PMC:7073332 / 38224-38876 JSONTXT

{"project":"LitCovid-PubTator","denotations":[{"id":"1087","span":{"begin":395,"end":398},"obj":"Gene"},{"id":"1088","span":{"begin":146,"end":155},"obj":"Species"},{"id":"1089","span":{"begin":156,"end":166},"obj":"Species"}],"attributes":[{"id":"A1087","pred":"tao:has_database_id","subj":"1087","obj":"Gene:6907"},{"id":"A1088","pred":"tao:has_database_id","subj":"1088","obj":"Tax:2697049"},{"id":"A1089","pred":"tao:has_database_id","subj":"1089","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":"Genome information and phylogenetic analysis\nIn total, we collected DNA sequences and protein sequences for 15 HCoVs, including three most recent 2019-nCoV/SARS-CoV-2 genomes, from the NCBI GenBank database (28 January 2020, Supplementary Table S1). Whole-genome alignment and protein sequence identity calculation were performed by Multiple Sequence Alignment in EMBL-EBI database (https://www.ebi.ac.uk/) with default parameters. The neighbor joining (NJ) tree was computed from the pairwise phylogenetic distance matrix using MEGA X84 with 1000 bootstrap replicates. The protein alignment and phylogenetic tree of HCoVs were constructed by MEGA X84."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T180","span":{"begin":0,"end":6},"obj":"Body_part"},{"id":"T181","span":{"begin":68,"end":71},"obj":"Body_part"},{"id":"T182","span":{"begin":86,"end":93},"obj":"Body_part"},{"id":"T183","span":{"begin":167,"end":174},"obj":"Body_part"},{"id":"T184","span":{"begin":256,"end":262},"obj":"Body_part"},{"id":"T185","span":{"begin":277,"end":284},"obj":"Body_part"},{"id":"T186","span":{"begin":574,"end":581},"obj":"Body_part"}],"attributes":[{"id":"A180","pred":"fma_id","subj":"T180","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A181","pred":"fma_id","subj":"T181","obj":"http://purl.org/sig/ont/fma/fma74412"},{"id":"A182","pred":"fma_id","subj":"T182","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A183","pred":"fma_id","subj":"T183","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A184","pred":"fma_id","subj":"T184","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A185","pred":"fma_id","subj":"T185","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A186","pred":"fma_id","subj":"T186","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"Genome information and phylogenetic analysis\nIn total, we collected DNA sequences and protein sequences for 15 HCoVs, including three most recent 2019-nCoV/SARS-CoV-2 genomes, from the NCBI GenBank database (28 January 2020, Supplementary Table S1). Whole-genome alignment and protein sequence identity calculation were performed by Multiple Sequence Alignment in EMBL-EBI database (https://www.ebi.ac.uk/) with default parameters. The neighbor joining (NJ) tree was computed from the pairwise phylogenetic distance matrix using MEGA X84 with 1000 bootstrap replicates. The protein alignment and phylogenetic tree of HCoVs were constructed by MEGA X84."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T157","span":{"begin":156,"end":164},"obj":"Disease"}],"attributes":[{"id":"A157","pred":"mondo_id","subj":"T157","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"Genome information and phylogenetic analysis\nIn total, we collected DNA sequences and protein sequences for 15 HCoVs, including three most recent 2019-nCoV/SARS-CoV-2 genomes, from the NCBI GenBank database (28 January 2020, Supplementary Table S1). Whole-genome alignment and protein sequence identity calculation were performed by Multiple Sequence Alignment in EMBL-EBI database (https://www.ebi.ac.uk/) with default parameters. The neighbor joining (NJ) tree was computed from the pairwise phylogenetic distance matrix using MEGA X84 with 1000 bootstrap replicates. The protein alignment and phylogenetic tree of HCoVs were constructed by MEGA X84."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T271","span":{"begin":245,"end":247},"obj":"http://purl.obolibrary.org/obo/CLO_0050050"}],"text":"Genome information and phylogenetic analysis\nIn total, we collected DNA sequences and protein sequences for 15 HCoVs, including three most recent 2019-nCoV/SARS-CoV-2 genomes, from the NCBI GenBank database (28 January 2020, Supplementary Table S1). Whole-genome alignment and protein sequence identity calculation were performed by Multiple Sequence Alignment in EMBL-EBI database (https://www.ebi.ac.uk/) with default parameters. The neighbor joining (NJ) tree was computed from the pairwise phylogenetic distance matrix using MEGA X84 with 1000 bootstrap replicates. The protein alignment and phylogenetic tree of HCoVs were constructed by MEGA X84."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T431","span":{"begin":68,"end":71},"obj":"Chemical"},{"id":"T432","span":{"begin":86,"end":93},"obj":"Chemical"},{"id":"T433","span":{"begin":277,"end":284},"obj":"Chemical"},{"id":"T434","span":{"begin":529,"end":533},"obj":"Chemical"},{"id":"T435","span":{"begin":574,"end":581},"obj":"Chemical"},{"id":"T436","span":{"begin":643,"end":647},"obj":"Chemical"}],"attributes":[{"id":"A431","pred":"chebi_id","subj":"T431","obj":"http://purl.obolibrary.org/obo/CHEBI_16991"},{"id":"A432","pred":"chebi_id","subj":"T432","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A433","pred":"chebi_id","subj":"T433","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A434","pred":"chebi_id","subj":"T434","obj":"http://purl.obolibrary.org/obo/CHEBI_6617"},{"id":"A435","pred":"chebi_id","subj":"T435","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A436","pred":"chebi_id","subj":"T436","obj":"http://purl.obolibrary.org/obo/CHEBI_6617"}],"text":"Genome information and phylogenetic analysis\nIn total, we collected DNA sequences and protein sequences for 15 HCoVs, including three most recent 2019-nCoV/SARS-CoV-2 genomes, from the NCBI GenBank database (28 January 2020, Supplementary Table S1). Whole-genome alignment and protein sequence identity calculation were performed by Multiple Sequence Alignment in EMBL-EBI database (https://www.ebi.ac.uk/) with default parameters. The neighbor joining (NJ) tree was computed from the pairwise phylogenetic distance matrix using MEGA X84 with 1000 bootstrap replicates. The protein alignment and phylogenetic tree of HCoVs were constructed by MEGA X84."}

{"project":"LitCovid-sentences","denotations":[{"id":"T235","span":{"begin":0,"end":44},"obj":"Sentence"},{"id":"T236","span":{"begin":45,"end":249},"obj":"Sentence"},{"id":"T237","span":{"begin":250,"end":431},"obj":"Sentence"},{"id":"T238","span":{"begin":432,"end":569},"obj":"Sentence"},{"id":"T239","span":{"begin":570,"end":652},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Genome information and phylogenetic analysis\nIn total, we collected DNA sequences and protein sequences for 15 HCoVs, including three most recent 2019-nCoV/SARS-CoV-2 genomes, from the NCBI GenBank database (28 January 2020, Supplementary Table S1). Whole-genome alignment and protein sequence identity calculation were performed by Multiple Sequence Alignment in EMBL-EBI database (https://www.ebi.ac.uk/) with default parameters. The neighbor joining (NJ) tree was computed from the pairwise phylogenetic distance matrix using MEGA X84 with 1000 bootstrap replicates. The protein alignment and phylogenetic tree of HCoVs were constructed by MEGA X84."}

{"project":"2_test","denotations":[{"id":"32194980-29722887-19614248","span":{"begin":535,"end":537},"obj":"29722887"},{"id":"32194980-29722887-19614249","span":{"begin":649,"end":651},"obj":"29722887"}],"text":"Genome information and phylogenetic analysis\nIn total, we collected DNA sequences and protein sequences for 15 HCoVs, including three most recent 2019-nCoV/SARS-CoV-2 genomes, from the NCBI GenBank database (28 January 2020, Supplementary Table S1). Whole-genome alignment and protein sequence identity calculation were performed by Multiple Sequence Alignment in EMBL-EBI database (https://www.ebi.ac.uk/) with default parameters. The neighbor joining (NJ) tree was computed from the pairwise phylogenetic distance matrix using MEGA X84 with 1000 bootstrap replicates. The protein alignment and phylogenetic tree of HCoVs were constructed by MEGA X84."}