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PMC:7126544 / 49810-53143 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T160 21-25 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T161 26-30 Body_part denotes Cell http://purl.org/sig/ont/fma/fma68646
T162 147-159 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T163 266-273 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T164 356-363 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T165 468-473 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T166 746-751 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T167 844-851 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T168 1015-1020 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T169 1030-1035 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T170 1070-1074 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T171 1636-1641 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T172 1758-1763 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T173 1776-1783 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T174 1912-1917 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T175 1989-1993 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T176 2780-2791 Body_part denotes hepatocytes http://purl.org/sig/ont/fma/fma14515
T177 2835-2840 Body_part denotes liver http://purl.org/sig/ont/fma/fma7197
T178 2841-2848 Body_part denotes tissues http://purl.org/sig/ont/fma/fma9637
T179 2855-2859 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T180 2860-2863 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T181 2918-2937 Body_part denotes respiratory systems http://purl.org/sig/ont/fma/fma7158
T182 3006-3010 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T183 3038-3042 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T184 3044-3053 Body_part denotes esophagus http://purl.org/sig/ont/fma/fma7131
T185 3064-3069 Body_part denotes ileum http://purl.org/sig/ont/fma/fma7208
T186 3074-3079 Body_part denotes colon http://purl.org/sig/ont/fma/fma14543
T187 3096-3112 Body_part denotes digestive system http://purl.org/sig/ont/fma/fma7152
T188 3203-3207 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T189 3212-3217 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T190 3219-3228 Body_part denotes esophagus http://purl.org/sig/ont/fma/fma7131
T191 3250-3266 Body_part denotes epithelial cells http://purl.org/sig/ont/fma/fma66768
T192 3261-3266 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T193 3290-3301 Body_part denotes enterocytes http://purl.org/sig/ont/fma/fma62122
T194 3311-3316 Body_part denotes ileum http://purl.org/sig/ont/fma/fma7208
T195 3321-3326 Body_part denotes colon http://purl.org/sig/ont/fma/fma14543

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T57 2835-2840 Body_part denotes liver http://purl.obolibrary.org/obo/UBERON_0002107
T58 2918-2937 Body_part denotes respiratory systems http://purl.obolibrary.org/obo/UBERON_0001004
T59 3038-3042 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T60 3044-3053 Body_part denotes esophagus http://purl.obolibrary.org/obo/UBERON_0001043
T61 3064-3069 Body_part denotes ileum http://purl.obolibrary.org/obo/UBERON_0002116
T62 3074-3079 Body_part denotes colon http://purl.obolibrary.org/obo/UBERON_0001155
T63 3096-3112 Body_part denotes digestive system http://purl.obolibrary.org/obo/UBERON_0001007
T64 3203-3207 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T65 3219-3228 Body_part denotes esophagus http://purl.obolibrary.org/obo/UBERON_0001043
T66 3311-3316 Body_part denotes ileum http://purl.obolibrary.org/obo/UBERON_0002116
T67 3321-3326 Body_part denotes colon http://purl.obolibrary.org/obo/UBERON_0001155

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T432 617-625 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T433 617-621 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T434 686-694 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T435 686-690 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T436 696-704 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T437 696-700 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T438 929-937 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T439 929-933 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T440 1088-1096 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T441 1088-1092 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T442 1251-1259 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T443 1251-1255 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T444 1305-1313 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T445 1305-1309 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T446 1384-1392 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T447 1384-1388 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T448 1468-1476 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T449 1468-1472 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T450 1518-1526 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T451 1518-1522 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T452 1572-1580 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T453 1572-1576 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T454 1606-1614 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T455 1606-1610 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T456 1675-1683 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T457 1675-1679 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T458 2564-2572 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T459 2564-2568 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T460 2577-2585 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T461 2577-2581 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T462 2655-2663 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T463 2655-2659 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T464 2682-2690 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T465 2682-2686 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T466 2699-2707 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T467 2699-2703 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T468 2961-2969 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T469 2961-2965 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T470 3152-3160 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T429 21-25 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T430 26-30 http://purl.obolibrary.org/obo/GO_0005623 denotes Cell
T431 137-138 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T432 417-423 http://purl.obolibrary.org/obo/SO_0000418 denotes signal
T433 424-431 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T434 446-451 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T435 468-473 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T436 490-493 http://purl.obolibrary.org/obo/CLO_0053001 denotes 114
T437 746-751 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T438 871-872 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T439 963-968 http://purl.obolibrary.org/obo/CLO_0007836 denotes mouse
T440 1015-1020 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T441 1030-1035 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T442 1070-1074 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T443 1203-1205 http://purl.obolibrary.org/obo/CLO_0001527 denotes 94
T444 1413-1416 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T445 1529-1532 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T446 1538-1543 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T447 1547-1552 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T448 1636-1641 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T449 1758-1763 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T450 1831-1832 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T451 1895-1903 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T452 1912-1917 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T453 1958-1960 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T454 1989-1993 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T455 2074-2076 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T456 2099-2100 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T457 2147-2149 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T458 2147-2149 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T459 2159-2162 http://purl.obolibrary.org/obo/CLO_0001053 denotes 121
T460 2199-2201 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T461 2260-2262 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T462 2301-2302 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T463 2376-2377 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T464 2835-2840 http://purl.obolibrary.org/obo/UBERON_0002107 denotes liver
T465 2835-2840 http://www.ebi.ac.uk/efo/EFO_0000887 denotes liver
T466 2855-2859 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T467 2918-2937 http://purl.obolibrary.org/obo/UBERON_0001004 denotes respiratory systems
T468 2941-2942 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T469 3006-3010 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T470 3038-3042 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T471 3038-3042 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T472 3044-3053 http://purl.obolibrary.org/obo/UBERON_0001043 denotes esophagus
T473 3064-3069 http://purl.obolibrary.org/obo/UBERON_0002116 denotes ileum
T474 3074-3079 http://purl.obolibrary.org/obo/UBERON_0001155 denotes colon
T475 3096-3112 http://purl.obolibrary.org/obo/UBERON_0001007 denotes digestive system
T476 3096-3112 http://www.ebi.ac.uk/efo/EFO_0000793 denotes digestive system
T477 3121-3122 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T478 3203-3207 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T479 3203-3207 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T480 3212-3217 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T481 3219-3228 http://purl.obolibrary.org/obo/UBERON_0001043 denotes esophagus
T482 3239-3266 http://purl.obolibrary.org/obo/CL_0000079 denotes stratified epithelial cells
T483 3311-3316 http://purl.obolibrary.org/obo/UBERON_0002116 denotes ileum
T484 3321-3326 http://purl.obolibrary.org/obo/UBERON_0001155 denotes colon

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T42865 147-159 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T26728 266-273 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T66150 356-363 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T53998 424-431 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T83174 504-515 Chemical denotes Angiotensin http://purl.obolibrary.org/obo/CHEBI_2719
T29108 844-851 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T28218 1776-1783 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T85504 2147-2149 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T53 5-25 http://purl.obolibrary.org/obo/GO_0044409 denotes Entry into host cell
T54 287-308 http://purl.obolibrary.org/obo/GO_0051701 denotes interaction with host
T55 446-473 http://purl.obolibrary.org/obo/GO_0046718 denotes virus entry into host cells
T56 452-467 http://purl.obolibrary.org/obo/GO_0044409 denotes entry into host
T57 730-745 http://purl.obolibrary.org/obo/GO_0044409 denotes entry into host
T58 1742-1757 http://purl.obolibrary.org/obo/GO_0044409 denotes entry into host

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T408 0-25 Sentence denotes 9.2 Entry into host cell
T409 26-120 Sentence denotes Cell entry is an essential component of cross-species transmission, especially for the β-CoVs.
T410 121-232 Sentence denotes All CoVs encode a surface glycoprotein, spike, which binds to the host receptor and mediates viral entry [111].
T411 233-318 Sentence denotes For β-CoVs, the RBD of the spike protein mediates the interaction with host receptor.
T412 319-503 Sentence denotes Upon binding the receptor, the spike protein is cleaved by nearby host proteases and releases the signal peptide to facilitate virus entry into host cells [[112], [113], [114], [115]].
T413 504-663 Sentence denotes Angiotensin converting enzyme 2 (ACE2) and dipeptidyl peptidase 4 (DPP4) are known host receptors for the β-CoVs SARS-CoV and MERS-CoV, respectively [116,117].
T414 664-752 Sentence denotes In similar fashion to SARS-CoV, SARS-CoV-2 also uses ACE2 to gain entry into host cells.
T415 753-896 Sentence denotes Hoffmann et al. found that the cellular protease MPRSS2 blocks entry by cleaving the spike protein and may constitute a treatment option [118].
T416 897-1207 Sentence denotes Zhou et al. also confirmed that SARS-CoV-2 is able to use all but mouse ACE2 as an entry receptor for ACE2-expressing cells, but not cells without ACE2, indicating that the cell receptor for SARS-CoV-2 could be ACE2, and not other coronavirus receptors such as aminopeptidase N and dipeptidyl peptidase 4 [94].
T417 1208-1350 Sentence denotes Huang also showed that the affinity of the SARS-CoV-2 S-RBD binding to ACE2 is less than that of SARS-CoV through Monte Carlo algorithm [119].
T418 1351-1586 Sentence denotes However, Wrapp et al. found that SARS-CoV-2 S binding to ACE2 has approximately 10- to 20- fold higher affinity than SARS-CoV S, which can provide one explanation why SARS-CoV-2 has more human-to human spread compared to SARS-CoV [97].
T419 1587-1769 Sentence denotes The combination of SARS-CoV-2 S and ACE2 of host cells is similar to the combination of SARS-CoV and ACE2, indicating that they have the same mechanism to entry into host cells [97].
T420 1770-1928 Sentence denotes The S protein of metastable prefusion conformation undergoes a series of structural rearrangements to combine with the viral membrane of host cells [111,120].
T421 1929-2164 Sentence denotes This process consists of the S1 subunit binding to the host cell receptor, triggering of the prefusion trimer's instability, and shedding of the S1 subunit, resulting in a highly stable post-fusion conformation of the S2 subunit [121].
T422 2165-2491 Sentence denotes During the binding of the subunit S1 to its cognate receptor, it is important to note that the S1 subunit exists in 2 different states, a “down” conformation and an “up” conformation state, which corresponds to a receptor-inaccessible state and an unstable receptor-accessible state, respectively [[122], [123], [124], [125]].
T423 2492-2698 Sentence denotes Unfortunately, there are significant conformational differences between SARS-CoV and SARS-CoV-2 such that the commercially available monoclonal antibodies against SARS-CoV do not react with SARS-CoV-2 [97].
T424 2699-2906 Sentence denotes SARS-CoV-2 may directly bind to ACE2 positive cholangiocytes but not necessarily hepatocytes via specific expression of ACE2 in healthy liver tissues using cell RNA-seq data of two independent cohorts [126].
T425 2907-3333 Sentence denotes Though the respiratory systems is a primary target of SARS-CoV-2, bioinformatic analysis of single-cell transcriptomes datasets of lung, esophagus, gastric, ileum and colon reveal that the digestive system is also a potential route of entry for COVID-19, as ACE2 was not only highly expressed in lung AT2 cells, esophagus upper and stratified epithelial cells but also in absorptive enterocytes from the ileum and colon [127].

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1316 161-166 Gene denotes spike Gene:43740568
1317 260-265 Gene denotes spike Gene:43740568
1318 350-355 Gene denotes spike Gene:43740568
1319 115-119 Species denotes CoVs Tax:11118
1320 125-129 Species denotes CoVs Tax:11118
1321 239-243 Species denotes CoVs Tax:11118
1350 537-541 Gene denotes ACE2 Gene:59272
1351 547-569 Gene denotes dipeptidyl peptidase 4 Gene:1803
1352 717-721 Gene denotes ACE2 Gene:59272
1353 838-843 Gene denotes spike Gene:43740568
1354 969-973 Gene denotes ACE2 Gene:70008
1355 999-1003 Gene denotes ACE2 Gene:70008
1356 1044-1048 Gene denotes ACE2 Gene:70008
1357 1108-1112 Gene denotes ACE2 Gene:59272
1358 1179-1201 Gene denotes dipeptidyl peptidase 4 Gene:1803
1359 1279-1283 Gene denotes ACE2 Gene:59272
1360 1408-1412 Gene denotes ACE2 Gene:59272
1361 612-616 Species denotes CoVs Tax:11118
1362 617-625 Species denotes SARS-CoV Tax:694009
1363 630-638 Species denotes MERS-CoV Tax:1335626
1364 686-694 Species denotes SARS-CoV Tax:694009
1365 696-706 Species denotes SARS-CoV-2 Tax:2697049
1366 929-939 Species denotes SARS-CoV-2 Tax:2697049
1367 963-968 Species denotes mouse Tax:10090
1368 1088-1098 Species denotes SARS-CoV-2 Tax:2697049
1369 1128-1139 Species denotes coronavirus Tax:11118
1370 1251-1261 Species denotes SARS-CoV-2 Tax:2697049
1371 1305-1313 Species denotes SARS-CoV Tax:694009
1372 1384-1394 Species denotes SARS-CoV-2 Tax:2697049
1373 1468-1476 Species denotes SARS-CoV Tax:694009
1374 1518-1528 Species denotes SARS-CoV-2 Tax:2697049
1375 1538-1543 Species denotes human Tax:9606
1376 1547-1552 Species denotes human Tax:9606
1377 1572-1580 Species denotes SARS-CoV Tax:694009
1386 1623-1627 Gene denotes ACE2 Gene:59272
1387 1688-1692 Gene denotes ACE2 Gene:59272
1388 1606-1616 Species denotes SARS-CoV-2 Tax:2697049
1389 1675-1683 Species denotes SARS-CoV Tax:694009
1390 2564-2572 Species denotes SARS-CoV Tax:694009
1391 2577-2587 Species denotes SARS-CoV-2 Tax:2697049
1392 2655-2663 Species denotes SARS-CoV Tax:694009
1393 2682-2692 Species denotes SARS-CoV-2 Tax:2697049
1401 2731-2735 Gene denotes ACE2 Gene:59272
1402 2819-2823 Gene denotes ACE2 Gene:59272
1403 3165-3169 Gene denotes ACE2 Gene:59272
1404 2699-2709 Species denotes SARS-CoV-2 Tax:2697049
1405 2961-2971 Species denotes SARS-CoV-2 Tax:2697049
1406 2918-2929 Species denotes respiratory Tax:12814
1407 3152-3160 Disease denotes COVID-19 MESH:C000657245

2_test

Id Subject Object Predicate Lexical cue
32143990-27578435-55637431 227-230 27578435 denotes 111
32143990-19321428-55637432 476-479 19321428 denotes 112
32143990-20926566-55637433 483-486 20926566 denotes 113
32143990-21994442-55637434 490-493 21994442 denotes 114
32143990-24121034-55637435 497-500 24121034 denotes 115
32143990-15549175-55637436 654-657 15549175 denotes 116
32143990-23486063-55637437 658-661 23486063 denotes 117
32143990-27578435-55637438 1919-1922 27578435 denotes 111
32143990-12885899-55637439 1923-1926 12885899 denotes 120
32143990-29073020-55637440 2159-2162 29073020 denotes 121
32143990-28008928-55637441 2464-2467 28008928 denotes 122
32143990-28807998-55637442 2471-2474 28807998 denotes 123