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PMC:7252096 / 11285-12816 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T72738 39-50 Body_part denotes Pneumocytes http://purl.org/sig/ont/fma/fma62499
T37841 62-67 Body_part denotes Lungs http://purl.org/sig/ont/fma/fma68877
T92961 133-137 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T78907 138-144 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T68232 260-262 Body_part denotes v1 http://purl.org/sig/ont/fma/fma13444|http://purl.org/sig/ont/fma/fma68614
T20260 303-307 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T30494 373-378 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T63361 398-402 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T10555 590-597 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T54627 661-664 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T41736 681-684 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T81740 737-741 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T27177 844-849 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T15384 886-890 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T58974 997-1002 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T91751 1032-1043 Body_part denotes pneumocytes http://purl.org/sig/ont/fma/fma62499
T93701 1181-1192 Body_part denotes pneumocytes http://purl.org/sig/ont/fma/fma62499
T72518 1259-1263 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T49230 1310-1315 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T85711 1382-1393 Body_part denotes pneumocytes http://purl.org/sig/ont/fma/fma62499

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T25 133-137 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T26 138-144 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T86 417-421 Disease denotes STAR http://purl.obolibrary.org/obo/MONDO_0010408

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T22343 62-67 http://www.ebi.ac.uk/efo/EFO_0000934 denotes Lungs
T70499 75-80 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T98814 81-89 http://purl.obolibrary.org/obo/NCBITaxon_9443 denotes Primates
T59631 91-92 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T79845 133-137 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T77319 133-137 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T56107 174-179 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T41263 180-188 http://purl.obolibrary.org/obo/NCBITaxon_9443 denotes primates
T54356 303-313 http://purl.obolibrary.org/obo/CL_0000000 denotes cell types
T37269 373-378 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T88766 398-402 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T66647 433-434 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T40116 496-497 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T55688 722-727 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T97901 737-746 http://purl.obolibrary.org/obo/CL_0000000 denotes cell type
T45113 754-756 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T83525 844-849 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T86594 878-879 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T79235 886-890 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T82704 997-1002 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T94942 1234-1236 http://purl.obolibrary.org/obo/CLO_0008935 denotes S9
T53007 1259-1268 http://purl.obolibrary.org/obo/CL_0000000 denotes cell type
T17987 1310-1315 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T36108 1321-1326 http://purl.obolibrary.org/obo/OGG_0000000002 denotes Genes
T72036 1508-1510 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T94552 1528-1530 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T39 36-38 Chemical denotes II http://purl.obolibrary.org/obo/CHEBI_74067
T40 590-597 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T41 1029-1031 Chemical denotes II http://purl.obolibrary.org/obo/CHEBI_74067
T42 1178-1180 Chemical denotes II http://purl.obolibrary.org/obo/CHEBI_74067
T43 1379-1381 Chemical denotes II http://purl.obolibrary.org/obo/CHEBI_74067

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T62 0-89 Sentence denotes Figure 1 Expression of ACE2 in Type II Pneumocytes in Healthy Lungs of Non-human Primates
T63 90-340 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 341-431 Sentence denotes UMAP projection of 3,793 single cells, points colored by cell identity (see STAR Methods).
T65 432-625 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 626-694 Sentence denotes Color coding is as follows: black, RNA positive; blue, RNA negative.
T67 695-811 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 812-1003 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 1004-1165 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 1166-1238 Sentence denotes Of all type II pneumocytes, 3.8% co-express ACE2 and TMPRSS2 (Table S9).
T71 1239-1316 Sentence denotes Red arrow indicates cell type with largest proportion of ACE2+TMPRSS2+ cells.
T72 1317-1512 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 1513-1531 Sentence denotes See also Table S1.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
318 23-27 Gene denotes ACE2 Gene:59272
319 75-80 Species denotes human Tax:9606
323 417-421 Gene denotes STAR Gene:6770
324 174-179 Species denotes human Tax:9606
325 190-200 Species denotes M. mulatta Tax:9544
330 531-535 Gene denotes ACE2 Gene:59272
331 567-574 Gene denotes TMPRSS2 Gene:7113
332 537-548 Species denotes coronavirus Tax:11118
333 576-587 Species denotes coronavirus Tax:11118
342 794-798 Gene denotes ACE2 Gene:59272
343 803-810 Gene denotes TMPRSS2 Gene:7113
344 1004-1008 Gene denotes ACE2 Gene:59272
345 1103-1110 Gene denotes TMPRSS2 Gene:7113
346 1210-1214 Gene denotes ACE2 Gene:59272
347 1219-1226 Gene denotes TMPRSS2 Gene:7113
348 1296-1300 Gene denotes ACE2 Gene:59272
349 1301-1308 Gene denotes TMPRSS2 Gene:7113
356 1358-1362 Gene denotes ACE2 Gene:59272
357 1368-1372 Gene denotes ACE2 Gene:59272
358 1436-1442 Gene denotes IFNGR2 Gene:3460
359 1444-1450 Gene denotes NT5DC1 Gene:221294
360 1452-1459 Gene denotes ARL6IP1 Gene:23204
361 1465-1471 Gene denotes TRIM27 Gene:5987