PMC:7140597 / 4277-5193 JSONTXT

{"project":"LitCovid-PubTator","denotations":[{"id":"78","span":{"begin":24,"end":34},"obj":"Species"},{"id":"79","span":{"begin":152,"end":159},"obj":"Species"},{"id":"80","span":{"begin":251,"end":261},"obj":"Species"},{"id":"81","span":{"begin":73,"end":81},"obj":"Disease"}],"attributes":[{"id":"A78","pred":"tao:has_database_id","subj":"78","obj":"Tax:2697049"},{"id":"A79","pred":"tao:has_database_id","subj":"79","obj":"Tax:9606"},{"id":"A80","pred":"tao:has_database_id","subj":"80","obj":"Tax:2697049"},{"id":"A81","pred":"tao:has_database_id","subj":"81","obj":"MESH:D007239"}],"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":"To analyse the obtained SARS-CoV-2 genomes respectively derived from the infected Chinese tourist (GISAID accession ID: EPI_ISL_412974) and the Italian patient (GISAID accession ID: EPI_ISL_412973) in a phylogenetic context, a dataset of 40 available SARS-Cov-2 complete genomes from different countries was retrieved from GISAID (https://www.gisaid.org/, last access 2 March 2020; Supplementary material). Sequence alignment was performed using MUltiple Sequence Comparison by Log- Expectation (MUSCLE) software (http://www.clustal.org) [6]. Estimation of the best fitting substitution model (Hasegawa, Kishino, and Yano, HKY model) and inference of the phylogenetic tree were conducted by a maximum likelihood approach using Molecular Evolutionary Genetics Analysis across Computing Platforms (MEGA X; https://www.megasoftware.net/) [7]. Support for the tree topology was estimated with 1,000 bootstrap replicates."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T14","span":{"begin":35,"end":42},"obj":"Body_part"},{"id":"T15","span":{"begin":271,"end":278},"obj":"Body_part"}],"attributes":[{"id":"A14","pred":"fma_id","subj":"T14","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A15","pred":"fma_id","subj":"T15","obj":"http://purl.org/sig/ont/fma/fma84116"}],"text":"To analyse the obtained SARS-CoV-2 genomes respectively derived from the infected Chinese tourist (GISAID accession ID: EPI_ISL_412974) and the Italian patient (GISAID accession ID: EPI_ISL_412973) in a phylogenetic context, a dataset of 40 available SARS-Cov-2 complete genomes from different countries was retrieved from GISAID (https://www.gisaid.org/, last access 2 March 2020; Supplementary material). Sequence alignment was performed using MUltiple Sequence Comparison by Log- Expectation (MUSCLE) software (http://www.clustal.org) [6]. Estimation of the best fitting substitution model (Hasegawa, Kishino, and Yano, HKY model) and inference of the phylogenetic tree were conducted by a maximum likelihood approach using Molecular Evolutionary Genetics Analysis across Computing Platforms (MEGA X; https://www.megasoftware.net/) [7]. Support for the tree topology was estimated with 1,000 bootstrap replicates."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T15","span":{"begin":24,"end":32},"obj":"Disease"},{"id":"T16","span":{"begin":251,"end":255},"obj":"Disease"}],"attributes":[{"id":"A15","pred":"mondo_id","subj":"T15","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A16","pred":"mondo_id","subj":"T16","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"To analyse the obtained SARS-CoV-2 genomes respectively derived from the infected Chinese tourist (GISAID accession ID: EPI_ISL_412974) and the Italian patient (GISAID accession ID: EPI_ISL_412973) in a phylogenetic context, a dataset of 40 available SARS-Cov-2 complete genomes from different countries was retrieved from GISAID (https://www.gisaid.org/, last access 2 March 2020; Supplementary material). Sequence alignment was performed using MUltiple Sequence Comparison by Log- Expectation (MUSCLE) software (http://www.clustal.org) [6]. Estimation of the best fitting substitution model (Hasegawa, Kishino, and Yano, HKY model) and inference of the phylogenetic tree were conducted by a maximum likelihood approach using Molecular Evolutionary Genetics Analysis across Computing Platforms (MEGA X; https://www.megasoftware.net/) [7]. Support for the tree topology was estimated with 1,000 bootstrap replicates."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T21","span":{"begin":201,"end":202},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T22","span":{"begin":225,"end":226},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T23","span":{"begin":496,"end":502},"obj":"http://purl.obolibrary.org/obo/UBERON_0001630"},{"id":"T24","span":{"begin":496,"end":502},"obj":"http://purl.obolibrary.org/obo/UBERON_0005090"},{"id":"T25","span":{"begin":496,"end":502},"obj":"http://www.ebi.ac.uk/efo/EFO_0000801"},{"id":"T26","span":{"begin":496,"end":502},"obj":"http://www.ebi.ac.uk/efo/EFO_0001949"},{"id":"T27","span":{"begin":691,"end":692},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"To analyse the obtained SARS-CoV-2 genomes respectively derived from the infected Chinese tourist (GISAID accession ID: EPI_ISL_412974) and the Italian patient (GISAID accession ID: EPI_ISL_412973) in a phylogenetic context, a dataset of 40 available SARS-Cov-2 complete genomes from different countries was retrieved from GISAID (https://www.gisaid.org/, last access 2 March 2020; Supplementary material). Sequence alignment was performed using MUltiple Sequence Comparison by Log- Expectation (MUSCLE) software (http://www.clustal.org) [6]. Estimation of the best fitting substitution model (Hasegawa, Kishino, and Yano, HKY model) and inference of the phylogenetic tree were conducted by a maximum likelihood approach using Molecular Evolutionary Genetics Analysis across Computing Platforms (MEGA X; https://www.megasoftware.net/) [7]. Support for the tree topology was estimated with 1,000 bootstrap replicates."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T1","span":{"begin":116,"end":118},"obj":"Chemical"},{"id":"T2","span":{"begin":178,"end":180},"obj":"Chemical"},{"id":"T3","span":{"begin":796,"end":800},"obj":"Chemical"}],"attributes":[{"id":"A1","pred":"chebi_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/CHEBI_141439"},{"id":"A2","pred":"chebi_id","subj":"T2","obj":"http://purl.obolibrary.org/obo/CHEBI_141439"},{"id":"A3","pred":"chebi_id","subj":"T3","obj":"http://purl.obolibrary.org/obo/CHEBI_6617"}],"text":"To analyse the obtained SARS-CoV-2 genomes respectively derived from the infected Chinese tourist (GISAID accession ID: EPI_ISL_412974) and the Italian patient (GISAID accession ID: EPI_ISL_412973) in a phylogenetic context, a dataset of 40 available SARS-Cov-2 complete genomes from different countries was retrieved from GISAID (https://www.gisaid.org/, last access 2 March 2020; Supplementary material). Sequence alignment was performed using MUltiple Sequence Comparison by Log- Expectation (MUSCLE) software (http://www.clustal.org) [6]. Estimation of the best fitting substitution model (Hasegawa, Kishino, and Yano, HKY model) and inference of the phylogenetic tree were conducted by a maximum likelihood approach using Molecular Evolutionary Genetics Analysis across Computing Platforms (MEGA X; https://www.megasoftware.net/) [7]. Support for the tree topology was estimated with 1,000 bootstrap replicates."}

{"project":"LitCovid-sentences","denotations":[{"id":"T28","span":{"begin":0,"end":406},"obj":"Sentence"},{"id":"T29","span":{"begin":407,"end":542},"obj":"Sentence"},{"id":"T30","span":{"begin":543,"end":839},"obj":"Sentence"},{"id":"T31","span":{"begin":840,"end":916},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"To analyse the obtained SARS-CoV-2 genomes respectively derived from the infected Chinese tourist (GISAID accession ID: EPI_ISL_412974) and the Italian patient (GISAID accession ID: EPI_ISL_412973) in a phylogenetic context, a dataset of 40 available SARS-Cov-2 complete genomes from different countries was retrieved from GISAID (https://www.gisaid.org/, last access 2 March 2020; Supplementary material). Sequence alignment was performed using MUltiple Sequence Comparison by Log- Expectation (MUSCLE) software (http://www.clustal.org) [6]. Estimation of the best fitting substitution model (Hasegawa, Kishino, and Yano, HKY model) and inference of the phylogenetic tree were conducted by a maximum likelihood approach using Molecular Evolutionary Genetics Analysis across Computing Platforms (MEGA X; https://www.megasoftware.net/) [7]. Support for the tree topology was estimated with 1,000 bootstrap replicates."}

{"project":"MyTest","denotations":[{"id":"32265007-15318951-29331402","span":{"begin":539,"end":540},"obj":"15318951"},{"id":"32265007-29722887-29331403","span":{"begin":836,"end":837},"obj":"29722887"}],"namespaces":[{"prefix":"_base","uri":"https://www.uniprot.org/uniprot/testbase"},{"prefix":"UniProtKB","uri":"https://www.uniprot.org/uniprot/"},{"prefix":"uniprot","uri":"https://www.uniprot.org/uniprotkb/"}],"text":"To analyse the obtained SARS-CoV-2 genomes respectively derived from the infected Chinese tourist (GISAID accession ID: EPI_ISL_412974) and the Italian patient (GISAID accession ID: EPI_ISL_412973) in a phylogenetic context, a dataset of 40 available SARS-Cov-2 complete genomes from different countries was retrieved from GISAID (https://www.gisaid.org/, last access 2 March 2020; Supplementary material). Sequence alignment was performed using MUltiple Sequence Comparison by Log- Expectation (MUSCLE) software (http://www.clustal.org) [6]. Estimation of the best fitting substitution model (Hasegawa, Kishino, and Yano, HKY model) and inference of the phylogenetic tree were conducted by a maximum likelihood approach using Molecular Evolutionary Genetics Analysis across Computing Platforms (MEGA X; https://www.megasoftware.net/) [7]. Support for the tree topology was estimated with 1,000 bootstrap replicates."}

{"project":"2_test","denotations":[{"id":"32265007-15318951-29331402","span":{"begin":539,"end":540},"obj":"15318951"},{"id":"32265007-29722887-29331403","span":{"begin":836,"end":837},"obj":"29722887"}],"text":"To analyse the obtained SARS-CoV-2 genomes respectively derived from the infected Chinese tourist (GISAID accession ID: EPI_ISL_412974) and the Italian patient (GISAID accession ID: EPI_ISL_412973) in a phylogenetic context, a dataset of 40 available SARS-Cov-2 complete genomes from different countries was retrieved from GISAID (https://www.gisaid.org/, last access 2 March 2020; Supplementary material). Sequence alignment was performed using MUltiple Sequence Comparison by Log- Expectation (MUSCLE) software (http://www.clustal.org) [6]. Estimation of the best fitting substitution model (Hasegawa, Kishino, and Yano, HKY model) and inference of the phylogenetic tree were conducted by a maximum likelihood approach using Molecular Evolutionary Genetics Analysis across Computing Platforms (MEGA X; https://www.megasoftware.net/) [7]. Support for the tree topology was estimated with 1,000 bootstrap replicates."}

{"project":"LitCovid-PMC-OGER-BB","denotations":[{"id":"T40","span":{"begin":24,"end":34},"obj":"SP_7"},{"id":"T41","span":{"begin":35,"end":42},"obj":"SO:0001026"},{"id":"T42","span":{"begin":251,"end":261},"obj":"SP_7"},{"id":"T43","span":{"begin":271,"end":278},"obj":"SO:0001026"},{"id":"T44","span":{"begin":623,"end":626},"obj":"PR:Q8NBH2"},{"id":"T26369","span":{"begin":24,"end":34},"obj":"SP_7"},{"id":"T82884","span":{"begin":35,"end":42},"obj":"SO:0001026"},{"id":"T69016","span":{"begin":251,"end":261},"obj":"SP_7"},{"id":"T23094","span":{"begin":271,"end":278},"obj":"SO:0001026"},{"id":"T75860","span":{"begin":623,"end":626},"obj":"PR:Q8NBH2"}],"text":"To analyse the obtained SARS-CoV-2 genomes respectively derived from the infected Chinese tourist (GISAID accession ID: EPI_ISL_412974) and the Italian patient (GISAID accession ID: EPI_ISL_412973) in a phylogenetic context, a dataset of 40 available SARS-Cov-2 complete genomes from different countries was retrieved from GISAID (https://www.gisaid.org/, last access 2 March 2020; Supplementary material). Sequence alignment was performed using MUltiple Sequence Comparison by Log- Expectation (MUSCLE) software (http://www.clustal.org) [6]. Estimation of the best fitting substitution model (Hasegawa, Kishino, and Yano, HKY model) and inference of the phylogenetic tree were conducted by a maximum likelihood approach using Molecular Evolutionary Genetics Analysis across Computing Platforms (MEGA X; https://www.megasoftware.net/) [7]. Support for the tree topology was estimated with 1,000 bootstrap replicates."}