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PMC:7214327 / 1499-4004 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T2 286-296 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T3 402-405 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T4 416-419 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T5 494-497 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T6 752-762 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T7 780-783 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T8 903-913 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T9 955-958 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T10 974-985 Body_part denotes nucleotides http://purl.org/sig/ont/fma/fma82740
T11 1754-1757 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T12 1825-1831 Body_part denotes serine http://purl.org/sig/ont/fma/fma82764
T13 2001-2004 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T14 2374-2377 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T15 2501-2504 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T8 118-123 Disease denotes Ebola http://purl.obolibrary.org/obo/MONDO_0005737
T9 243-247 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T10 600-608 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T11 613-621 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T12 1262-1270 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T13 1275-1283 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T14 2222-2230 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T15 2299-2307 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T16 2343-2351 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T8 52-53 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T9 83-91 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T10 105-112 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T11 170-175 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T12 197-198 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T13 284-285 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T14 375-376 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T15 455-458 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T16 511-512 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T17 639-642 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T18 810-813 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T19 867-868 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T20 1081-1084 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T21 1197-1204 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T22 1360-1363 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T23 1462-1463 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T24 1534-1535 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T25 1678-1679 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T26 1782-1785 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T27 1956-1957 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T28 2070-2077 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T29 2166-2167 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T30 2234-2236 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T31 2309-2315 http://purl.obolibrary.org/obo/CLO_0001236 denotes 2. (A)
T32 2423-2424 http://purl.obolibrary.org/obo/CLO_0001021 denotes B

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T13 13-18 Chemical denotes drugs http://purl.obolibrary.org/obo/CHEBI_23888
T14 22-32 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T15 286-296 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T16 319-331 Chemical denotes triphosphate http://purl.obolibrary.org/obo/CHEBI_18036
T17 355-357 Chemical denotes TP http://purl.obolibrary.org/obo/CHEBI_73662
T18 666-668 Chemical denotes TP http://purl.obolibrary.org/obo/CHEBI_73662
T19 692-714 Chemical denotes Adenosine triphosphate http://purl.obolibrary.org/obo/CHEBI_15422
T20 692-701 Chemical denotes Adenosine http://purl.obolibrary.org/obo/CHEBI_16335
T21 702-714 Chemical denotes triphosphate http://purl.obolibrary.org/obo/CHEBI_18036
T22 716-719 Chemical denotes ATP http://purl.obolibrary.org/obo/CHEBI_15422|http://purl.obolibrary.org/obo/CHEBI_30616
T24 721-729 Chemical denotes molecule http://purl.obolibrary.org/obo/CHEBI_25367
T25 752-762 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T26 836-850 Chemical denotes hydroxyl group http://purl.obolibrary.org/obo/CHEBI_43176
T27 836-844 Chemical denotes hydroxyl http://purl.obolibrary.org/obo/CHEBI_29191
T28 845-850 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T29 858-860 Chemical denotes TP http://purl.obolibrary.org/obo/CHEBI_73662
T30 903-913 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T31 974-985 Chemical denotes nucleotides http://purl.obolibrary.org/obo/CHEBI_36976
T32 1043-1045 Chemical denotes TP http://purl.obolibrary.org/obo/CHEBI_73662
T33 1527-1529 Chemical denotes TP http://purl.obolibrary.org/obo/CHEBI_73662
T34 1825-1839 Chemical denotes serine residue http://purl.obolibrary.org/obo/CHEBI_32848
T35 1825-1831 Chemical denotes serine http://purl.obolibrary.org/obo/CHEBI_17822
T36 2143-2145 Chemical denotes TP http://purl.obolibrary.org/obo/CHEBI_73662

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T4 494-507 http://purl.obolibrary.org/obo/GO_0032774 denotes RNA synthesis
T5 498-507 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T6 780-793 http://purl.obolibrary.org/obo/GO_0032774 denotes RNA synthesis
T7 784-793 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T8 936-945 http://purl.obolibrary.org/obo/GO_0009058 denotes formation
T9 955-968 http://purl.obolibrary.org/obo/GO_0032774 denotes RNA synthesis
T10 959-968 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T11 1754-1767 http://purl.obolibrary.org/obo/GO_0032774 denotes RNA synthesis
T12 1758-1767 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T13 2001-2014 http://purl.obolibrary.org/obo/GO_0032774 denotes RNA synthesis
T14 2005-2014 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T15 2374-2387 http://purl.obolibrary.org/obo/GO_0032774 denotes RNA synthesis
T16 2378-2387 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T17 2482-2491 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T16 0-269 Sentence denotes One of these drugs is remdesivir (RDV), which shows a broad spectrum of anti-viral activity against many viruses like Ebola (4,5), Nipah (6, 7, 8), respiratory syncytial virus (RSV) family (8) and a diverse category of coronaviruses including SARS CoV and MERS CoV (9).
T17 270-635 Sentence denotes Remdesivir is a nucleotide analogue (4), and the triphosphate form of RDV, i.e., RDV-TP is being used as a substrate for many viral RNA-dependent RNA polymerase (RdRp) complexes and it has been reported to inhibit the viral RNA synthesis by a specific mechanism of delayed chain termination for all three coronaviruses (MERS-CoV, SARS-CoV and SARS-CoV-2) RdRp (10).
T18 636-806 Sentence denotes It has been observed that RDV-TP resembles specifically Adenosine triphosphate (ATP) molecule and competes with the nucleotide during the viral RNA synthesis (Figure 1 ).
T19 807-1067 Sentence denotes It has been reported that 3′ hydroxyl group of RDV-TP forms a phosphodiester bond with the next nucleotide but it terminates the formation of viral RNA synthesis at 3 nucleotides downstream, precisely at i + 3 position, whereas the RDV-TP is the i-th position.
T20 1068-1342 Sentence denotes Moreover, it has also been fascinating to note that the underlying mechanism of chain termination is more or less common in many viruses including all the recent coronaviruses, namely MERS-CoV, SARS-CoV and SARS-CoV-2, though the precise molecular mechanism remains elusive.
T21 1343-1563 Sentence denotes Additionally, it has been reported very recently that the main reason of chain termination at i + 4 position is due to a steric clash between 1′-CN substituent of the incorporated RDV-TP and a specific residue S861 (10).
T22 1564-1768 Sentence denotes It is consistent with the chain termination at i + 3 position due to the imposed inability of RdRp to translocate a single position downstream, so eventually it terminates the nascent viral RNA synthesis.
T23 1769-1874 Sentence denotes Moreover, it has also been imperative to note that this serine residue is conserved in all coronaviruses.
T24 1875-2015 Sentence denotes Though, the actual molecular mechanism is still not very clear but this could be a plausible explanation of termination viral RNA synthesis.
T25 2016-2238 Sentence denotes Recently, scientists also expressed RdRp of different viruses and measure kinetic parameters to infer its interaction with RDV-TP and also determined a score of 0.77 mmol half maximal concentration against SARS-CoV-2 (11).
T26 2239-2505 Sentence denotes Figure 1 Probable molecular mechanism of Remdisivir against SARS-CoV- 2. (A) Thematic diagram shows the SARS-CoV-2 viral entry and its RNA synthesis which can be block by Remdisivir. (B) Detail molecular mechanism of Remdisivir to inhibit the synthesis of viral RNA.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
31 2299-2310 Species denotes SARS-CoV- 2 Tax:2697049
32 2343-2353 Species denotes SARS-CoV-2 Tax:2697049
33 2280-2290 Chemical denotes Remdisivir
34 2410-2420 Chemical denotes Remdisivir
35 2456-2466 Chemical denotes Remdisivir
69 432-436 Gene denotes RdRp Gene:43740578
70 625-629 Gene denotes RdRp Gene:43740578
71 1658-1662 Gene denotes RdRp Gene:43740578
72 2052-2056 Gene denotes RdRp Gene:43740578
73 118-123 Species denotes Ebola Tax:1570291
74 148-175 Species denotes respiratory syncytial virus Tax:12814
75 219-232 Species denotes coronaviruses Tax:11118
76 243-251 Species denotes SARS CoV Tax:694009
77 256-264 Species denotes MERS CoV Tax:1335626
78 575-588 Species denotes coronaviruses Tax:11118
79 590-598 Species denotes MERS-CoV Tax:1335626
80 600-608 Species denotes SARS-CoV Tax:694009
81 613-623 Species denotes SARS-CoV-2 Tax:2697049
82 1230-1243 Species denotes coronaviruses Tax:11118
83 1252-1260 Species denotes MERS-CoV Tax:1335626
84 1262-1270 Species denotes SARS-CoV Tax:694009
85 1275-1285 Species denotes SARS-CoV-2 Tax:2697049
86 1860-1873 Species denotes coronaviruses Tax:11118
87 2222-2232 Species denotes SARS-CoV-2 Tax:2697049
88 177-180 Species denotes RSV Tax:12814
89 22-32 Chemical denotes remdesivir MESH:C000606551
90 34-37 Chemical denotes RDV MESH:C000606551
91 270-280 Chemical denotes Remdesivir MESH:C000606551
92 340-343 Chemical denotes RDV MESH:C000606551
93 351-354 Chemical denotes RDV MESH:C000606551
94 662-665 Chemical denotes RDV MESH:C000606551
95 692-701 Chemical denotes Adenosine MESH:D000241
96 716-719 Chemical denotes ATP MESH:D000255
97 854-857 Chemical denotes RDV MESH:C000606551
98 1039-1042 Chemical denotes RDV MESH:C000606551
99 1523-1526 Chemical denotes RDV MESH:C000606551
100 1825-1831 Chemical denotes serine MESH:D012694
101 2139-2142 Chemical denotes RDV MESH:C000606551