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PMC:7519301 / 42104-44378 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T121 1317-1323 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T182 1225-1233 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T183 1225-1229 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T184 1306-1314 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T185 1306-1310 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T186 1639-1647 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T187 1639-1643 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T188 1702-1710 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T189 1702-1706 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T190 1975-1983 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T191 1975-1979 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T192 2038-2046 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T193 2038-2042 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T302 343-344 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T303 389-391 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T304 568-569 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T305 629-635 http://purl.obolibrary.org/obo/CLO_0002045 denotes b(t)=b
T306 669-673 http://purl.obolibrary.org/obo/CLO_0002040 denotes b(t)
T307 684-685 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T308 816-818 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T309 832-834 http://purl.obolibrary.org/obo/CLO_0053794 denotes 41
T310 1199-1202 http://purl.obolibrary.org/obo/NCBITaxon_314295 denotes ape
T311 1783-1784 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T312 1809-1813 http://purl.obolibrary.org/obo/CLO_0002040 denotes b(t)
T313 2141-2145 http://purl.obolibrary.org/obo/CLO_0001550 denotes a 10
T314 2265-2268 http://purl.obolibrary.org/obo/NCBITaxon_314295 denotes ape

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
507 1225-1235 Species denotes SARS-CoV-2 Tax:2697049
513 1306-1316 Species denotes SARS-CoV-2 Tax:2697049
514 1639-1649 Species denotes SARS-CoV-2 Tax:2697049
515 1702-1712 Species denotes SARS-CoV-2 Tax:2697049
516 1975-1985 Species denotes SARS-CoV-2 Tax:2697049
517 2038-2048 Species denotes SARS-CoV-2 Tax:2697049

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T260 0-57 Sentence denotes Time-Dependent Estimates of Phylogenetic Diversification.
T261 58-397 Sentence denotes Time-dependent estimates of phylogenetic diversification were measured by extracting the branches descending from each internal node (above the root) of each phylogeny and calculating the peak height (η) of the spectral density profile of the graph Laplacian of each subtree, which is a measure of the density of branching events (36, 37).
T262 398-512 Sentence denotes The code to perform the analysis is available for download at https://www.hivresearch.org/publication-supplements.
T263 514-534 Sentence denotes Simulation analyses.
T264 535-846 Sentence denotes Phylogenies were simulated using a time-forward branching process under constant birth rates (b(t)=b) and time-dependent birth rates (b(t)=beαt) for b = 0.01, 0.03, 0.05, 0.07, and 0.09 and α = ±0.01, ±0.11, ±0.21, ±0.31, and ±0.41, for 20, 220, 420, 620, and 820 tips, and for 1, 11, 21, 31, and 41 time units.
T265 847-916 Sentence denotes Simulated phylogenies were downsampled at 0%, 10%, 30%, 50%, and 70%.
T266 917-967 Sentence denotes For each scenario, 100 phylogenies were simulated.
T267 968-1089 Sentence denotes Time-dependent diversification (i.e., η across subtrees) was calculated for each phylogeny simulated under each scenario.
T268 1090-1208 Sentence denotes Simulations were conducted using the R packages RPANDA (R Phylogenetic ANalyses of DiversificAtion) (61) and ape (53).
T269 1210-1246 Sentence denotes Comparisons to SARS-CoV-2 phylogeny.
T270 1247-1494 Sentence denotes Phylogenies downsampled at 10% from the full (18,514 tips) SARS-CoV-2 genome phylogeny (following the subsampling strategy described above) were used to calculate the phylogenetic η for each subtree (above the root) for each downsampled phylogeny.
T271 1495-1660 Sentence denotes Neutral phylogenies were simulated under stochastic branching by randomly sampling from the distribution of branch lengths from one downsampled SARS-CoV-2 phylogeny.
T272 1661-1725 Sentence denotes This was iterated across all downsampled SARS-CoV-2 phylogenies.
T273 1726-1996 Sentence denotes Positive time-dependent phylogenies were simulated using a time-dependent process (b(t)=0.01eαt) for α = 0.001, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, and 1, with branch lengths restricted to the distribution of branch lengths from one downsampled SARS-CoV-2 phylogeny.
T274 1997-2072 Sentence denotes This was iterated across all downsampled SARS-CoV-2 phylogenies for each α.
T275 2073-2165 Sentence denotes Neutral and positive time-dependent phylogenies were simulated with a 10% sampling fraction.
T276 2166-2200 Sentence denotes Polytomies were randomly resolved.
T277 2201-2274 Sentence denotes Simulations were conducted using the R packages RPANDA (61) and ape (53).

2_test

Id Subject Object Predicate Lexical cue
32868447-26658901-132542431 389-391 26658901 denotes 36
32868447-31700680-132542432 393-395 31700680 denotes 37
32868447-30016406-132542433 1204-1206 30016406 denotes 53
32868447-30016406-132542434 2270-2272 30016406 denotes 53