PMC:7519301 / 35757-36322 JSONTXT

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T3","span":{"begin":382,"end":385},"obj":"Body_part"}],"attributes":[{"id":"A3","pred":"uberon_id","subj":"T3","obj":"http://purl.obolibrary.org/obo/UBERON_2001840"}],"text":"To identify individual sequences that were much more divergent than expected, given their sampling date, which likely reflected sequencing artifacts rather than evolution, we obtained a tree using FastTree v2.10.1 compiled with double precision under the general time reversible (GTR) model with gamma heterogeneity (51). This tree was rooted at the reference sequence, and root-to-tip regression was performed following TempEst using the ape package in R (52, 53). Outliers were defined as sequences that had studentized residuals greater than 3, and were removed."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T279","span":{"begin":184,"end":185},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T280","span":{"begin":439,"end":442},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_314295"},{"id":"T281","span":{"begin":457,"end":459},"obj":"http://purl.obolibrary.org/obo/CLO_0001407"}],"text":"To identify individual sequences that were much more divergent than expected, given their sampling date, which likely reflected sequencing artifacts rather than evolution, we obtained a tree using FastTree v2.10.1 compiled with double precision under the general time reversible (GTR) model with gamma heterogeneity (51). This tree was rooted at the reference sequence, and root-to-tip regression was performed following TempEst using the ape package in R (52, 53). Outliers were defined as sequences that had studentized residuals greater than 3, and were removed."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T97","span":{"begin":296,"end":301},"obj":"Chemical"}],"attributes":[{"id":"A97","pred":"chebi_id","subj":"T97","obj":"http://purl.obolibrary.org/obo/CHEBI_30212"}],"text":"To identify individual sequences that were much more divergent than expected, given their sampling date, which likely reflected sequencing artifacts rather than evolution, we obtained a tree using FastTree v2.10.1 compiled with double precision under the general time reversible (GTR) model with gamma heterogeneity (51). This tree was rooted at the reference sequence, and root-to-tip regression was performed following TempEst using the ape package in R (52, 53). Outliers were defined as sequences that had studentized residuals greater than 3, and were removed."}

{"project":"LitCovid-sentences","denotations":[{"id":"T217","span":{"begin":0,"end":321},"obj":"Sentence"},{"id":"T218","span":{"begin":322,"end":465},"obj":"Sentence"},{"id":"T219","span":{"begin":466,"end":565},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"To identify individual sequences that were much more divergent than expected, given their sampling date, which likely reflected sequencing artifacts rather than evolution, we obtained a tree using FastTree v2.10.1 compiled with double precision under the general time reversible (GTR) model with gamma heterogeneity (51). This tree was rooted at the reference sequence, and root-to-tip regression was performed following TempEst using the ape package in R (52, 53). Outliers were defined as sequences that had studentized residuals greater than 3, and were removed."}

{"project":"2_test","denotations":[{"id":"32868447-20224823-132542413","span":{"begin":317,"end":319},"obj":"20224823"},{"id":"32868447-27774300-132542414","span":{"begin":457,"end":459},"obj":"27774300"},{"id":"32868447-30016406-132542415","span":{"begin":461,"end":463},"obj":"30016406"}],"text":"To identify individual sequences that were much more divergent than expected, given their sampling date, which likely reflected sequencing artifacts rather than evolution, we obtained a tree using FastTree v2.10.1 compiled with double precision under the general time reversible (GTR) model with gamma heterogeneity (51). This tree was rooted at the reference sequence, and root-to-tip regression was performed following TempEst using the ape package in R (52, 53). Outliers were defined as sequences that had studentized residuals greater than 3, and were removed."}