
PMC:7519301 / 20081-23837
Annnotations
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 |