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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T82 643-650 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T83 743-750 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T84 1612-1620 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T85 2030-2038 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T86 2629-2644 Body_part denotes structural gene http://purl.org/sig/ont/fma/fma74402
T87 2979-2983 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T88 3178-3184 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T89 3455-3461 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T97 1715-1723 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T98 1715-1719 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T99 2080-2088 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T100 2080-2084 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T101 2316-2324 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T102 2316-2320 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T103 2413-2421 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T104 2413-2417 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T105 3161-3169 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T106 3161-3165 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T107 3438-3446 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T108 3438-3442 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T109 3695-3703 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T110 3695-3699 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T178 823-833 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes, the
T179 1327-1328 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T180 1628-1630 http://purl.obolibrary.org/obo/CLO_0008935 denotes S9
T181 1644-1646 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T182 1678-1680 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T183 1923-1927 http://purl.obolibrary.org/obo/CLO_0002040 denotes b(t)
T184 2188-2192 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T185 2528-2529 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T186 2640-2644 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T187 2647-2648 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T188 2828-2829 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T189 2902-2903 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T190 2979-2983 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T191 3146-3147 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T192 3211-3212 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T193 3273-3274 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T194 3332-3336 http://purl.obolibrary.org/obo/CLO_0002040 denotes b(t)
T195 3667-3671 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T69 1609-1611 Chemical denotes SI http://purl.obolibrary.org/obo/CHEBI_90326
T70 2027-2029 Chemical denotes SI http://purl.obolibrary.org/obo/CHEBI_90326
T71 2989-2991 Chemical denotes Ln http://purl.obolibrary.org/obo/CHEBI_33319
T72 3259-3263 Chemical denotes gold http://purl.obolibrary.org/obo/CHEBI_29287|http://purl.obolibrary.org/obo/CHEBI_30050

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
305 1715-1725 Species denotes SARS-CoV-2 Tax:2697049
306 2080-2090 Species denotes SARS-CoV-2 Tax:2697049
307 2316-2326 Species denotes SARS-CoV-2 Tax:2697049
308 2413-2423 Species denotes SARS-CoV-2 Tax:2697049
309 436-443 Disease denotes fitness MESH:D012640
310 1499-1512 Disease denotes viral fitness
311 2439-2452 Disease denotes viral fitness
315 3161-3171 Species denotes SARS-CoV-2 Tax:2697049
316 3438-3448 Species denotes SARS-CoV-2 Tax:2697049
317 3695-3705 Species denotes SARS-CoV-2 Tax:2697049

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T125 0-55 Sentence denotes No Evidence of Differentiation of the Viral Population.
T126 56-268 Sentence denotes While there was only limited evidence of diversification at selected sites, we also assessed whether subpopulations among the globally circulating viral population had become genetically differentiated over time.
T127 269-487 Sentence denotes To do so, we used two measures of population differentiation, the GST and D statistics, which characterize changes in allele frequency across populations and can show fitness differences between subpopulations (30–32).
T128 488-617 Sentence denotes Genetic distances between two subpopulations can range between 0 and 1, indicating no and complete differentiation, respectively.
T129 618-789 Sentence denotes We initially compared 30 genomes sampled from the initial outbreak in Wuhan, China, with subsampled alignments of the 18,484 genomes sampled subsequently across the globe.
T130 790-1069 Sentence denotes Although distances varied across genes, the median genetic distance between these subpopulations was small for both GST (0.0049 ± 0.0047) and D (0.0053 ± 0.0272), indicating little differentiation between the initial outbreak and its global derivatives in the pandemic (Fig. 4A).
T131 1070-1149 Sentence denotes We then compared subpopulations sampled before and after each consecutive week.
T132 1150-1336 Sentence denotes Similarly, genetic distances between subpopulations were small for both GST (0.0058 ± 0.0096) and D (0.0098 ± 0.0650) and tended to narrow over time rather than diverge (Fig. 4 B and C).
T133 1337-1431 Sentence denotes Signatures of host adaptation can also be seen in the branching patterns of viral phylogenies.
T134 1432-1627 Sentence denotes Bursts in transmissibility are emblematic of increases in relative viral fitness and are reflected in imbalances in the phylogeny, which can be estimated at each internal node (SI Appendix, Figs.
T135 1628-1648 Sentence denotes S9 and S10) (33–35).
T136 1649-1938 Sentence denotes We estimated phylogenetic η (36, 37) at each internal node of the SARS-CoV-2 phylogeny reconstructed from subsampled (10%) alignments and compared the distribution of estimates through time to phylogenies simulated under models of neutral and positive time-dependent rates (b(t) = beα(t)).
T137 1939-2050 Sentence denotes Simulation analyses demonstrated that this metric was robust against sampling fraction (SI Appendix, Fig. S10).
T138 2051-2301 Sentence denotes The distribution of η in the SARS-CoV-2 phylogenies adhered to expectations of the neutral model and deviated significantly (Student’s t test, P < 0.001) from those of positive time-dependent rates for selection coefficients α ≥ 0.2 (Fig. 4 D and E).
T139 2302-2461 Sentence denotes Together, the SARS-CoV-2 population and phylogenetic dynamics showed little evidence that the global spread of SARS-CoV-2 was related to viral fitness effects.
T140 2462-2469 Sentence denotes Fig. 4.
T141 2471-2813 Sentence denotes Limited evidence of adaptation of the viral population. (A–C) Bootstrapped global estimates of Nei’s GST and Jost’s D for population differentiation for each structural gene. (A) Estimates of Nei’s GST (closed circles) and Jost’s D (open circles) comparing sequences sampled from the Hubei province to sequences subsequently sampled globally.
T142 2814-2918 Sentence denotes Estimates of (B) Nei’s GST and (C) Jost’s D comparing sequences sampled before or after a specific date.
T143 2919-3595 Sentence denotes Lines connect the median estimates across datasets for each gene. (D) Ln-transformed phylogenetic η, indicative of the number of iterative events in the sampled subtree, for subtrees from each internal node (after the root) of a down-sampled SARS-CoV-2 whole-genome phylogeny (dark gray), of a phylogeny simulated under neutral parameters (gold), and of a phylogeny simulated under positive time-dependent rates (b(t) = 0.01e0.4t, green). (E) Box plot of ln-transformed phylogenetic η estimates across all down-sampled SARS-CoV-2 whole-genome phylogenies, phylogenies simulated under neutral parameters, and phylogenies simulated under different positive time dependencies, α.
T144 3596-3756 Sentence denotes Asterisks indicate significant differences in mean values (Student’s t test, P < 0.05) between the SARS-CoV-2 and positive time-dependent phylogenies at each α.

2_test

Id Subject Object Predicate Lexical cue
32868447-4519626-132542397 480-482 4519626 denotes 30
32868447-19238703-132542397 480-482 19238703 denotes 30
32868447-22883857-132542397 480-482 22883857 denotes 30
32868447-26147205-132542398 1641-1643 26147205 denotes 33
32868447-28472435-132542398 1641-1643 28472435 denotes 33
32868447-26658901-132542399 1678-1680 26658901 denotes 36
32868447-31700680-132542400 1682-1684 31700680 denotes 37