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PMC:7519301 / 15334-17848 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T57 418-422 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T58 458-466 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T59 756-766 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T60 887-895 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T61 1058-1066 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T62 1073-1077 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T63 1201-1209 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T64 1275-1282 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T65 1941-1945 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T66 1974-1978 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T67 2079-2087 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T68 2142-2151 Body_part denotes leukocyte http://purl.org/sig/ont/fma/fma62852
T69 2161-2164 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T70 2295-2299 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T71 2360-2368 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T72 2495-2503 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T91 2091-2099 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T92 2091-2095 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T135 3-7 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T136 174-175 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T137 312-316 http://purl.obolibrary.org/obo/CLO_0001550 denotes a 10
T138 418-422 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T139 439-443 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T140 550-551 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T141 712-713 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T142 1071-1077 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T143 1130-1132 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T144 1137-1139 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T145 1137-1139 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T146 1216-1218 http://purl.obolibrary.org/obo/CLO_0008933 denotes S5
T147 1381-1383 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T148 1939-1945 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T149 1970-1971 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T150 1972-1978 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T151 2029-2032 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T152 2037-2040 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T153 2109-2113 http://purl.obolibrary.org/obo/CLO_0007653 denotes M, E
T154 2136-2141 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T155 2191-2192 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T156 2293-2299 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T40 455-457 Chemical denotes SI http://purl.obolibrary.org/obo/CHEBI_90326
T41 473-475 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T42 756-766 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T43 756-761 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T44 762-766 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T45 855-857 Chemical denotes dN http://purl.obolibrary.org/obo/CHEBI_33793
T46 884-886 Chemical denotes SI http://purl.obolibrary.org/obo/CHEBI_90326
T47 902-904 Chemical denotes S4 http://purl.obolibrary.org/obo/CHEBI_29401
T48 1137-1139 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T49 1198-1200 Chemical denotes SI http://purl.obolibrary.org/obo/CHEBI_90326
T50 1216-1218 Chemical denotes S5 http://purl.obolibrary.org/obo/CHEBI_29386
T51 1275-1282 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T52 2041-2048 Chemical denotes epitope http://purl.obolibrary.org/obo/CHEBI_53000
T53 2079-2087 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T54 2152-2159 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T55 2357-2359 Chemical denotes SI http://purl.obolibrary.org/obo/CHEBI_90326
T56 2492-2494 Chemical denotes SI http://purl.obolibrary.org/obo/CHEBI_90326
T57 2510-2512 Chemical denotes S8 http://purl.obolibrary.org/obo/CHEBI_29385

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id tao:has_standard_notation
266 1513-1517 Gene denotes ACE2 Gene:59272
267 1600-1604 Gene denotes ACE2 Gene:59272
268 2029-2032 Gene denotes CD8 Gene:925
269 2037-2040 Gene denotes CD4 Gene:920
270 2109-2110 Gene denotes M Gene:43740571
271 2106-2107 Gene denotes N Gene:43740575
272 2103-2104 Gene denotes S Gene:43740568
273 1306-1307 Gene denotes S Gene:43740568
274 481-482 Gene denotes S Gene:43740568
275 2091-2101 Species denotes SARS-CoV-2 Tax:2697049
276 2136-2141 Species denotes human Tax:9606
277 2161-2164 Gene denotes HLA Gene:3113
278 855-857 Chemical denotes dN MESH:C022306
279 858-860 Chemical denotes dS MESH:D003903
280 1323-1328 Mutation denotes D614G p.D614G
281 1017-1022 Mutation denotes D614G p.D614G

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T101 0-275 Sentence denotes To test whether this site was under selection, we used likelihood-based, phylogenetically informed models that assume branch-specific substitution rates (29) and implemented a sampling strategy to circumvent computational limitations imposed by the large number of sequences.
T102 276-477 Sentence denotes Subsampled alignments (100 times at a 10% sampling fraction) had diversity estimates statistically similar to the complete alignment for each gene (Mann−Whitney U test, P > 0.09; SI Appendix, Fig. S3).
T103 478-906 Sentence denotes In S, only site 614 was estimated to be under diversifying selection in a majority of subsampled alignments (58%); evidence of diversifying selection indicates that genetic diversity increases in the viral population (i.e., there was a higher proportion of mutations causing an amino acid change than not at site 614, or, the nonsynonymous/synonymous substitution rates ratio, dN/dS, was over 1, P < 0.1) (SI Appendix, Fig. S4).
T104 907-1088 Sentence denotes Because diversifying selection is often associated with the host adaptive response, we considered whether the D614G mutation coincided with targets of antibody and T cell responses.
T105 1089-1220 Sentence denotes Site 614 is at the interface between the S1 and S2 subunits and is thus not highly accessible to antibodies (SI Appendix, Fig. S5).
T106 1221-1389 Sentence denotes Therefore, we predict that antibodies to the native S protein would cross-react with S containing the D614G mutation, in agreement with recent reports (24, 25, 27, 28).
T107 1390-1659 Sentence denotes Many known neutralizing antibodies target the RBD, yet we found little evidence that mutations could affect binding to the ACE2 receptor, as only five shared mutations were identified at contact sites with the ACE2 receptor, and all were found in 10 or fewer sequences.
T108 1660-1753 Sentence denotes Of these, one mutation, at position 489, was synonymous and found in three sequences (0.02%).
T109 1754-1887 Sentence denotes The others were nonsynonymous: G476S (n = 10 sequences, 0.05%), Y453F (n = 5, 0.02%), G446V (n = 3, 0.02%), and A475V (n = 2, 0.01%).
T110 1888-2210 Sentence denotes To predict the potential immune pressure linked to T cell responses, we developed a T cell immunogenicity index which takes into account the CD8 and CD4 epitope repertoires in the structural proteins of SARS-CoV-2 (S, N, M, E) and the frequency of human leukocyte antigen (HLA) alleles or haplotypes in a given population.
T111 2211-2375 Sentence denotes We found that sites with mutations, including 614 in S, were not colocalized with T cell epitopes frequently identified in different populations (SI Appendix, Figs.
T112 2376-2514 Sentence denotes S6 and S7), and there was no significant relationship between the number of mutations and the immunogenicity index (SI Appendix, Fig. S8).

2_test

Id Subject Object Predicate Lexical cue
32868447-22807683-132542394 154-156 22807683 denotes 29
32868447-32697968-132542395 1373-1375 32697968 denotes 24