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PMC:7111504 / 5933-10162 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
105 21-30 Species denotes 2019-nCoV Tax:2697049
108 162-170 Species denotes SARS CoV Tax:694009
109 254-263 Species denotes 2019-nCoV Tax:2697049
111 430-439 Species denotes 2019-nCoV Tax:2697049
115 882-891 Species denotes 2019-nCoV Tax:2697049
116 1217-1225 Species denotes SARS CoV Tax:694009
117 1312-1324 Species denotes Homo sapiens Tax:9606
119 1405-1414 Species denotes 2019-nCoV Tax:2697049
123 1738-1747 Species denotes 2019-nCov Tax:2697049
124 1978-1987 Species denotes 2019-nCoV Tax:2697049
125 2123-2132 Species denotes 2019-nCov Tax:2697049
127 2380-2389 Species denotes 2019-nCoV Tax:2697049
129 2272-2281 Species denotes 2019-nCoV Tax:2697049
131 3540-3549 Species denotes 2019-nCoV Tax:2697049
133 3560-3569 Species denotes 2019-nCoV Tax:2697049

LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T71 21-30 SP_7 denotes 2019-nCoV
T72 94-105 CHEBI:60816;CHEBI:60816 denotes immunogenic
T73 106-111 NCBITaxon:10239 denotes viral
T74 162-170 SP_10 denotes SARS CoV
T75 191-195 UBERON:0002415 denotes tail
T76 254-263 SP_7 denotes 2019-nCoV
T77 264-268 SO:0000236 denotes ORFs
T78 430-439 SP_7 denotes 2019-nCoV
T79 482-493 CHEBI:60816;CHEBI:60816 denotes immunogenic
T80 665-673 NCBITaxon:1 denotes organism
T81 728-736 BV_9 denotes epitopes
T82 882-891 SP_7 denotes 2019-nCoV
T83 1217-1225 SP_10 denotes SARS CoV
T84 1312-1324 SP_6;NCBITaxon:9606 denotes Homo sapiens
T85 1405-1414 SP_7 denotes 2019-nCoV
T86 1458-1472 BV_15 denotes immunogenicity
T87 1525-1539 BV_15 denotes immunogenicity
T88 1575-1589 BV_15 denotes immunogenicity
T89 1691-1705 BV_15 denotes immunogenicity
T90 1738-1747 SP_7 denotes 2019-nCov
T91 1788-1802 BV_15 denotes immunogenicity
T92 1910-1924 BV_15 denotes immunogenicity
T93 1978-1987 SP_7 denotes 2019-nCoV
T94 2077-2088 CHEBI:60816;CHEBI:60816 denotes immunogenic
T95 2123-2132 SP_7 denotes 2019-nCov
T96 2212-2226 BV_15 denotes immunogenicity
T97 2272-2281 SP_7 denotes 2019-nCoV
T98 2317-2331 BV_15 denotes immunogenicity
T99 3500-3514 BV_15 denotes immunogenicity
T100 3524-3535 CHEBI:60816;CHEBI:60816 denotes immunogenic
T101 3540-3549 SP_7 denotes 2019-nCoV
T102 3560-3569 SP_7 denotes 2019-nCoV
T103 3616-3627 CHEBI:60816;CHEBI:60816 denotes immunogenic
T104 3679-3693 BV_15 denotes immunogenicity
T105 3770-3784 BV_15 denotes immunogenicity
T106 3895-3909 BV_15 denotes immunogenicity
T107 4014-4025 CHEBI:60816;CHEBI:60816 denotes immunogenic
T108 4091-4102 CHEBI:60816;CHEBI:60816 denotes immunogenic
T109 4110-4121 CHEBI:60816;CHEBI:60816 denotes immunogenic
T110 4194-4208 BV_15 denotes immunogenicity
T77904 21-30 SP_7 denotes 2019-nCoV
T67615 94-105 CHEBI:60816;CHEBI:60816 denotes immunogenic
T6301 106-111 NCBITaxon:10239 denotes viral
T83775 162-170 SP_10 denotes SARS CoV
T79489 191-195 UBERON:0002415 denotes tail
T30840 254-263 SP_7 denotes 2019-nCoV
T18704 264-268 SO:0000236 denotes ORFs
T25028 430-439 SP_7 denotes 2019-nCoV
T38195 482-493 CHEBI:60816;CHEBI:60816 denotes immunogenic
T91224 665-673 NCBITaxon:1 denotes organism
T26522 728-736 BV_9 denotes epitopes
T51283 882-891 SP_7 denotes 2019-nCoV
T83402 1217-1225 SP_10 denotes SARS CoV
T38460 1312-1324 SP_6;NCBITaxon:9606 denotes Homo sapiens
T18430 1405-1414 SP_7 denotes 2019-nCoV
T78372 1458-1472 BV_15 denotes immunogenicity
T32405 1525-1539 BV_15 denotes immunogenicity
T57245 1575-1589 BV_15 denotes immunogenicity
T4440 1691-1705 BV_15 denotes immunogenicity
T13636 1738-1747 SP_7 denotes 2019-nCov
T61633 1788-1802 BV_15 denotes immunogenicity
T19852 1910-1924 BV_15 denotes immunogenicity
T63857 1978-1987 SP_7 denotes 2019-nCoV
T42242 2077-2088 CHEBI:60816;CHEBI:60816 denotes immunogenic
T74171 2123-2132 SP_7 denotes 2019-nCov
T89996 2212-2226 BV_15 denotes immunogenicity
T99846 2272-2281 SP_7 denotes 2019-nCoV
T22698 2317-2331 BV_15 denotes immunogenicity
T23450 3500-3514 BV_15 denotes immunogenicity
T46975 3524-3535 CHEBI:60816;CHEBI:60816 denotes immunogenic
T97466 3540-3549 SP_7 denotes 2019-nCoV
T87936 3560-3569 SP_7 denotes 2019-nCoV
T30689 3616-3627 CHEBI:60816;CHEBI:60816 denotes immunogenic
T76745 3679-3693 BV_15 denotes immunogenicity
T34290 3770-3784 BV_15 denotes immunogenicity
T17780 3895-3909 BV_15 denotes immunogenicity
T91242 4014-4025 CHEBI:60816;CHEBI:60816 denotes immunogenic
T28529 4091-4102 CHEBI:60816;CHEBI:60816 denotes immunogenic
T28382 4110-4121 CHEBI:60816;CHEBI:60816 denotes immunogenic
T58994 4194-4208 BV_15 denotes immunogenicity

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 191-195 Body_part denotes tail http://purl.obolibrary.org/obo/UBERON_0002415

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T12 162-166 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T13 1217-1221 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T82 18-20 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T83 31-39 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T84 112-120 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T85 184-185 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T86 191-195 http://purl.obolibrary.org/obo/UBERON_0002415 denotes tail
T87 285-293 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T88 440-448 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T89 494-502 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T90 512-513 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T91 569-577 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T92 612-613 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T93 632-640 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T94 665-673 http://purl.obolibrary.org/obo/OBI_0100026 denotes organism
T95 665-673 http://purl.obolibrary.org/obo/UBERON_0000468 denotes organism
T96 679-687 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T97 856-857 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T98 892-900 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T99 978-980 http://purl.obolibrary.org/obo/CLO_0053799 denotes 45
T100 985-987 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T101 988-996 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T102 1087-1095 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T103 1157-1158 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T104 1165-1167 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T105 1168-1176 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T106 1312-1324 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Homo sapiens
T107 1434-1442 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T108 1487-1495 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T109 1504-1505 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T110 1620-1628 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T111 1660-1661 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T112 1717-1718 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T113 1748-1756 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T114 1833-1835 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48
T115 1941-1949 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T116 1965-1967 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T117 1975-1977 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48
T118 1988-1996 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T119 2133-2141 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T120 2147-2148 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T121 2184-2186 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T122 2204-2205 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T123 2269-2271 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T124 2282-2290 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T125 2298-2299 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T126 2356-2364 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T127 3550-3558 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T128 3570-3578 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T129 3586-3587 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T130 3628-3636 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T131 3794-3795 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T132 3796-3803 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T133 3827-3828 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T134 3985-3986 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T135 4026-4034 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T136 4139-4142 http://purl.obolibrary.org/obo/CLO_0001755 denotes ask

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T47 31-39 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T48 112-120 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T49 285-293 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T50 440-448 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T51 494-502 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T52 569-577 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T53 632-640 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T54 679-687 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T55 892-900 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T56 988-996 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T57 1087-1095 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T58 1168-1176 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T59 1434-1442 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T60 1487-1495 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T61 1620-1628 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T62 1748-1756 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T63 1941-1949 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T64 1988-1996 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T65 2133-2141 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T66 2282-2290 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T67 2356-2364 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T68 2876-2878 Chemical denotes WN http://purl.obolibrary.org/obo/CHEBI_141447
T69 3550-3558 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T70 3570-3578 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T71 3628-3636 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T72 3796-3803 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T73 4026-4034 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T65 0-120 Sentence denotes Identification of 22 2019-nCoV peptides with high degree of similarity to previously reported immunogenic viral peptides
T66 121-316 Sentence denotes In addition to 28 identical hits against SARS CoV, we observed a long tail in distribution of normalized alignment scores between 10 2019-nCoV ORFs and 35,225 IEDB peptides ( Figure 1A, Methods).
T67 317-418 Sentence denotes We therefore set out to further investigate potential vaccine targets among highly similar sequences.
T68 419-428 Sentence denotes Figure 1.
T69 430-511 Sentence denotes 2019-nCoV peptides with high sequence similarity to immunogenic peptides in IEDB.
T70 512-514 Sentence denotes A.
T71 515-611 Sentence denotes Comparison of normalized sequence alignment score for peptides with exact and non-exact matches.
T72 612-614 Sentence denotes B.
T73 615-674 Sentence denotes Number of target peptides grouped by their source organism.
T74 675-797 Sentence denotes The peptides having an exact sequence alignment with epitopes in IEDB had normalized alignment scores ranging from 4 to 6.
T75 798-936 Sentence denotes Taking the normalized alignment score of exact matches as a reference, we extracted 2019-nCoV peptides having score greater or equal to 4.
T76 937-1075 Sentence denotes As illustrated in Figure 1A, we observed 45 and 11 peptides having normalized alignment score ≥ 4 and ≥ 5 respectively ( Figure 1A inset).
T77 1076-1226 Sentence denotes The target peptides were originated from 10 different sources ( Figure 1B) where a total 36 peptides were derived from strains associated to SARS CoV.
T78 1227-1325 Sentence denotes Of interest, we also observed 7 hits having high sequence similarity to targets from Homo sapiens.
T79 1326-1646 Sentence denotes In order to investigate the extent to which the difference between the source (2019-nCoV) and target (IEDB) peptides influences the immunogenicity of the source peptides we used a recently published immunogenicity model 5 to predict and compare the immunogenicity between the source and target peptides (Data Table 2 4).
T80 1647-1822 Sentence denotes We could see a similar (close to identical) immunogenicity scores for a number of IEDB and 2019-nCov peptides especially for those with high immunogenicity scores ( Figure 2).
T81 1823-1950 Sentence denotes While all 48 can be potential targets, of particular interest were those having higher immunogenicity score than IEDB peptides.
T82 1951-2100 Sentence denotes Here, we list 22 out of 48 2019-nCoV peptides that scored higher compared to their targets that have been characterized to be immunogenic ( Table 2).
T83 2101-2250 Sentence denotes In this list 15 (68%) 2019-nCov peptides have a score higher than 0.5 whereas only 11(50%) of IEDB get a score immunogenicity score greater than 0.5.
T84 2251-2259 Sentence denotes Table 2.
T85 2261-2365 Sentence denotes List of 22 2019-nCoV peptides having a higher predicted immunogenicity score than their target peptides.
T86 2366-2419 Sentence denotes IEDB.peptide 2019-nCoV.pattern IEDB.prob nCol.prob
T87 2420-2457 Sentence denotes WYMWLGARY WYIWLG 0.999249 0.999441
T88 2458-2498 Sentence denotes GLMWLSYFV GLMWLSYFI 0.995073 0.998216
T89 2499-2538 Sentence denotes GLVFLCLQY GIVFMCVEY 0.98123 0.984127
T90 2539-2611 Sentence denotes TWLTYHGAIKLDDKDPQFKDNVILL TWLTYTGAIKLDDKDPNFKDQVILL 0.925862 0.975242
T91 2612-2663 Sentence denotes IGMEVTPSGTWLTYH IGMEVTPSGTWLTY 0.903518 0.919184
T92 2664-2716 Sentence denotes GETALALLLLDRLNQ GDAALALLLLDRLNQ 0.853114 0.900655
T93 2717-2769 Sentence denotes TPSGTWLTYHGAIKL TPSGTWLTYTGAIKL 0.620894 0.662417
T94 2770-2810 Sentence denotes SIVAYTMSL SIIAYTMSL 0.589694 0.693763
T95 2811-2863 Sentence denotes RRPQGLPNNIASWFT RRPQGLPNNTASWFT 0.533253 0.584355
T96 2864-2898 Sentence denotes YNLKWN YNL-WN 0.520244 0.765309
T97 2899-2956 Sentence denotes AGCLIGAEHVDTSYECDI AGCLIGAEHVNNSYECDI 0.503905 0.56813
T98 2957-3015 Sentence denotes GFMKQYGECLGDINARDL GFIKQYGDCLGDIAARDL 0.471939 0.506817
T99 3016-3068 Sentence denotes ANKEGIVWVATEGAL ANKDGIIWVATEGAL 0.367723 0.404796
T100 3069-3103 Sentence denotes WNPDDY WNADLY 0.355018 0.584726
T101 3104-3138 Sentence denotes PDDYGG PDDFTG 0.334887 0.527287
T102 3139-3196 Sentence denotes TWLTYHGAIKLDDKDPQF TWLTYTGAIKLDDKDPNF 0.27017 0.529675
T103 3197-3230 Sentence denotes DEVNQI DEVRQI 0.18504 0.187797
T104 3231-3283 Sentence denotes SSKRFQPFQQFGRDV SNKKFLPFQQFGRDI 0.098384 0.119472
T105 3284-3323 Sentence denotes NHDSPDAEL NHTSPDVDL 0.067808 0.17889
T106 3324-3366 Sentence denotes TKQYNVTQAF TKAYNVTQAF 0.054818 0.171488
T107 3367-3425 Sentence denotes VKQMYKTPTLKYFGGFNF VKQIYKTPPIKDFGGFNF 0.018685 0.135681
T108 3426-3478 Sentence denotes QKRTATKQYNVTQAF QKRTATKAYNVTQAF 0.004891 0.037776
T109 3479-3488 Sentence denotes Figure 2.
T110 3490-3559 Sentence denotes Predicted immunogenicity for IEDB immunogenic vs. 2019-nCoV peptides.
T111 3560-3723 Sentence denotes 2019-nCoV peptides having a high sequence similarity to immunogenic peptides and their targets were analysed for their immunogenicity potential by iPred algorithm.
T112 3724-3957 Sentence denotes It is worth noting that in general predicting immunogenicity of given a peptide is challenging and not a fully solved problem, and therefore current models for predicting immunogenicity are suboptimal. iPred is also not an exception.
T113 3958-4123 Sentence denotes In fact, we could see that a substantial number of IEDB immunogenic peptides were scored < 0.5 (the threshold score used to classify immunogenic vs non-immunogenic).
T114 4124-4229 Sentence denotes This led us to ask whether we can gather any other evidence of either immunogenicity or cross-reactivity.

MyTest

Id Subject Object Predicate Lexical cue
32269766-30144804-30420971 1546-1548 30144804 denotes 5

2_test

Id Subject Object Predicate Lexical cue
32269766-30144804-30420971 1546-1547 30144804 denotes 5