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PMC:7214327 / 654-4378 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T2 1131-1141 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T3 1247-1250 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T4 1261-1264 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T5 1339-1342 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T6 1597-1607 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T7 1625-1628 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T8 1748-1758 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T9 1800-1803 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T10 1819-1830 Body_part denotes nucleotides http://purl.org/sig/ont/fma/fma82740
T11 2599-2602 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T12 2670-2676 Body_part denotes serine http://purl.org/sig/ont/fma/fma82764
T13 2846-2849 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T14 3219-3222 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T15 3346-3349 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T16 3668-3672 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T5 21-29 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T6 64-72 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T7 98-108 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T8 963-968 Disease denotes Ebola http://purl.obolibrary.org/obo/MONDO_0005737
T9 1088-1092 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T10 1445-1453 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T11 1458-1466 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T12 2107-2115 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T13 2120-2128 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T14 3067-3075 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T15 3144-3152 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T16 3188-3196 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T17 3520-3535 Disease denotes viral infection http://purl.obolibrary.org/obo/MONDO_0005108
T18 3526-3535 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 43-44 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T2 204-205 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T3 516-517 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T4 638-643 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T5 675-676 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T6 700-701 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T7 771-772 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T8 897-898 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T9 928-936 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T10 950-957 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T11 1015-1020 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T12 1042-1043 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T13 1129-1130 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T14 1220-1221 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T15 1300-1303 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T16 1356-1357 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T17 1484-1487 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T18 1655-1658 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T19 1712-1713 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T20 1926-1929 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T21 2042-2049 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T22 2205-2208 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T23 2307-2308 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T24 2379-2380 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T25 2523-2524 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T26 2627-2630 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T27 2801-2802 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T28 2915-2922 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T29 3011-3012 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T30 3079-3081 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T31 3154-3160 http://purl.obolibrary.org/obo/CLO_0001236 denotes 2. (A)
T32 3268-3269 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T33 3415-3416 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T34 3449-3457 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T35 3490-3491 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T36 3567-3572 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T37 3616-3617 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T38 3668-3672 http://purl.obolibrary.org/obo/GO_0005623 denotes cell

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T9 367-371 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T10 583-588 Chemical denotes drugs http://purl.obolibrary.org/obo/CHEBI_23888
T11 692-696 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T12 750-754 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T13 858-863 Chemical denotes drugs http://purl.obolibrary.org/obo/CHEBI_23888
T14 867-877 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T15 1131-1141 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T16 1164-1176 Chemical denotes triphosphate http://purl.obolibrary.org/obo/CHEBI_18036
T17 1200-1202 Chemical denotes TP http://purl.obolibrary.org/obo/CHEBI_73662
T18 1511-1513 Chemical denotes TP http://purl.obolibrary.org/obo/CHEBI_73662
T19 1537-1559 Chemical denotes Adenosine triphosphate http://purl.obolibrary.org/obo/CHEBI_15422
T20 1537-1546 Chemical denotes Adenosine http://purl.obolibrary.org/obo/CHEBI_16335
T21 1547-1559 Chemical denotes triphosphate http://purl.obolibrary.org/obo/CHEBI_18036
T22 1561-1564 Chemical denotes ATP http://purl.obolibrary.org/obo/CHEBI_15422|http://purl.obolibrary.org/obo/CHEBI_30616
T24 1566-1574 Chemical denotes molecule http://purl.obolibrary.org/obo/CHEBI_25367
T25 1597-1607 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T26 1681-1695 Chemical denotes hydroxyl group http://purl.obolibrary.org/obo/CHEBI_43176
T27 1681-1689 Chemical denotes hydroxyl http://purl.obolibrary.org/obo/CHEBI_29191
T28 1690-1695 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T29 1703-1705 Chemical denotes TP http://purl.obolibrary.org/obo/CHEBI_73662
T30 1748-1758 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T31 1819-1830 Chemical denotes nucleotides http://purl.obolibrary.org/obo/CHEBI_36976
T32 1888-1890 Chemical denotes TP http://purl.obolibrary.org/obo/CHEBI_73662
T33 2372-2374 Chemical denotes TP http://purl.obolibrary.org/obo/CHEBI_73662
T34 2670-2684 Chemical denotes serine residue http://purl.obolibrary.org/obo/CHEBI_32848
T35 2670-2676 Chemical denotes serine http://purl.obolibrary.org/obo/CHEBI_17822
T36 2988-2990 Chemical denotes TP http://purl.obolibrary.org/obo/CHEBI_73662

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T4 1339-1352 http://purl.obolibrary.org/obo/GO_0032774 denotes RNA synthesis
T5 1343-1352 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T6 1625-1638 http://purl.obolibrary.org/obo/GO_0032774 denotes RNA synthesis
T7 1629-1638 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T8 1781-1790 http://purl.obolibrary.org/obo/GO_0009058 denotes formation
T9 1800-1813 http://purl.obolibrary.org/obo/GO_0032774 denotes RNA synthesis
T10 1804-1813 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T11 2599-2612 http://purl.obolibrary.org/obo/GO_0032774 denotes RNA synthesis
T12 2603-2612 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T13 2846-2859 http://purl.obolibrary.org/obo/GO_0032774 denotes RNA synthesis
T14 2850-2859 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T15 3219-3232 http://purl.obolibrary.org/obo/GO_0032774 denotes RNA synthesis
T16 3223-3232 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T17 3327-3336 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T18 3520-3535 http://purl.obolibrary.org/obo/GO_0016032 denotes viral infection

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T11 0-75 Sentence denotes The current pandemic COVID-19 is caused by a novel coronavirus, SARS-CoV-2.
T12 76-238 Sentence denotes The disease is highly infectious like other coronaviral disease and causing already more than 2.3 lacs deaths worldwide, posing a serious threat to mankind (1,2).
T13 239-422 Sentence denotes Scientists, doctors and other health professional are working very hard to combat this current situation, but still there is no drug or vaccine available to treat this morbid disease.
T14 423-482 Sentence denotes But researchers are trying to develop new therapeutics (3).
T15 483-844 Sentence denotes However this situation initiates a global effort to find out effective measures or discovery of new drugs or vaccines to stop the spreading of this deadly virus, but, since the development of a new vaccine or drug is a time-consuming process, repurposing of existing drug could be act as a brilliant alternative with potential to combat the disease effectively.
T16 845-1114 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 1115-1480 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 1481-1651 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 1652-1912 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 1913-2187 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 2188-2408 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 2409-2613 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 2614-2719 Sentence denotes Moreover, it has also been imperative to note that this serine residue is conserved in all coronaviruses.
T24 2720-2860 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 2861-3083 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 3084-3350 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.
T27 3351-3724 Sentence denotes It can be concluded that this chain termination method could be a general mechanism of anti-viral activity of this particular substrate to a broad spectrum of different viral infection, but still the availability of human trial and safety data is pending, and also a detailed anti-viral profiling of this compound in cell culture study is highly appreciated at this moment.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
21 45-62 Species denotes novel coronavirus Tax:2697049
22 64-74 Species denotes SARS-CoV-2 Tax:2697049
23 120-131 Species denotes coronaviral Tax:11118
24 21-29 Disease denotes COVID-19 MESH:C000657245
25 179-185 Disease denotes deaths MESH:D003643
31 3144-3155 Species denotes SARS-CoV- 2 Tax:2697049
32 3188-3198 Species denotes SARS-CoV-2 Tax:2697049
33 3125-3135 Chemical denotes Remdisivir
34 3255-3265 Chemical denotes Remdisivir
35 3301-3311 Chemical denotes Remdisivir
69 1277-1281 Gene denotes RdRp Gene:43740578
70 1470-1474 Gene denotes RdRp Gene:43740578
71 2503-2507 Gene denotes RdRp Gene:43740578
72 2897-2901 Gene denotes RdRp Gene:43740578
73 963-968 Species denotes Ebola Tax:1570291
74 993-1020 Species denotes respiratory syncytial virus Tax:12814
75 1064-1077 Species denotes coronaviruses Tax:11118
76 1088-1096 Species denotes SARS CoV Tax:694009
77 1101-1109 Species denotes MERS CoV Tax:1335626
78 1420-1433 Species denotes coronaviruses Tax:11118
79 1435-1443 Species denotes MERS-CoV Tax:1335626
80 1445-1453 Species denotes SARS-CoV Tax:694009
81 1458-1468 Species denotes SARS-CoV-2 Tax:2697049
82 2075-2088 Species denotes coronaviruses Tax:11118
83 2097-2105 Species denotes MERS-CoV Tax:1335626
84 2107-2115 Species denotes SARS-CoV Tax:694009
85 2120-2130 Species denotes SARS-CoV-2 Tax:2697049
86 2705-2718 Species denotes coronaviruses Tax:11118
87 3067-3077 Species denotes SARS-CoV-2 Tax:2697049
88 1022-1025 Species denotes RSV Tax:12814
89 867-877 Chemical denotes remdesivir MESH:C000606551
90 879-882 Chemical denotes RDV MESH:C000606551
91 1115-1125 Chemical denotes Remdesivir MESH:C000606551
92 1185-1188 Chemical denotes RDV MESH:C000606551
93 1196-1199 Chemical denotes RDV MESH:C000606551
94 1507-1510 Chemical denotes RDV MESH:C000606551
95 1537-1546 Chemical denotes Adenosine MESH:D000241
96 1561-1564 Chemical denotes ATP MESH:D000255
97 1699-1702 Chemical denotes RDV MESH:C000606551
98 1884-1887 Chemical denotes RDV MESH:C000606551
99 2368-2371 Chemical denotes RDV MESH:C000606551
100 2670-2676 Chemical denotes serine MESH:D012694
101 2984-2987 Chemical denotes RDV MESH:C000606551
104 3567-3572 Species denotes human Tax:9606
105 3520-3535 Disease denotes viral infection MESH:D001102