PMC:7519301 / 44425-45562 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T123","span":{"begin":12,"end":19},"obj":"Body_part"},{"id":"T124","span":{"begin":57,"end":67},"obj":"Body_part"},{"id":"T125","span":{"begin":608,"end":619},"obj":"Body_part"},{"id":"T126","span":{"begin":637,"end":647},"obj":"Body_part"},{"id":"T127","span":{"begin":965,"end":972},"obj":"Body_part"}],"attributes":[{"id":"A123","pred":"fma_id","subj":"T123","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A124","pred":"fma_id","subj":"T124","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A125","pred":"fma_id","subj":"T125","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A126","pred":"fma_id","subj":"T126","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A127","pred":"fma_id","subj":"T127","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"Ancestral S protein sequences were reconstructed from an amino acid alignment of 30 SARS-CoV-2 sequences sampled from the Hubei province, a coronavirus sampled from bat (Yunnan RaTG13), and six SARS-CoV-2-like coronaviruses sampled from pangolins using maximum posterior probability and returning a unique residue at each site assuming a Jones-Taylor-Thornton (JTT) model with gamma heterogeneity (62). The JTT model was the most appropriate model available in the software (62). The bat sequence was retrieved from GenBank, and the pangolin sequences were retrieved from GISAID (63). A sliding window of 10 amino acids (and a step of 1 amino acid) was used to compare the cumulative number of mutations in the human−bat and human−bat−pangolin ancestors with respect to the human ancestral sequence. Median values for each window were compared to a null window (computed as a normal distribution of 10 values with a mean equal to the mean value across the entire S protein, 0.046 mutations) using a one-tailed t test. An alignment including the reconstructed sequences is available at https://www.hivresearch.org/publication-supplements."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T194","span":{"begin":84,"end":92},"obj":"Disease"},{"id":"T195","span":{"begin":84,"end":88},"obj":"Disease"},{"id":"T196","span":{"begin":194,"end":202},"obj":"Disease"},{"id":"T197","span":{"begin":194,"end":198},"obj":"Disease"}],"attributes":[{"id":"A194","pred":"mondo_id","subj":"T194","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A195","pred":"mondo_id","subj":"T195","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A196","pred":"mondo_id","subj":"T196","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A197","pred":"mondo_id","subj":"T197","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"Ancestral S protein sequences were reconstructed from an amino acid alignment of 30 SARS-CoV-2 sequences sampled from the Hubei province, a coronavirus sampled from bat (Yunnan RaTG13), and six SARS-CoV-2-like coronaviruses sampled from pangolins using maximum posterior probability and returning a unique residue at each site assuming a Jones-Taylor-Thornton (JTT) model with gamma heterogeneity (62). The JTT model was the most appropriate model available in the software (62). The bat sequence was retrieved from GenBank, and the pangolin sequences were retrieved from GISAID (63). A sliding window of 10 amino acids (and a step of 1 amino acid) was used to compare the cumulative number of mutations in the human−bat and human−bat−pangolin ancestors with respect to the human ancestral sequence. Median values for each window were compared to a null window (computed as a normal distribution of 10 values with a mean equal to the mean value across the entire S protein, 0.046 mutations) using a one-tailed t test. An alignment including the reconstructed sequences is available at https://www.hivresearch.org/publication-supplements."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T315","span":{"begin":138,"end":139},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T316","span":{"begin":165,"end":168},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9397"},{"id":"T317","span":{"begin":261,"end":270},"obj":"http://purl.obolibrary.org/obo/UBERON_0001353"},{"id":"T318","span":{"begin":297,"end":298},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T319","span":{"begin":336,"end":337},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T320","span":{"begin":484,"end":487},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9397"},{"id":"T321","span":{"begin":585,"end":586},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T322","span":{"begin":625,"end":626},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T323","span":{"begin":711,"end":716},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T324","span":{"begin":717,"end":720},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9397"},{"id":"T325","span":{"begin":725,"end":730},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T326","span":{"begin":731,"end":734},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9397"},{"id":"T327","span":{"begin":774,"end":779},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T328","span":{"begin":847,"end":848},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T329","span":{"begin":874,"end":875},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T330","span":{"begin":914,"end":915},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T331","span":{"begin":997,"end":998},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T332","span":{"begin":1003,"end":1009},"obj":"http://purl.obolibrary.org/obo/UBERON_0002415"},{"id":"T333","span":{"begin":1012,"end":1016},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"}],"text":"Ancestral S protein sequences were reconstructed from an amino acid alignment of 30 SARS-CoV-2 sequences sampled from the Hubei province, a coronavirus sampled from bat (Yunnan RaTG13), and six SARS-CoV-2-like coronaviruses sampled from pangolins using maximum posterior probability and returning a unique residue at each site assuming a Jones-Taylor-Thornton (JTT) model with gamma heterogeneity (62). The JTT model was the most appropriate model available in the software (62). The bat sequence was retrieved from GenBank, and the pangolin sequences were retrieved from GISAID (63). A sliding window of 10 amino acids (and a step of 1 amino acid) was used to compare the cumulative number of mutations in the human−bat and human−bat−pangolin ancestors with respect to the human ancestral sequence. Median values for each window were compared to a null window (computed as a normal distribution of 10 values with a mean equal to the mean value across the entire S protein, 0.046 mutations) using a one-tailed t test. An alignment including the reconstructed sequences is available at https://www.hivresearch.org/publication-supplements."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T109","span":{"begin":12,"end":19},"obj":"Chemical"},{"id":"T110","span":{"begin":57,"end":67},"obj":"Chemical"},{"id":"T111","span":{"begin":57,"end":62},"obj":"Chemical"},{"id":"T112","span":{"begin":63,"end":67},"obj":"Chemical"},{"id":"T113","span":{"begin":377,"end":382},"obj":"Chemical"},{"id":"T114","span":{"begin":608,"end":619},"obj":"Chemical"},{"id":"T115","span":{"begin":608,"end":613},"obj":"Chemical"},{"id":"T116","span":{"begin":614,"end":619},"obj":"Chemical"},{"id":"T117","span":{"begin":637,"end":647},"obj":"Chemical"},{"id":"T118","span":{"begin":637,"end":642},"obj":"Chemical"},{"id":"T119","span":{"begin":643,"end":647},"obj":"Chemical"},{"id":"T120","span":{"begin":965,"end":972},"obj":"Chemical"}],"attributes":[{"id":"A109","pred":"chebi_id","subj":"T109","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A110","pred":"chebi_id","subj":"T110","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"},{"id":"A111","pred":"chebi_id","subj":"T111","obj":"http://purl.obolibrary.org/obo/CHEBI_46882"},{"id":"A112","pred":"chebi_id","subj":"T112","obj":"http://purl.obolibrary.org/obo/CHEBI_37527"},{"id":"A113","pred":"chebi_id","subj":"T113","obj":"http://purl.obolibrary.org/obo/CHEBI_30212"},{"id":"A114","pred":"chebi_id","subj":"T114","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"},{"id":"A115","pred":"chebi_id","subj":"T115","obj":"http://purl.obolibrary.org/obo/CHEBI_46882"},{"id":"A116","pred":"chebi_id","subj":"T116","obj":"http://purl.obolibrary.org/obo/CHEBI_37527"},{"id":"A117","pred":"chebi_id","subj":"T117","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"},{"id":"A118","pred":"chebi_id","subj":"T118","obj":"http://purl.obolibrary.org/obo/CHEBI_46882"},{"id":"A119","pred":"chebi_id","subj":"T119","obj":"http://purl.obolibrary.org/obo/CHEBI_37527"},{"id":"A120","pred":"chebi_id","subj":"T120","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"}],"text":"Ancestral S protein sequences were reconstructed from an amino acid alignment of 30 SARS-CoV-2 sequences sampled from the Hubei province, a coronavirus sampled from bat (Yunnan RaTG13), and six SARS-CoV-2-like coronaviruses sampled from pangolins using maximum posterior probability and returning a unique residue at each site assuming a Jones-Taylor-Thornton (JTT) model with gamma heterogeneity (62). The JTT model was the most appropriate model available in the software (62). The bat sequence was retrieved from GenBank, and the pangolin sequences were retrieved from GISAID (63). A sliding window of 10 amino acids (and a step of 1 amino acid) was used to compare the cumulative number of mutations in the human−bat and human−bat−pangolin ancestors with respect to the human ancestral sequence. Median values for each window were compared to a null window (computed as a normal distribution of 10 values with a mean equal to the mean value across the entire S protein, 0.046 mutations) using a one-tailed t test. An alignment including the reconstructed sequences is available at https://www.hivresearch.org/publication-supplements."}

{"project":"LitCovid-PubTator","denotations":[{"id":"528","span":{"begin":10,"end":11},"obj":"Gene"},{"id":"529","span":{"begin":84,"end":94},"obj":"Species"},{"id":"530","span":{"begin":140,"end":151},"obj":"Species"},{"id":"531","span":{"begin":194,"end":204},"obj":"Species"},{"id":"532","span":{"begin":210,"end":223},"obj":"Species"},{"id":"533","span":{"begin":711,"end":716},"obj":"Species"},{"id":"534","span":{"begin":725,"end":730},"obj":"Species"},{"id":"535","span":{"begin":774,"end":779},"obj":"Species"}],"attributes":[{"id":"A528","pred":"tao:has_database_id","subj":"528","obj":"Gene:43740568"},{"id":"A529","pred":"tao:has_database_id","subj":"529","obj":"Tax:2697049"},{"id":"A530","pred":"tao:has_database_id","subj":"530","obj":"Tax:11118"},{"id":"A531","pred":"tao:has_database_id","subj":"531","obj":"Tax:2697049"},{"id":"A532","pred":"tao:has_database_id","subj":"532","obj":"Tax:11118"},{"id":"A533","pred":"tao:has_database_id","subj":"533","obj":"Tax:9606"},{"id":"A534","pred":"tao:has_database_id","subj":"534","obj":"Tax:9606"},{"id":"A535","pred":"tao:has_database_id","subj":"535","obj":"Tax:9606"}],"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":"Ancestral S protein sequences were reconstructed from an amino acid alignment of 30 SARS-CoV-2 sequences sampled from the Hubei province, a coronavirus sampled from bat (Yunnan RaTG13), and six SARS-CoV-2-like coronaviruses sampled from pangolins using maximum posterior probability and returning a unique residue at each site assuming a Jones-Taylor-Thornton (JTT) model with gamma heterogeneity (62). The JTT model was the most appropriate model available in the software (62). The bat sequence was retrieved from GenBank, and the pangolin sequences were retrieved from GISAID (63). A sliding window of 10 amino acids (and a step of 1 amino acid) was used to compare the cumulative number of mutations in the human−bat and human−bat−pangolin ancestors with respect to the human ancestral sequence. Median values for each window were compared to a null window (computed as a normal distribution of 10 values with a mean equal to the mean value across the entire S protein, 0.046 mutations) using a one-tailed t test. An alignment including the reconstructed sequences is available at https://www.hivresearch.org/publication-supplements."}

{"project":"LitCovid-sentences","denotations":[{"id":"T279","span":{"begin":0,"end":402},"obj":"Sentence"},{"id":"T280","span":{"begin":403,"end":479},"obj":"Sentence"},{"id":"T281","span":{"begin":480,"end":584},"obj":"Sentence"},{"id":"T282","span":{"begin":585,"end":799},"obj":"Sentence"},{"id":"T283","span":{"begin":800,"end":1017},"obj":"Sentence"},{"id":"T284","span":{"begin":1018,"end":1137},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Ancestral S protein sequences were reconstructed from an amino acid alignment of 30 SARS-CoV-2 sequences sampled from the Hubei province, a coronavirus sampled from bat (Yunnan RaTG13), and six SARS-CoV-2-like coronaviruses sampled from pangolins using maximum posterior probability and returning a unique residue at each site assuming a Jones-Taylor-Thornton (JTT) model with gamma heterogeneity (62). The JTT model was the most appropriate model available in the software (62). The bat sequence was retrieved from GenBank, and the pangolin sequences were retrieved from GISAID (63). A sliding window of 10 amino acids (and a step of 1 amino acid) was used to compare the cumulative number of mutations in the human−bat and human−bat−pangolin ancestors with respect to the human ancestral sequence. Median values for each window were compared to a null window (computed as a normal distribution of 10 values with a mean equal to the mean value across the entire S protein, 0.046 mutations) using a one-tailed t test. An alignment including the reconstructed sequences is available at https://www.hivresearch.org/publication-supplements."}

{"project":"2_test","denotations":[{"id":"32868447-10833195-132542435","span":{"begin":398,"end":400},"obj":"10833195"},{"id":"32868447-10833195-132542436","span":{"begin":475,"end":477},"obj":"10833195"},{"id":"32868447-31565258-132542437","span":{"begin":580,"end":582},"obj":"31565258"}],"text":"Ancestral S protein sequences were reconstructed from an amino acid alignment of 30 SARS-CoV-2 sequences sampled from the Hubei province, a coronavirus sampled from bat (Yunnan RaTG13), and six SARS-CoV-2-like coronaviruses sampled from pangolins using maximum posterior probability and returning a unique residue at each site assuming a Jones-Taylor-Thornton (JTT) model with gamma heterogeneity (62). The JTT model was the most appropriate model available in the software (62). The bat sequence was retrieved from GenBank, and the pangolin sequences were retrieved from GISAID (63). A sliding window of 10 amino acids (and a step of 1 amino acid) was used to compare the cumulative number of mutations in the human−bat and human−bat−pangolin ancestors with respect to the human ancestral sequence. Median values for each window were compared to a null window (computed as a normal distribution of 10 values with a mean equal to the mean value across the entire S protein, 0.046 mutations) using a one-tailed t test. An alignment including the reconstructed sequences is available at https://www.hivresearch.org/publication-supplements."}