PMC:7519301 / 43314-44378 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T121","span":{"begin":107,"end":113},"obj":"Body_part"}],"attributes":[{"id":"A121","pred":"fma_id","subj":"T121","obj":"http://purl.org/sig/ont/fma/fma84116"}],"text":"Comparisons to SARS-CoV-2 phylogeny.\nPhylogenies 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. Neutral phylogenies were simulated under stochastic branching by randomly sampling from the distribution of branch lengths from one downsampled SARS-CoV-2 phylogeny. This was iterated across all downsampled SARS-CoV-2 phylogenies. 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. This was iterated across all downsampled SARS-CoV-2 phylogenies for each α. Neutral and positive time-dependent phylogenies were simulated with a 10% sampling fraction. Polytomies were randomly resolved. Simulations were conducted using the R packages RPANDA (61) and ape (53)."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T182","span":{"begin":15,"end":23},"obj":"Disease"},{"id":"T183","span":{"begin":15,"end":19},"obj":"Disease"},{"id":"T184","span":{"begin":96,"end":104},"obj":"Disease"},{"id":"T185","span":{"begin":96,"end":100},"obj":"Disease"},{"id":"T186","span":{"begin":429,"end":437},"obj":"Disease"},{"id":"T187","span":{"begin":429,"end":433},"obj":"Disease"},{"id":"T188","span":{"begin":492,"end":500},"obj":"Disease"},{"id":"T189","span":{"begin":492,"end":496},"obj":"Disease"},{"id":"T190","span":{"begin":765,"end":773},"obj":"Disease"},{"id":"T191","span":{"begin":765,"end":769},"obj":"Disease"},{"id":"T192","span":{"begin":828,"end":836},"obj":"Disease"},{"id":"T193","span":{"begin":828,"end":832},"obj":"Disease"}],"attributes":[{"id":"A182","pred":"mondo_id","subj":"T182","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A183","pred":"mondo_id","subj":"T183","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A184","pred":"mondo_id","subj":"T184","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A185","pred":"mondo_id","subj":"T185","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A186","pred":"mondo_id","subj":"T186","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A187","pred":"mondo_id","subj":"T187","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A188","pred":"mondo_id","subj":"T188","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A189","pred":"mondo_id","subj":"T189","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A190","pred":"mondo_id","subj":"T190","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A191","pred":"mondo_id","subj":"T191","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A192","pred":"mondo_id","subj":"T192","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A193","pred":"mondo_id","subj":"T193","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"Comparisons to SARS-CoV-2 phylogeny.\nPhylogenies 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. Neutral phylogenies were simulated under stochastic branching by randomly sampling from the distribution of branch lengths from one downsampled SARS-CoV-2 phylogeny. This was iterated across all downsampled SARS-CoV-2 phylogenies. 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. This was iterated across all downsampled SARS-CoV-2 phylogenies for each α. Neutral and positive time-dependent phylogenies were simulated with a 10% sampling fraction. Polytomies were randomly resolved. Simulations were conducted using the R packages RPANDA (61) and ape (53)."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T311","span":{"begin":573,"end":574},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T312","span":{"begin":599,"end":603},"obj":"http://purl.obolibrary.org/obo/CLO_0002040"},{"id":"T313","span":{"begin":931,"end":935},"obj":"http://purl.obolibrary.org/obo/CLO_0001550"},{"id":"T314","span":{"begin":1055,"end":1058},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_314295"}],"text":"Comparisons to SARS-CoV-2 phylogeny.\nPhylogenies 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. Neutral phylogenies were simulated under stochastic branching by randomly sampling from the distribution of branch lengths from one downsampled SARS-CoV-2 phylogeny. This was iterated across all downsampled SARS-CoV-2 phylogenies. 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. This was iterated across all downsampled SARS-CoV-2 phylogenies for each α. Neutral and positive time-dependent phylogenies were simulated with a 10% sampling fraction. Polytomies were randomly resolved. Simulations were conducted using the R packages RPANDA (61) and ape (53)."}

{"project":"LitCovid-PubTator","denotations":[{"id":"507","span":{"begin":15,"end":25},"obj":"Species"},{"id":"513","span":{"begin":96,"end":106},"obj":"Species"},{"id":"514","span":{"begin":429,"end":439},"obj":"Species"},{"id":"515","span":{"begin":492,"end":502},"obj":"Species"},{"id":"516","span":{"begin":765,"end":775},"obj":"Species"},{"id":"517","span":{"begin":828,"end":838},"obj":"Species"}],"attributes":[{"id":"A507","pred":"tao:has_database_id","subj":"507","obj":"Tax:2697049"},{"id":"A513","pred":"tao:has_database_id","subj":"513","obj":"Tax:2697049"},{"id":"A514","pred":"tao:has_database_id","subj":"514","obj":"Tax:2697049"},{"id":"A515","pred":"tao:has_database_id","subj":"515","obj":"Tax:2697049"},{"id":"A516","pred":"tao:has_database_id","subj":"516","obj":"Tax:2697049"},{"id":"A517","pred":"tao:has_database_id","subj":"517","obj":"Tax:2697049"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"Comparisons to SARS-CoV-2 phylogeny.\nPhylogenies 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. Neutral phylogenies were simulated under stochastic branching by randomly sampling from the distribution of branch lengths from one downsampled SARS-CoV-2 phylogeny. This was iterated across all downsampled SARS-CoV-2 phylogenies. 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. This was iterated across all downsampled SARS-CoV-2 phylogenies for each α. Neutral and positive time-dependent phylogenies were simulated with a 10% sampling fraction. Polytomies were randomly resolved. Simulations were conducted using the R packages RPANDA (61) and ape (53)."}

{"project":"LitCovid-sentences","denotations":[{"id":"T269","span":{"begin":0,"end":36},"obj":"Sentence"},{"id":"T270","span":{"begin":37,"end":284},"obj":"Sentence"},{"id":"T271","span":{"begin":285,"end":450},"obj":"Sentence"},{"id":"T272","span":{"begin":451,"end":515},"obj":"Sentence"},{"id":"T273","span":{"begin":516,"end":786},"obj":"Sentence"},{"id":"T274","span":{"begin":787,"end":862},"obj":"Sentence"},{"id":"T275","span":{"begin":863,"end":955},"obj":"Sentence"},{"id":"T276","span":{"begin":956,"end":990},"obj":"Sentence"},{"id":"T277","span":{"begin":991,"end":1064},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Comparisons to SARS-CoV-2 phylogeny.\nPhylogenies 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. Neutral phylogenies were simulated under stochastic branching by randomly sampling from the distribution of branch lengths from one downsampled SARS-CoV-2 phylogeny. This was iterated across all downsampled SARS-CoV-2 phylogenies. 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. This was iterated across all downsampled SARS-CoV-2 phylogenies for each α. Neutral and positive time-dependent phylogenies were simulated with a 10% sampling fraction. Polytomies were randomly resolved. Simulations were conducted using the R packages RPANDA (61) and ape (53)."}

{"project":"2_test","denotations":[{"id":"32868447-30016406-132542434","span":{"begin":1060,"end":1062},"obj":"30016406"}],"text":"Comparisons to SARS-CoV-2 phylogeny.\nPhylogenies 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. Neutral phylogenies were simulated under stochastic branching by randomly sampling from the distribution of branch lengths from one downsampled SARS-CoV-2 phylogeny. This was iterated across all downsampled SARS-CoV-2 phylogenies. 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. This was iterated across all downsampled SARS-CoV-2 phylogenies for each α. Neutral and positive time-dependent phylogenies were simulated with a 10% sampling fraction. Polytomies were randomly resolved. Simulations were conducted using the R packages RPANDA (61) and ape (53)."}