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PMC:7067204 / 10264-13197 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
643 2055-2058 Gene denotes the Gene:25085
644 2397-2399 Gene denotes of Gene:6688
645 2091-2093 Gene denotes of Gene:6688
646 2063-2065 Gene denotes of Gene:6688
647 2168-2176 Gene denotes helicase Gene:164045
650 1349-1351 Gene denotes as Gene:112935892
651 1309-1311 Gene denotes of Gene:6688
658 2570-2573 Gene denotes bat Gene:570
659 2783-2788 Gene denotes Spike Gene:43740568
660 2885-2889 Gene denotes Orf8 Gene:43740577
661 2544-2553 Species denotes 2019-nCoV Tax:2697049
662 2554-2563 Species denotes 2019-nCoV Tax:2697049
663 2590-2598 Species denotes SARS-CoV Tax:694009
668 2444-2447 Gene denotes the Gene:25085
669 2448-2470 Species denotes 2019 novel coronavirus Tax:2697049
670 2475-2500 Species denotes bat SARS-like coronavirus Tax:1508227
671 2510-2518 Species denotes SARS-CoV Tax:694009
704 843-852 Gene denotes helicase) Gene:164045
705 1018-1020 Gene denotes of Gene:6688
706 1065-1068 Gene denotes The Gene:25085
707 1000-1003 Gene denotes the Gene:25085
708 935-938 Gene denotes the Gene:25085
709 898-901 Gene denotes the Gene:25085
710 556-559 Gene denotes the Gene:25085
711 535-538 Gene denotes the Gene:25085
712 482-485 Gene denotes the Gene:25085
713 423-426 Gene denotes The Gene:25085
714 306-309 Gene denotes The Gene:25085
715 238-241 Gene denotes The Gene:25085
716 151-154 Gene denotes the Gene:25085
717 1219-1221 Gene denotes to Gene:6999
718 361-363 Gene denotes to Gene:6999
719 1173-1178 Gene denotes Spike Gene:43740568
720 1131-1136 Gene denotes Spike Gene:43740568
721 1186-1190 Gene denotes orf8 Gene:43740577
722 1141-1145 Gene denotes orf8 Gene:43740577
723 322-325 Gene denotes UTR Gene:2837
724 1042-1044 Gene denotes of Gene:6688
725 932-934 Gene denotes of Gene:6688
726 553-555 Gene denotes of Gene:6688
727 412-414 Gene denotes of Gene:6688
728 370-372 Gene denotes of Gene:6688
729 336-338 Gene denotes of Gene:6688
730 89-91 Gene denotes of Gene:6688
731 339-348 Species denotes 2019-nCoV Tax:2697049
732 1021-1030 Species denotes 2019-nCoV Tax:2697049
733 1045-1053 Species denotes SARS-CoV Tax:694009
734 1095-1104 Species denotes SARSr-CoV Tax:694009
735 1109-1117 Species denotes SARS-CoV Tax:694009

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T47 155-161 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T48 274-285 Body_part denotes nucleotides http://purl.org/sig/ont/fma/fma82740
T49 390-400 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T50 560-566 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T51 622-630 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T52 678-686 Body_part denotes cysteine http://purl.org/sig/ont/fma/fma82751
T53 798-801 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T54 812-815 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T55 1329-1337 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T56 1410-1420 Body_part denotes Amino acid http://purl.org/sig/ont/fma/fma82739
T57 1562-1564 Body_part denotes PL http://purl.org/sig/ont/fma/fma273007
T58 1908-1911 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T59 1912-1915 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T60 2107-2110 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T61 2121-2124 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T62 2209-2213 Body_part denotes ExoN http://purl.org/sig/ont/fma/fma84120
T63 2416-2426 Body_part denotes Amino acid http://purl.org/sig/ont/fma/fma82739
T64 2520-2530 Body_part denotes Amino acid http://purl.org/sig/ont/fma/fma82739

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T53 1045-1053 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T54 1109-1117 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T55 2479-2483 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T56 2510-2518 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T57 2549-2558 Disease denotes nCoV 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T58 2590-2598 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T108 76-77 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T109 120-121 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T110 526-527 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T111 939-944 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T112 1179-1181 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T113 1347-1348 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T114 1489-1491 http://purl.obolibrary.org/obo/CLO_0007448 denotes M1
T115 1489-1491 http://purl.obolibrary.org/obo/CLO_0050175 denotes M1
T116 1924-1932 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T117 2044-2051 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T118 2215-2219 http://purl.obolibrary.org/obo/CLO_0001000 denotes 3′–5
T119 2344-2349 http://purl.obolibrary.org/obo/CLO_0007888 denotes MT: 2
T120 2475-2478 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T121 2504-2509 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T122 2570-2573 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T123 2835-2843 http://purl.obolibrary.org/obo/UBERON_0000158 denotes Membrane
T124 2855-2857 http://purl.obolibrary.org/obo/CLO_0001527 denotes 94
T125 2896-2898 http://purl.obolibrary.org/obo/CLO_0001527 denotes 94
T126 2916-2918 http://purl.obolibrary.org/obo/CLO_0001527 denotes 94
T127 2919-2921 http://purl.obolibrary.org/obo/CLO_0001527 denotes 94

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T42 274-285 Chemical denotes nucleotides http://purl.obolibrary.org/obo/CHEBI_36976
T43 390-400 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T44 622-630 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T45 678-686 Chemical denotes cysteine http://purl.obolibrary.org/obo/CHEBI_15356
T46 1329-1337 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T47 1410-1420 Chemical denotes Amino acid http://purl.obolibrary.org/obo/CHEBI_33704
T48 1416-1420 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T49 1465-1474 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T50 1489-1491 Chemical denotes M1 http://purl.obolibrary.org/obo/CHEBI_51079|http://purl.obolibrary.org/obo/CHEBI_139019|http://purl.obolibrary.org/obo/CHEBI_140152|http://purl.obolibrary.org/obo/CHEBI_34826
T54 1562-1564 Chemical denotes PL http://purl.obolibrary.org/obo/CHEBI_74791|http://purl.obolibrary.org/obo/CHEBI_81588
T56 1912-1915 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T57 2044-2051 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T58 2273-2280 Chemical denotes poly(U) http://purl.obolibrary.org/obo/CHEBI_73279
T59 2344-2346 Chemical denotes MT http://purl.obolibrary.org/obo/CHEBI_73614
T60 2353-2359 Chemical denotes ribose http://purl.obolibrary.org/obo/CHEBI_33942|http://purl.obolibrary.org/obo/CHEBI_47013
T62 2416-2426 Chemical denotes Amino acid http://purl.obolibrary.org/obo/CHEBI_33704
T63 2422-2426 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T64 2520-2530 Chemical denotes Amino acid http://purl.obolibrary.org/obo/CHEBI_33704
T65 2526-2530 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T66 2574-2576 Chemical denotes SL http://purl.obolibrary.org/obo/CHEBI_74815

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T3 165-178 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription
T4 902-915 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription
T5 1635-1644 http://purl.obolibrary.org/obo/GO_0009058 denotes formation
T6 1751-1760 http://purl.obolibrary.org/obo/GO_0009058 denotes formation

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T95 0-237 Sentence denotes There are 12 putative, functional open reading frames (orfs) expressed from a nested set of 9 subgenomic mRNAs carrying a conserved leader sequence in the genome, 9 transcription-regulatory sequences, and 2 terminal untranslated regions.
T96 238-305 Sentence denotes The 5′- and 3′-UTRs are 265 and 358 nucleotides long, respectively.
T97 306-422 Sentence denotes The 5′- and 3 ′-UTR sequences of 2019-nCoV are similar to those of other βCoVs with nucleotide identities of ⩾83.6%.
T98 423-638 Sentence denotes The large replicase polyproteins pp1a and pp1ab encoded by the partially overlapping 5′-terminal orf1a/b within the 5′ two-thirds of the genome is proteolytic cleaved into 16 putative non-structural proteins (nsps).
T99 639-955 Sentence denotes These putative nsps included two viral cysteine proteases, namely, nsp3 (papain-like protease) and nsp5 (chymotrypsin-like, 3C-like, or main protease), nsp12 (RNA-dependent RNA polymerase [RdRp]), nsp13 (helicase), and other nsps which are likely involved in the transcription and replication of the virus (Table 2).
T100 956-1064 Sentence denotes There are no remarkable differences between the orfs and nsps of 2019-nCoV with those of SARS-CoV (Table 3).
T101 1065-1249 Sentence denotes The major distinction between SARSr-CoV and SARS-CoV is in orf3b, Spike and orf8 but especially variable in Spike S1 and orf8 which were previously shown to be recombination hot spots.
T102 1250-1258 Sentence denotes Table 2.
T103 1259-1380 Sentence denotes Putative functions and proteolytic cleavage sites of 16 nonstructural proteins in orf1a/b as predicted by bioinformatics.
T104 1381-1450 Sentence denotes NSP Putative function/domain Amino acid position Putative cleave site
T105 1451-1510 Sentence denotes nsp1 suppress antiviral host response M1 – G180 (LNGG'AYTR)
T106 1511-1547 Sentence denotes nsp2 unknown A181 – G818 (LKGG'APTK)
T107 1548-1600 Sentence denotes nsp3 putative PL-pro domain A819 – G2763 (LKGG'KIVN)
T108 1601-1670 Sentence denotes nsp4 complex with nsp3 and 6: DMV formation K2764 – Q3263 (AVLQ'SGFR)
T109 1671-1716 Sentence denotes nsp5 3CL-pro domain S3264 – Q3569 (VTFQ'SAVK)
T110 1717-1786 Sentence denotes nsp6 complex with nsp3 and 4: DMV formation S3570 – Q3859 (ATVQ'SKMS)
T111 1787-1844 Sentence denotes nsp7 complex with nsp8: primase S3860 – Q3942 (ATLQ'AIAS)
T112 1845-1902 Sentence denotes nsp8 complex with nsp7: primase A3943 – Q4140 (VKLQ'NNEL)
T113 1903-1958 Sentence denotes nsp9 RNA/DNA binding activity N4141 – Q4253 (VRLQ'AGNA)
T114 1959-2031 Sentence denotes nsp10 complex with nsp14: replication fidelity A4254 – Q4392 (PMLQ'SADA)
T115 2032-2100 Sentence denotes nsp11 short peptide at the end of orf1a S4393 – V4405 (end of orf1a)
T116 2101-2161 Sentence denotes nsp12 RNA-dependent RNA polymerase S4393 – Q5324 (TVLQ'AVGA)
T117 2162-2202 Sentence denotes nsp13 helicase A5325 – Q5925 (ATLQ'AENV)
T118 2203-2214 Sentence denotes nsp14 ExoN:
T119 2215-2258 Sentence denotes 3′–5′ exonuclease A5926 – Q6452 (TRLQ'SLEN)
T120 2259-2332 Sentence denotes nsp15 XendoU: poly(U)-specific endoribonuclease S6453 – Q6798 (PKLQ'SSQA)
T121 2333-2347 Sentence denotes nsp16 2'-O-MT:
T122 2348-2406 Sentence denotes 2'-O-ribose methyltransferase S6799 – N7096 (end of orf1b)
T123 2407-2415 Sentence denotes Table 3.
T124 2416-2519 Sentence denotes Amino acid identity between the 2019 novel coronavirus and bat SARS-like coronavirus or human SARS-CoV.
T125 2520-2563 Sentence denotes Amino acid identity (%) 2019-nCoV 2019-nCoV
T126 2564-2598 Sentence denotes   vs. bat-SL-CoVZXC21 vs. SARS-CoV
T127 2599-2609 Sentence denotes NSP1 96 84
T128 2610-2620 Sentence denotes NSP2 96 68
T129 2621-2631 Sentence denotes NSP3 93 76
T130 2632-2642 Sentence denotes NSP4 96 80
T131 2643-2653 Sentence denotes NSP5 99 96
T132 2654-2664 Sentence denotes NSP6 98 88
T133 2665-2675 Sentence denotes NSP7 99 99
T134 2676-2686 Sentence denotes NSP8 96 97
T135 2687-2697 Sentence denotes NSP9 96 97
T136 2698-2709 Sentence denotes NSP10 98 97
T137 2710-2721 Sentence denotes NSP11 85 85
T138 2722-2733 Sentence denotes NSP12 96 96
T139 2734-2746 Sentence denotes NSP13 99 100
T140 2747-2758 Sentence denotes NSP14 95 95
T141 2759-2770 Sentence denotes NSP15 88 89
T142 2771-2782 Sentence denotes NSP16 98 93
T143 2783-2794 Sentence denotes Spike 80 76
T144 2795-2806 Sentence denotes Orf3a 92 72
T145 2807-2818 Sentence denotes Orf3b 32 32
T146 2819-2834 Sentence denotes Envelope 100 95
T147 2835-2849 Sentence denotes Membrane 99 91
T148 2850-2860 Sentence denotes Orf6 94 69
T149 2861-2872 Sentence denotes Orf7a 89 85
T150 2873-2884 Sentence denotes Orf7b 93 81
T151 2885-2901 Sentence denotes Orf8/Orf8b 94 40
T152 2902-2921 Sentence denotes Nucleoprotein 94 94
T153 2922-2933 Sentence denotes Orf9b 73 73