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PMC:7081066 / 10025-12901 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
294 146-151 Gene denotes spike Gene:43740568
295 412-416 Gene denotes CCR5 Gene:1234
296 420-425 Gene denotes CXCR4 Gene:7852
297 595-599 Gene denotes ACE2 Gene:59272
298 758-762 Gene denotes ACE2 Gene:59272
299 74-84 Species denotes SARS-CoV-2 Tax:2697049
300 105-114 Species denotes SARS-CoVs Tax:694009
301 119-127 Species denotes SARS-CoV Tax:694009
302 589-594 Species denotes human Tax:9606
303 703-713 Species denotes SARS-CoV-2 Tax:2697049
304 999-1009 Species denotes SARS-CoV-2 Tax:2697049
305 1022-1030 Species denotes SARS-CoV Tax:694009
306 276-289 Disease denotes HIV infection MESH:D015658
307 1108-1117 Disease denotes infection MESH:D007239
331 2099-2103 Gene denotes ACE2 Gene:59272
332 2249-2253 Gene denotes ACE2 Gene:59272
333 2335-2340 Gene denotes spike Gene:43740568
334 2519-2524 Gene denotes spike Gene:43740568
335 2603-2608 Gene denotes spike Gene:43740568
336 1661-1666 Gene denotes spike Gene:43740568
337 1182-1192 Species denotes SARS-CoV-2 Tax:2697049
338 1360-1373 Species denotes coronaviruses Tax:11118
339 1409-1419 Species denotes SARS-CoV-2 Tax:2697049
340 1455-1474 Species denotes Rhinolophus affinis Tax:59477
341 1586-1591 Species denotes human Tax:9606
342 1650-1655 Species denotes human Tax:9606
343 1722-1730 Species denotes SARS-CoV Tax:694009
344 1735-1745 Species denotes SARS-CoV-2 Tax:2697049
345 1918-1928 Species denotes SARS-CoV-2 Tax:2697049
346 1979-1998 Species denotes Rhinolophus affinis Tax:59477
347 2270-2280 Species denotes SARS-CoV-2 Tax:2697049
348 2352-2362 Species denotes SARS-CoV-2 Tax:2697049
349 2781-2789 Species denotes SARS-CoV Tax:694009
350 2794-2804 Species denotes SARS-CoV-2 Tax:2697049
351 1515-1523 Chemical denotes Pangolin
352 2652-2661 Disease denotes infection MESH:D007239
353 2847-2855 Disease denotes zoonotic MESH:D015047

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T45 19-29 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T46 152-159 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T47 276-279 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T48 362-370 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T49 893-903 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T50 1325-1332 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T51 1810-1817 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T52 1874-1885 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T53 2053-2064 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T54 2341-2348 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T55 2410-2420 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T56 2525-2532 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T57 2609-2616 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid_AGAC

Id Subject Object Predicate Lexical cue
p24456s3 395-410 MPA denotes co-receptor use
p24456s14 442-460 MPA denotes viral pathogenesis
p24458s16 723-732 PosReg denotes promoting
p24458s18 737-748 MPA denotes interaction
p24458s24 773-782 PosReg denotes improving
p24458s26 787-794 MPA denotes binding
p24459s14 977-995 MPA denotes binding affinities

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T49 74-82 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T50 105-109 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T51 119-127 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T52 276-289 Disease denotes HIV infection http://purl.obolibrary.org/obo/MONDO_0005109
T53 280-289 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T54 703-711 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T55 999-1007 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T56 1022-1030 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T57 1108-1117 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T58 1182-1190 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T59 1409-1417 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T60 1722-1730 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T61 1735-1743 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T62 1918-1926 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T63 2270-2278 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T64 2352-2360 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T65 2652-2661 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T66 2781-2789 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T67 2794-2802 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T57 188-189 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T58 190-195 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T59 293-294 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T60 589-594 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T61 1157-1162 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T62 1193-1196 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T63 1291-1293 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T64 1304-1305 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T65 1561-1562 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T66 1586-1591 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T67 1592-1597 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T68 1642-1645 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T69 1650-1655 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T70 1858-1861 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T71 1955-1962 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T72 2145-2147 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T73 2236-2243 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T59 19-29 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T60 19-24 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T61 25-29 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T62 152-159 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T63 362-370 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T64 840-845 Chemical denotes atoms http://purl.obolibrary.org/obo/CHEBI_33250
T65 893-903 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T66 893-898 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T67 899-903 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T68 1325-1332 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T69 1810-1817 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T70 1874-1885 Chemical denotes amino acids http://purl.obolibrary.org/obo/CHEBI_33709
T71 1874-1879 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T72 1880-1885 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T73 2053-2064 Chemical denotes amino acids http://purl.obolibrary.org/obo/CHEBI_33709
T74 2053-2058 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T75 2059-2064 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T76 2341-2348 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T77 2410-2420 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T78 2410-2415 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T79 2416-2420 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T80 2525-2532 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T81 2609-2616 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T2 177-184 http://purl.obolibrary.org/obo/GO_0009606 denotes tropism
T3 237-249 http://purl.obolibrary.org/obo/GO_0009405 denotes pathogenesis
T4 325-332 http://purl.obolibrary.org/obo/GO_0009606 denotes tropism
T5 420-425 http://purl.obolibrary.org/obo/GO_0038147 denotes CXCR4
T6 448-460 http://purl.obolibrary.org/obo/GO_0009405 denotes pathogenesis

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T83 0-10 Sentence denotes Discussion
T84 11-128 Sentence denotes Several amino acid substitutions in RBD were identified in the SARS-CoV-2 RBD compared to Bat-SARS-CoVs and SARS-CoV.
T85 129-275 Sentence denotes Mutations in the spike protein could change the tropism of a virus, including new hosts or increasing viral pathogenesis (Shang et al., 2020[13]).
T86 276-371 Sentence denotes HIV infection is a good model of change in viral tropism by mutations in the envelope proteins.
T87 372-478 Sentence denotes These mutations switch co-receptor use (CCR5 to CXCR4) increasing the viral pathogenesis (Mosier 2009[7]).
T88 479-658 Sentence denotes Interestingly, our data showed that these changes are not only related to the ability of interaction with the human ACE2 receptor but also for improving this receptor recognition.
T89 659-869 Sentence denotes The presence of two loops around the RBD of SARS-CoV-2 might be promoting the interaction with the ACE2 receptor, improving the binding to this receptor by increasing the number of atoms involved (Tables 1(Tab.
T90 870-883 Sentence denotes 1) and 2(Tab.
T91 884-888 Sentence denotes 2)).
T92 889-1044 Sentence denotes The amino acid substitutions and the longer capping loops could explain the increase in binding affinities in SARS-CoV-2 compared to SARS-CoV (Table 1(Tab.
T93 1045-1049 Sentence denotes 1)).
T94 1050-1163 Sentence denotes Higher affinity values might be related to the dynamic of infection and the rapid spread observed for this virus.
T95 1164-1223 Sentence denotes The origin of the SARS-CoV-2 has been not fully elucidated.
T96 1224-1484 Sentence denotes While this study was in course, another study of Wong et al. (2020[18]), showed a high similarity at protein level in the RBD among the coronaviruses isolated from the recent outbreak (SARS-CoV-2), those isolated from pangolin and Rhinolophus affinis (RaTG13).
T97 1485-1656 Sentence denotes The authors also suggest that Pangolin might be the intermediate host, with a 98 % identity with the human virus, at the receptor binding motif, between the bat and human.
T98 1657-1805 Sentence denotes The spike model of RaTG13 is quite similar to that obtained from SARS-CoV and SARS-CoV-2 and the loops in the RBD are also present (data not shown).
T99 1806-1886 Sentence denotes The protein sequence of the receptor binding motif, has 5 important amino acids.
T100 1887-2150 Sentence denotes When comparing the sequence of SARS-CoV-2 with that of the isolated viruses of pangolin and Rhinolophus affinis, 1 and 4 differences are observed respectively in the amino acids considered key for the union with ACE2 (Yan et al., 2020[20]; Wong et al., 2020[18]).
T101 2151-2302 Sentence denotes These differences should mean slightly less favorable binding energies between these viruses with ACE2 compared to the SARS-CoV-2, shown in this study.
T102 2303-2533 Sentence denotes Thus, the loops observed in the spike protein of SARS-CoV-2 could play an important role together with the amino acid substitutions, being an interesting clue to determine the host receptor specificity for the viral spike protein.
T103 2534-2691 Sentence denotes Altogether, structural changes and residues composition in the viral spike protein could be associated with increased infection kinetics and viral spreading.
T104 2692-2876 Sentence denotes Comparative studies to determine the impact in vitro of the mutation and loops in RBD of SARS-CoV and SARS-CoV-2 are required in order to predict possible zoonotic event in the future.

MyTest

Id Subject Object Predicate Lexical cue
32210742-32150576-29811238 270-272 32150576 denotes 13
32210742-19339951-29811239 474-475 19339951 denotes 7

2_test

Id Subject Object Predicate Lexical cue
32210742-32150576-29811238 270-272 32150576 denotes 13
32210742-19339951-29811239 474-475 19339951 denotes 7