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PMC:7111504 / 10164-12359 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
135 42-51 Species denotes 2019-nCoV Tax:2697049
145 564-569 Gene denotes HLA-A Gene:3105
146 577-582 Gene denotes HLA-A Gene:3105
147 590-595 Gene denotes HLA-B Gene:3106
148 603-608 Gene denotes HLA-B Gene:3106
149 619-624 Gene denotes HLA-C Gene:3107
150 386-389 Gene denotes MHC Gene:3107
151 167-176 Species denotes 2019-nCov Tax:2697049
152 219-228 Species denotes 2019-nCoV Tax:2697049
153 428-437 Chemical denotes NetMHCpan
155 666-669 Gene denotes MHC Gene:3107
158 1061-1070 Species denotes 2019-nCoV Tax:2697049
159 1131-1140 Chemical denotes NetMHCpan
162 1980-1983 Gene denotes MHC Gene:3107
163 1956-1965 Species denotes 2019-nCoV Tax:2697049
171 2031-2034 Gene denotes MHC Gene:3107
172 2061-2066 Gene denotes HLA-A Gene:3105
173 2074-2079 Gene denotes HLA-A Gene:3105
174 2087-2092 Gene denotes HLA-B Gene:3106
175 2100-2105 Gene denotes HLA-B Gene:3106
176 2116-2121 Gene denotes HLA-C Gene:3107
177 2139-2148 Chemical denotes NetMHCpan

LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T111 18-29 CHEBI:60816;CHEBI:60816 denotes immunogenic
T112 42-51 SP_7 denotes 2019-nCoV
T113 134-145 CHEBI:60816;CHEBI:60816 denotes immunogenic
T114 167-176 SP_7 denotes 2019-nCov
T115 209-213 SP_9 denotes mers
T116 219-228 SP_7 denotes 2019-nCoV
T117 322-336 BV_15 denotes immunogenicity
T118 386-389 GO:0042611 denotes MHC
T119 495-505 SO:0001024 denotes haplotypes
T120 564-569 PR:000002009 denotes HLA-A
T121 577-582 PR:000002009 denotes HLA-A
T122 590-595 PR:000002010 denotes HLA-B
T123 603-608 PR:000002010 denotes HLA-B
T124 619-624 PR:000002011 denotes HLA-C
T125 631-638 SO:0001023 denotes alleles
T126 666-669 GO:0042611 denotes MHC
T127 687-701 BV_15 denotes immunogenicity
T128 771-778 SO:0001023 denotes alleles
T129 801-815 BV_15 denotes immunogenicity
T130 897-911 BV_15 denotes immunogenicity
T131 991-1002 CHEBI:60816;CHEBI:60816 denotes immunogenic
T132 1061-1070 SP_7 denotes 2019-nCoV
T133 1120-1127 SO:0001023 denotes alleles
T134 1182-1189 SO:0001023 denotes alleles
T135 1194-1208 BV_15 denotes immunogenicity
T136 1245-1252 SO:0001023 denotes alleles
T137 1325-1331 SO:0001023 denotes allele
T138 1956-1965 SP_7 denotes 2019-nCoV
T139 1980-1983 GO:0042611 denotes MHC
T140 2001-2015 BV_15 denotes immunogenicity
T141 2031-2034 GO:0042611 denotes MHC
T142 2061-2066 PR:000002009 denotes HLA-A
T143 2074-2079 PR:000002009 denotes HLA-A
T144 2087-2092 PR:000002010 denotes HLA-B
T145 2100-2105 PR:000002010 denotes HLA-B
T146 2116-2121 PR:000002011 denotes HLA-C
T147 2128-2135 SO:0001023 denotes alleles
T148 2157-2171 BV_15 denotes immunogenicity
T62473 18-29 CHEBI:60816;CHEBI:60816 denotes immunogenic
T49303 42-51 SP_7 denotes 2019-nCoV
T4279 134-145 CHEBI:60816;CHEBI:60816 denotes immunogenic
T6626 167-176 SP_7 denotes 2019-nCov
T90148 209-213 SP_9 denotes mers
T85766 219-228 SP_7 denotes 2019-nCoV
T90107 322-336 BV_15 denotes immunogenicity
T45797 386-389 GO:0042611 denotes MHC
T63293 495-505 SO:0001024 denotes haplotypes
T59388 564-569 PR:000002009 denotes HLA-A
T64753 577-582 PR:000002009 denotes HLA-A
T67356 590-595 PR:000002010 denotes HLA-B
T99742 603-608 PR:000002010 denotes HLA-B
T8696 619-624 PR:000002011 denotes HLA-C
T3771 631-638 SO:0001023 denotes alleles
T81007 666-669 GO:0042611 denotes MHC
T71652 687-701 BV_15 denotes immunogenicity
T43291 771-778 SO:0001023 denotes alleles
T65127 801-815 BV_15 denotes immunogenicity
T76335 897-911 BV_15 denotes immunogenicity
T29057 991-1002 CHEBI:60816;CHEBI:60816 denotes immunogenic
T69709 1061-1070 SP_7 denotes 2019-nCoV
T97652 1120-1127 SO:0001023 denotes alleles
T30189 1182-1189 SO:0001023 denotes alleles
T17570 1194-1208 BV_15 denotes immunogenicity
T56623 1245-1252 SO:0001023 denotes alleles
T32084 1325-1331 SO:0001023 denotes allele
T12377 1956-1965 SP_7 denotes 2019-nCoV
T98397 1980-1983 GO:0042611 denotes MHC
T94145 2001-2015 BV_15 denotes immunogenicity
T75496 2031-2034 GO:0042611 denotes MHC
T7224 2061-2066 PR:000002009 denotes HLA-A
T38753 2074-2079 PR:000002009 denotes HLA-A
T92877 2087-2092 PR:000002010 denotes HLA-B
T36156 2100-2105 PR:000002010 denotes HLA-B
T68789 2116-2121 PR:000002011 denotes HLA-C
T46318 2128-2135 SO:0001023 denotes alleles
T4457 2157-2171 BV_15 denotes immunogenicity

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T55 257-268 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T56 290-300 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T57 386-389 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T58 456-459 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T59 564-567 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T60 577-580 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T61 590-593 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T62 603-606 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T63 619-622 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T64 666-669 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T65 767-770 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T66 879-882 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T67 1116-1119 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T68 1178-1181 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T69 1321-1324 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T70 1424-1427 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T71 1980-1983 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T72 2031-2034 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T73 2061-2064 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T74 2074-2077 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T75 2087-2090 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T76 2100-2103 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T77 2116-2119 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T14 1366-1368 Disease denotes NB http://purl.obolibrary.org/obo/MONDO_0005072
T15 1376-1378 Disease denotes NB http://purl.obolibrary.org/obo/MONDO_0005072
T16 1386-1388 Disease denotes NB http://purl.obolibrary.org/obo/MONDO_0005072
T17 1396-1398 Disease denotes NB http://purl.obolibrary.org/obo/MONDO_0005072
T18 1406-1408 Disease denotes NB http://purl.obolibrary.org/obo/MONDO_0005072

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T137 30-38 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T138 64-65 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T139 114-115 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T140 146-154 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T141 243-244 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T142 346-354 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T143 484-491 http://purl.obolibrary.org/obo/CLO_0009985 denotes focused
T144 568-569 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T145 581-582 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T146 594-595 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T147 607-608 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T148 651-654 http://purl.obolibrary.org/obo/CLO_0001302 denotes 3 4
T149 728-736 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T150 973-974 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T151 1077-1085 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T152 1452-1456 http://purl.obolibrary.org/obo/CLO_0053733 denotes 1 1
T153 1458-1465 http://purl.obolibrary.org/obo/CLO_0053001 denotes 1 1 4
T154 1490-1494 http://purl.obolibrary.org/obo/CLO_0053733 denotes 1 1
T155 1496-1503 http://purl.obolibrary.org/obo/CLO_0053001 denotes 1 1 4
T156 1525-1529 http://purl.obolibrary.org/obo/CLO_0053733 denotes 1 1
T157 1563-1567 http://purl.obolibrary.org/obo/CLO_0053733 denotes 1 1
T158 1600-1604 http://purl.obolibrary.org/obo/CLO_0053733 denotes 1 1
T159 1685-1689 http://purl.obolibrary.org/obo/CLO_0053733 denotes 1 1
T160 1790-1794 http://purl.obolibrary.org/obo/CLO_0053733 denotes 1 1
T161 1828-1832 http://purl.obolibrary.org/obo/CLO_0053733 denotes 1 1
T162 1869-1873 http://purl.obolibrary.org/obo/CLO_0053733 denotes 1 1
T163 1966-1974 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T164 2065-2066 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T165 2078-2079 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T166 2091-2092 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T167 2104-2105 http://purl.obolibrary.org/obo/CLO_0001021 denotes B

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T74 30-38 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T75 146-154 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T76 257-268 Chemical denotes amino acids http://purl.obolibrary.org/obo/CHEBI_33709
T77 257-262 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T78 263-268 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T79 290-300 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T80 290-295 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T81 296-300 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T82 346-354 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T83 728-736 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T84 1077-1085 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T85 1966-1974 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T115 0-60 Sentence denotes De novo search of immunogenic peptides in 2019-nCoV proteome
T116 61-195 Sentence denotes As a complementary reciprocal approach, we conducted a de novo search of immunogenic peptides against the 2019-nCov proteome sequence.
T117 196-317 Sentence denotes We scanned 9-mers from 2019-nCoV proteome with a window of 9 amino acids and step length of 1 amino acid (9613 in total).
T118 318-466 Sentence denotes The immunogenicity of 9-mer peptides were predicted using iPred and MHC presentation scores were gauged using NetMHCpan 4.0 6 for various HLA types.
T119 467-656 Sentence denotes In this task, we focused on haplotypes common in Chinese and European populations, which include HLA-A*02:01, HLA-A*01:01, HLA-B*07:02, HLA-B*40:01 and HLA-C*07:02 alleles (Data Table 3 4).
T120 657-835 Sentence denotes Based on MHC presentation and immunogenicity prediction, we detected 5 peptides predicted to bind 4 different HLA alleles of which 2 had strong immunogenicity scores ( Figure 3).
T121 836-936 Sentence denotes For those 65 strong binders to 3 different HLA types, 39 had immunogenicity scores ≥ 0.5 ( Table 3).
T122 937-1050 Sentence denotes Collectively this analysis suggests a number of 9-mer immunogenic candidates for further experimental validation.
T123 1051-1059 Sentence denotes Table 3.
T124 1061-1230 Sentence denotes 2019-nCoV 9-mer peptides predicted to bind 4 different HLA alleles by NetMHCpan 4.0, and those predicted to bind ≥ 3 HLA alleles and immunogenicity score ≥ 0.9 by iPred.
T125 1231-1332 Sentence denotes For different alleles, 0 denotes non-binding and 1 denotes binding predicted for specific HLA allele.
T126 1333-1427 Sentence denotes Antigen.epitope Imm.prob A0101.NB A0201.NB B0702.NB B4001.NB C0702.NB Total binding HLA
T127 1428-1465 Sentence denotes VQMAPISAM 0.893938 0 1 1 1 1 4
T128 1466-1503 Sentence denotes AMYTPHTVL 0.862427 0 1 1 1 1 4
T129 1504-1541 Sentence denotes TLDSKTQSL 0.254998 1 1 1 0 1 4
T130 1542-1579 Sentence denotes KVDGVVQQL 0.191786 1 1 1 0 1 4
T131 1580-1616 Sentence denotes KVDGVDVEL 0.18632 1 1 1 0 1 4
T132 1617-1654 Sentence denotes MADQAMTQM 0.991227 1 0 1 0 1 3
T133 1655-1692 Sentence denotes LEAPFLYLY 0.983072 1 0 0 1 1 3
T134 1693-1730 Sentence denotes RTAPHGHVM 0.972153 1 0 1 0 1 3
T135 1731-1768 Sentence denotes IPFAMQMAY 0.961569 1 0 1 0 1 3
T136 1769-1806 Sentence denotes FLTENLLLY 0.951715 1 1 0 0 1 3
T137 1807-1844 Sentence denotes YLQPRTFLL 0.947743 1 1 0 0 1 3
T138 1845-1882 Sentence denotes MMISAGFSL 0.941318 0 1 1 0 1 3
T139 1883-1920 Sentence denotes ATLPKGIMM 0.926603 1 0 1 0 1 3
T140 1921-1930 Sentence denotes Figure 3.
T141 1932-2026 Sentence denotes De novo search of 9-mer 2019-nCoV peptides with MHC presentation and immunogenicity potential.
T142 2027-2195 Sentence denotes The MHC binding was predicted for HLA-A*02:01, HLA-A*01:01, HLA-B*07:02, HLA-B*40:01 and HLA-C*07:02 alleles by NetMHCpan 4.0 and immunogenicity was predicted by iPred.

MyTest

Id Subject Object Predicate Lexical cue
32269766-28978689-30420972 442-444 28978689 denotes 6

2_test

Id Subject Object Predicate Lexical cue
32269766-28978689-30420972 442-443 28978689 denotes 6