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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T61053 21-26 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T38580 48-55 Body_part denotes tissues http://purl.org/sig/ont/fma/fma9637
T4254 157-161 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T46063 276-280 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T8984 281-287 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T79059 369-371 Body_part denotes v1 http://purl.org/sig/ont/fma/fma13444|http://purl.org/sig/ont/fma/fma68614
T85470 436-440 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T2796 596-612 Body_part denotes epithelial cells http://purl.org/sig/ont/fma/fma66768
T62378 607-612 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T64743 635-646 Body_part denotes pneumocytes http://purl.org/sig/ont/fma/fma62499
T35128 758-763 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T18720 808-818 Body_part denotes pneumocyte http://purl.org/sig/ont/fma/fma62499
T83814 890-895 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T23477 906-922 Body_part denotes epithelial cells http://purl.org/sig/ont/fma/fma66768
T1445 917-922 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T92758 935-946 Body_part denotes pneumocytes http://purl.org/sig/ont/fma/fma62499
T97944 1015-1026 Body_part denotes pneumocytes http://purl.org/sig/ont/fma/fma62499
T72738 1089-1100 Body_part denotes Pneumocytes http://purl.org/sig/ont/fma/fma62499
T37841 1112-1117 Body_part denotes Lungs http://purl.org/sig/ont/fma/fma68877
T92961 1183-1187 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T78907 1188-1194 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T68232 1310-1312 Body_part denotes v1 http://purl.org/sig/ont/fma/fma13444|http://purl.org/sig/ont/fma/fma68614
T20260 1353-1357 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T30494 1423-1428 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T63361 1448-1452 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T10555 1640-1647 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T54627 1711-1714 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T41736 1731-1734 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T81740 1787-1791 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T27177 1894-1899 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T15384 1936-1940 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T58974 2047-2052 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T91751 2082-2093 Body_part denotes pneumocytes http://purl.org/sig/ont/fma/fma62499
T93701 2231-2242 Body_part denotes pneumocytes http://purl.org/sig/ont/fma/fma62499
T72518 2309-2313 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T49230 2360-2365 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T85711 2432-2443 Body_part denotes pneumocytes http://purl.org/sig/ont/fma/fma62499

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T23 276-280 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T24 281-287 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T25 1183-1187 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T26 1188-1194 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T83 73-81 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T84 73-77 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T85 536-540 Disease denotes STAR http://purl.obolibrary.org/obo/MONDO_0010408
T86 1467-1471 Disease denotes STAR http://purl.obolibrary.org/obo/MONDO_0010408

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T22651 21-26 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T95022 34-39 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T6005 157-167 http://purl.obolibrary.org/obo/CL_0000000 denotes cell types
T65779 208-209 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T21693 260-274 http://purl.obolibrary.org/obo/NCBITaxon_9544 denotes Macaca mulatta
T78816 276-280 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T69580 276-280 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T95293 330-337 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animals
T91672 436-446 http://purl.obolibrary.org/obo/CL_0000000 denotes cell types
T86810 520-521 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T29504 532-534 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T74686 596-606 http://purl.obolibrary.org/obo/CL_0000066 denotes epithelial
T68973 607-612 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T53098 758-763 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T93726 890-895 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T79600 906-916 http://purl.obolibrary.org/obo/CL_0000066 denotes epithelial
T66664 917-932 http://purl.obolibrary.org/obo/CL_0000000 denotes cells, and type
T13219 1045-1047 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T22343 1112-1117 http://www.ebi.ac.uk/efo/EFO_0000934 denotes Lungs
T70499 1125-1130 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T98814 1131-1139 http://purl.obolibrary.org/obo/NCBITaxon_9443 denotes Primates
T59631 1141-1142 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T79845 1183-1187 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T77319 1183-1187 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T56107 1224-1229 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T41263 1230-1238 http://purl.obolibrary.org/obo/NCBITaxon_9443 denotes primates
T54356 1353-1363 http://purl.obolibrary.org/obo/CL_0000000 denotes cell types
T37269 1423-1428 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T88766 1448-1452 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T66647 1483-1484 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T40116 1546-1547 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T55688 1772-1777 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T97901 1787-1796 http://purl.obolibrary.org/obo/CL_0000000 denotes cell type
T45113 1804-1806 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T83525 1894-1899 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T86594 1928-1929 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T79235 1936-1940 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T82704 2047-2052 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T94942 2284-2286 http://purl.obolibrary.org/obo/CLO_0008935 denotes S9
T53007 2309-2318 http://purl.obolibrary.org/obo/CL_0000000 denotes cell type
T17987 2360-2365 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T36108 2371-2376 http://purl.obolibrary.org/obo/OGG_0000000002 denotes Genes
T72036 2558-2560 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T94552 2578-2580 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T36 632-634 Chemical denotes II http://purl.obolibrary.org/obo/CHEBI_74067
T37 805-807 Chemical denotes II http://purl.obolibrary.org/obo/CHEBI_74067
T38 1012-1014 Chemical denotes II http://purl.obolibrary.org/obo/CHEBI_74067
T39 1086-1088 Chemical denotes II http://purl.obolibrary.org/obo/CHEBI_74067
T40 1640-1647 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T41 2079-2081 Chemical denotes II http://purl.obolibrary.org/obo/CHEBI_74067
T42 2228-2230 Chemical denotes II http://purl.obolibrary.org/obo/CHEBI_74067
T43 2429-2431 Chemical denotes II http://purl.obolibrary.org/obo/CHEBI_74067

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T58 0-204 Sentence denotes To investigate which cells within human and NHP tissues represent likely SARS-CoV-2 targets, we analyzed new and existing scRNA-seq datasets to assess which cell types express ACE2, alone or with TMPRSS2.
T59 205-550 Sentence denotes In a previously unpublished dataset consisting of NHP (Macaca mulatta) lung tissue collected after necropsy of healthy adult animals and analyzed by using Seq-Well v1 (Gierahn et al., 2017), we recovered at least 17 distinct major cell types, including various lymphoid, myeloid, and stromal populations (Figures 1 A–1C; Table S1; STAR Methods).
T60 551-723 Sentence denotes ACE2 and TMPRSS2 were primarily expressed in epithelial cells, with 6.7% of type II pneumocytes expressing ACE2 and 3.8% co-expressing ACE2 and TMPRSS2 (Figures 1B and 1C).
T61 724-1049 Sentence denotes Notably, the only double-positive cells observed were classified within the type II pneumocyte population; however, we also identified TMPRSS2 expression within club cells, ciliated epithelial cells, and type I pneumocytes, albeit at diminished abundance and frequency compared with type II pneumocytes (Figure 1C; Table S1).
T62 1050-1139 Sentence denotes Figure 1 Expression of ACE2 in Type II Pneumocytes in Healthy Lungs of Non-human Primates
T63 1140-1390 Sentence denotes (A) Schematic of protocol for isolation of lung tissue at necropsy from healthy non-human primates (M. mulatta, n = 3), creation of scRNA-seq libraries by using Seq-Well v1, and computational analysis to identify cell types by using unbiased methods.
T64 1391-1481 Sentence denotes UMAP projection of 3,793 single cells, points colored by cell identity (see STAR Methods).
T65 1482-1675 Sentence denotes (B) Uniform manifold approximation and projection (UMAP) as in (A), points colored by detection of ACE2 (coronavirus receptor, top) or TMPRSS2 (coronavirus S protein priming for entry, bottom).
T66 1676-1744 Sentence denotes Color coding is as follows: black, RNA positive; blue, RNA negative.
T67 1745-1861 Sentence denotes (C) Dot plot of 2 defining genes for each cell type (Table S1) (Bonferroni-adjusted p < 0.001) and ACE2 and TMPRSS2.
T68 1862-2053 Sentence denotes Dot size represents fraction of cells within that type expressing a given gene, and color intensity represents binned count-based expression amount (log(scaled UMI+1)) among expressing cells.
T69 2054-2215 Sentence denotes ACE2 is enriched in type II pneumocytes (6.7% expressing, Bonferroni-adjusted p = 8.62E−33), as is TMPRSS2 (29.5% expressing, Bonferroni-adjusted p = 8.73E−153).
T70 2216-2288 Sentence denotes Of all type II pneumocytes, 3.8% co-express ACE2 and TMPRSS2 (Table S9).
T71 2289-2366 Sentence denotes Red arrow indicates cell type with largest proportion of ACE2+TMPRSS2+ cells.
T72 2367-2562 Sentence denotes (D) Genes differentially expressed among ACE2+ and ACE2− type II pneumocytes. (SCDE package, FDR-adjusted p < 0.05 for IFNGR2, NT5DC1, ARL6IP1, and TRIM27; full results can be found in Table S1).
T73 2563-2581 Sentence denotes See also Table S1.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
318 1073-1077 Gene denotes ACE2 Gene:59272
319 1125-1130 Species denotes human Tax:9606
323 1467-1471 Gene denotes STAR Gene:6770
324 1224-1229 Species denotes human Tax:9606
325 1240-1250 Species denotes M. mulatta Tax:9544
330 1581-1585 Gene denotes ACE2 Gene:59272
331 1617-1624 Gene denotes TMPRSS2 Gene:7113
332 1587-1598 Species denotes coronavirus Tax:11118
333 1626-1637 Species denotes coronavirus Tax:11118
342 1844-1848 Gene denotes ACE2 Gene:59272
343 1853-1860 Gene denotes TMPRSS2 Gene:7113
344 2054-2058 Gene denotes ACE2 Gene:59272
345 2153-2160 Gene denotes TMPRSS2 Gene:7113
346 2260-2264 Gene denotes ACE2 Gene:59272
347 2269-2276 Gene denotes TMPRSS2 Gene:7113
348 2346-2350 Gene denotes ACE2 Gene:59272
349 2351-2358 Gene denotes TMPRSS2 Gene:7113
356 2408-2412 Gene denotes ACE2 Gene:59272
357 2418-2422 Gene denotes ACE2 Gene:59272
358 2486-2492 Gene denotes IFNGR2 Gene:3460
359 2494-2500 Gene denotes NT5DC1 Gene:221294
360 2502-2509 Gene denotes ARL6IP1 Gene:23204
361 2515-2521 Gene denotes TRIM27 Gene:5987
374 176-180 Gene denotes ACE2 Gene:59272
375 196-203 Gene denotes TMPRSS2 Gene:7113
376 551-555 Gene denotes ACE2 Gene:712790
377 560-567 Gene denotes TMPRSS2 Gene:715138
378 658-662 Gene denotes ACE2 Gene:712790
379 686-690 Gene denotes ACE2 Gene:712790
380 695-702 Gene denotes TMPRSS2 Gene:715138
381 859-866 Gene denotes TMPRSS2 Gene:715138
382 536-540 Gene denotes STAR Gene:699515
383 34-39 Species denotes human Tax:9606
384 73-83 Species denotes SARS-CoV-2 Tax:2697049
385 260-274 Species denotes Macaca mulatta Tax:9544

2_test

Id Subject Object Predicate Lexical cue
32413319-28192419-20790459 389-393 28192419 denotes 2017