PMC:7033698 / 7236-8142 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T56","span":{"begin":122,"end":126},"obj":"Body_part"},{"id":"T57","span":{"begin":429,"end":436},"obj":"Body_part"},{"id":"T58","span":{"begin":441,"end":444},"obj":"Body_part"},{"id":"T59","span":{"begin":742,"end":745},"obj":"Body_part"},{"id":"T60","span":{"begin":815,"end":817},"obj":"Body_part"},{"id":"T62","span":{"begin":818,"end":820},"obj":"Body_part"}],"attributes":[{"id":"A56","pred":"fma_id","subj":"T56","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A57","pred":"fma_id","subj":"T57","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A58","pred":"fma_id","subj":"T58","obj":"http://purl.org/sig/ont/fma/fma278683"},{"id":"A59","pred":"fma_id","subj":"T59","obj":"http://purl.org/sig/ont/fma/fma278683"},{"id":"A60","pred":"fma_id","subj":"T60","obj":"http://purl.org/sig/ont/fma/fma13444"},{"id":"A61","pred":"fma_id","subj":"T60","obj":"http://purl.org/sig/ont/fma/fma68614"},{"id":"A62","pred":"fma_id","subj":"T62","obj":"http://purl.org/sig/ont/fma/fma13443"},{"id":"A63","pred":"fma_id","subj":"T62","obj":"http://purl.org/sig/ont/fma/fma68615"}],"text":"Figure 1. Sequence and structure analysis of 2019-nCoV and bat coronaviruses. (A) Phylogenetic tree analysis of the spike gene sequences. (B) Sequence alignment of suspected insertion sites between the 2019-nCoV and bat coronavirus sequences. The deletions in the alignment are shown as dashes. The numbers of insertions are indicated at the top of the alignment. (C) Structure comparison of the four insertions in the CoV spike protein and HIV-1 gp120. 2019-nCoV structure was modelled using I-TASSER server with default parameters. Only relevant domains with residues 1 to 708 (exclude residues from 305 to 603) were presented as ribbon diagram. The four insertions were labelled and coloured in red, blue, green and magenta, respectively. HIV-1 gp120 structure (PDB 1GC1) is presented as ribbon diagram. V4, V5, V1/V2 and LE loops were labelled and coloured in red, blue, green, and black, respectively."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T73","span":{"begin":59,"end":62},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9397"},{"id":"T74","span":{"begin":79,"end":80},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T75","span":{"begin":122,"end":126},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T76","span":{"begin":139,"end":140},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T77","span":{"begin":216,"end":219},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9397"},{"id":"T78","span":{"begin":673,"end":681},"obj":"http://purl.obolibrary.org/obo/CLO_0007225"},{"id":"T79","span":{"begin":839,"end":847},"obj":"http://purl.obolibrary.org/obo/CLO_0007225"}],"text":"Figure 1. Sequence and structure analysis of 2019-nCoV and bat coronaviruses. (A) Phylogenetic tree analysis of the spike gene sequences. (B) Sequence alignment of suspected insertion sites between the 2019-nCoV and bat coronavirus sequences. The deletions in the alignment are shown as dashes. The numbers of insertions are indicated at the top of the alignment. (C) Structure comparison of the four insertions in the CoV spike protein and HIV-1 gp120. 2019-nCoV structure was modelled using I-TASSER server with default parameters. Only relevant domains with residues 1 to 708 (exclude residues from 305 to 603) were presented as ribbon diagram. The four insertions were labelled and coloured in red, blue, green and magenta, respectively. HIV-1 gp120 structure (PDB 1GC1) is presented as ribbon diagram. V4, V5, V1/V2 and LE loops were labelled and coloured in red, blue, green, and black, respectively."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T12","span":{"begin":429,"end":436},"obj":"Chemical"},{"id":"T13","span":{"begin":719,"end":726},"obj":"Chemical"},{"id":"T14","span":{"begin":825,"end":827},"obj":"Chemical"}],"attributes":[{"id":"A12","pred":"chebi_id","subj":"T12","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A13","pred":"chebi_id","subj":"T13","obj":"http://purl.obolibrary.org/obo/CHEBI_87661"},{"id":"A14","pred":"chebi_id","subj":"T14","obj":"http://purl.obolibrary.org/obo/CHEBI_74531"}],"text":"Figure 1. Sequence and structure analysis of 2019-nCoV and bat coronaviruses. (A) Phylogenetic tree analysis of the spike gene sequences. (B) Sequence alignment of suspected insertion sites between the 2019-nCoV and bat coronavirus sequences. The deletions in the alignment are shown as dashes. The numbers of insertions are indicated at the top of the alignment. (C) Structure comparison of the four insertions in the CoV spike protein and HIV-1 gp120. 2019-nCoV structure was modelled using I-TASSER server with default parameters. Only relevant domains with residues 1 to 708 (exclude residues from 305 to 603) were presented as ribbon diagram. The four insertions were labelled and coloured in red, blue, green and magenta, respectively. HIV-1 gp120 structure (PDB 1GC1) is presented as ribbon diagram. V4, V5, V1/V2 and LE loops were labelled and coloured in red, blue, green, and black, respectively."}

{"project":"LitCovid-sentences","denotations":[{"id":"T61","span":{"begin":0,"end":9},"obj":"Sentence"},{"id":"T62","span":{"begin":10,"end":242},"obj":"Sentence"},{"id":"T63","span":{"begin":243,"end":294},"obj":"Sentence"},{"id":"T64","span":{"begin":295,"end":453},"obj":"Sentence"},{"id":"T65","span":{"begin":454,"end":533},"obj":"Sentence"},{"id":"T66","span":{"begin":534,"end":647},"obj":"Sentence"},{"id":"T67","span":{"begin":648,"end":741},"obj":"Sentence"},{"id":"T68","span":{"begin":742,"end":806},"obj":"Sentence"},{"id":"T69","span":{"begin":807,"end":906},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Figure 1. Sequence and structure analysis of 2019-nCoV and bat coronaviruses. (A) Phylogenetic tree analysis of the spike gene sequences. (B) Sequence alignment of suspected insertion sites between the 2019-nCoV and bat coronavirus sequences. The deletions in the alignment are shown as dashes. The numbers of insertions are indicated at the top of the alignment. (C) Structure comparison of the four insertions in the CoV spike protein and HIV-1 gp120. 2019-nCoV structure was modelled using I-TASSER server with default parameters. Only relevant domains with residues 1 to 708 (exclude residues from 305 to 603) were presented as ribbon diagram. The four insertions were labelled and coloured in red, blue, green and magenta, respectively. HIV-1 gp120 structure (PDB 1GC1) is presented as ribbon diagram. V4, V5, V1/V2 and LE loops were labelled and coloured in red, blue, green, and black, respectively."}

{"project":"LitCovid-PubTator","denotations":[{"id":"171","span":{"begin":116,"end":121},"obj":"Gene"},{"id":"172","span":{"begin":447,"end":452},"obj":"Gene"},{"id":"173","span":{"begin":748,"end":753},"obj":"Gene"},{"id":"174","span":{"begin":423,"end":428},"obj":"Gene"},{"id":"175","span":{"begin":45,"end":54},"obj":"Species"},{"id":"176","span":{"begin":63,"end":76},"obj":"Species"},{"id":"177","span":{"begin":202,"end":211},"obj":"Species"},{"id":"178","span":{"begin":216,"end":231},"obj":"Species"},{"id":"179","span":{"begin":419,"end":422},"obj":"Species"},{"id":"180","span":{"begin":441,"end":446},"obj":"Species"},{"id":"181","span":{"begin":454,"end":463},"obj":"Species"},{"id":"182","span":{"begin":742,"end":747},"obj":"Species"},{"id":"183","span":{"begin":174,"end":183},"obj":"Species"}],"attributes":[{"id":"A171","pred":"tao:has_database_id","subj":"171","obj":"Gene:43740568"},{"id":"A172","pred":"tao:has_database_id","subj":"172","obj":"Gene:3700"},{"id":"A173","pred":"tao:has_database_id","subj":"173","obj":"Gene:3700"},{"id":"A174","pred":"tao:has_database_id","subj":"174","obj":"Gene:43740568"},{"id":"A175","pred":"tao:has_database_id","subj":"175","obj":"Tax:2697049"},{"id":"A176","pred":"tao:has_database_id","subj":"176","obj":"Tax:11118"},{"id":"A177","pred":"tao:has_database_id","subj":"177","obj":"Tax:2697049"},{"id":"A178","pred":"tao:has_database_id","subj":"178","obj":"Tax:1508220"},{"id":"A179","pred":"tao:has_database_id","subj":"179","obj":"Tax:11118"},{"id":"A180","pred":"tao:has_database_id","subj":"180","obj":"Tax:11676"},{"id":"A181","pred":"tao:has_database_id","subj":"181","obj":"Tax:2697049"},{"id":"A182","pred":"tao:has_database_id","subj":"182","obj":"Tax:11676"},{"id":"A183","pred":"tao:has_database_id","subj":"183","obj":"Tax:2673"}],"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":"Figure 1. Sequence and structure analysis of 2019-nCoV and bat coronaviruses. (A) Phylogenetic tree analysis of the spike gene sequences. (B) Sequence alignment of suspected insertion sites between the 2019-nCoV and bat coronavirus sequences. The deletions in the alignment are shown as dashes. The numbers of insertions are indicated at the top of the alignment. (C) Structure comparison of the four insertions in the CoV spike protein and HIV-1 gp120. 2019-nCoV structure was modelled using I-TASSER server with default parameters. Only relevant domains with residues 1 to 708 (exclude residues from 305 to 603) were presented as ribbon diagram. The four insertions were labelled and coloured in red, blue, green and magenta, respectively. HIV-1 gp120 structure (PDB 1GC1) is presented as ribbon diagram. V4, V5, V1/V2 and LE loops were labelled and coloured in red, blue, green, and black, respectively."}