977 Gene denotes Ace2 Gene:59272
1317 1025-1029 Gene denotes Ace2 Gene:59272
1325 1184-1189 Gene denotes IFNγR Gene:15979
1326 1349-1354 Gene denotes Epcam Gene:4072
1327 1194-1198 Species denotes mice Tax:10090
1328 1231-1237 Species denotes murine Tax:10090
1329 1244-1255 Species denotes herpesvirus Tax:39059
1330 1260-1265 Species denotes MHV68 Tax:1440122
1331 1204-1212 Disease denotes infected MESH:D007239
1334 1383-1387 Gene denotes Ace2 Gene:70008
1335 1428-1432 Species denotes mice Tax:10090
1339 1532-1536 Gene denotes Ace2 Gene:70008
1340 1596-1600 Species denotes mice Tax:10090
1341 1573-1582 Disease denotes infection MESH:D007239
1352 1697-1701 Gene denotes Ace2 Gene:59272
1353 1828-1833 Gene denotes IFNγR Gene:15979
1354 1852-1856 Gene denotes Ace2 Gene:70008
1355 1886-1890 Gene denotes Ace2 Gene:70008
1356 1764-1769 Species denotes MHV68 Tax:1440122
1357 1779-1784 Species denotes mouse Tax:10090
1358 1786-1791 Species denotes MHV68 Tax:1440122
1359 1808-1813 Species denotes mouse Tax:10090
1360 1712-1721 Disease denotes infection MESH:D007239
1361 1770-1778 Disease denotes infected MESH:D007239
1367 1959-1964 Species denotes human Tax:9606
1368 2005-2022 Species denotes influenza A virus Tax:11320
1369 2029-2033 Species denotes H3N2 Tax:119210
1370 2024-2027 Species denotes IAV Tax:11320
1371 2048-2057 Disease denotes infection MESH:D007239
1375 2078-2105 Gene denotes SFTPC (surfactant protein C Gene:6440
1376 2147-2151 Gene denotes ACE2 Gene:59272
1377 2163-2171 Disease denotes infected MESH:D007239
1381 2303-2308 Gene denotes SFTPC Gene:6440
1382 2359-2362 Species denotes IAV Tax:11320
1383 2363-2372 Disease denotes infection MESH:D007239
1387 2456-2460 Gene denotes ACE2 Gene:59272
1388 2511-2514 Species denotes IAV Tax:11320
1389 2515-2524 Disease denotes infection MESH:D007239
1397 2788-2792 Gene denotes IFNγ Gene:3458
1398 2850-2854 Gene denotes ACE2 Gene:59272
1399 2905-2909 Gene denotes IFNγ Gene:3458
1400 2985-2990 Gene denotes GAPDH Gene:2597
1401 2713-2718 Species denotes human Tax:9606
1402 2944-2951 Species denotes patient Tax:9606
1403 2731-2737 Disease denotes asthma MESH:D001249

2_test

Id Subject Object Predicate Lexical cue
32413319-31826721-20790494 1950-1954 31826721 denotes 2019