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    LitCovid-PubTator

    {"project":"LitCovid-PubTator","denotations":[{"id":"58","span":{"begin":664,"end":667},"obj":"Gene"},{"id":"59","span":{"begin":478,"end":481},"obj":"Gene"},{"id":"60","span":{"begin":175,"end":177},"obj":"Gene"},{"id":"61","span":{"begin":1393,"end":1396},"obj":"Gene"},{"id":"62","span":{"begin":1360,"end":1363},"obj":"Gene"},{"id":"63","span":{"begin":1318,"end":1321},"obj":"Gene"},{"id":"64","span":{"begin":1229,"end":1232},"obj":"Gene"},{"id":"65","span":{"begin":1132,"end":1135},"obj":"Gene"},{"id":"66","span":{"begin":1074,"end":1077},"obj":"Gene"},{"id":"67","span":{"begin":714,"end":717},"obj":"Gene"},{"id":"68","span":{"begin":660,"end":663},"obj":"Gene"},{"id":"69","span":{"begin":538,"end":541},"obj":"Gene"},{"id":"70","span":{"begin":421,"end":424},"obj":"Gene"},{"id":"71","span":{"begin":230,"end":233},"obj":"Gene"},{"id":"72","span":{"begin":68,"end":70},"obj":"Gene"},{"id":"73","span":{"begin":740,"end":745},"obj":"Gene"},{"id":"74","span":{"begin":579,"end":584},"obj":"Gene"},{"id":"75","span":{"begin":1096,"end":1100},"obj":"Gene"},{"id":"76","span":{"begin":482,"end":486},"obj":"Gene"},{"id":"77","span":{"begin":945,"end":949},"obj":"Gene"},{"id":"78","span":{"begin":1404,"end":1406},"obj":"Gene"},{"id":"79","span":{"begin":1254,"end":1256},"obj":"Gene"},{"id":"80","span":{"begin":772,"end":774},"obj":"Gene"},{"id":"81","span":{"begin":737,"end":739},"obj":"Gene"},{"id":"82","span":{"begin":657,"end":659},"obj":"Gene"},{"id":"83","span":{"begin":561,"end":563},"obj":"Gene"},{"id":"84","span":{"begin":519,"end":521},"obj":"Gene"},{"id":"85","span":{"begin":432,"end":434},"obj":"Gene"},{"id":"86","span":{"begin":107,"end":109},"obj":"Gene"},{"id":"87","span":{"begin":22,"end":24},"obj":"Gene"},{"id":"88","span":{"begin":139,"end":156},"obj":"Species"},{"id":"89","span":{"begin":178,"end":200},"obj":"Species"},{"id":"90","span":{"begin":202,"end":211},"obj":"Species"},{"id":"91","span":{"begin":323,"end":330},"obj":"Species"},{"id":"92","span":{"begin":391,"end":402},"obj":"Species"},{"id":"93","span":{"begin":435,"end":444},"obj":"Species"},{"id":"94","span":{"begin":528,"end":536},"obj":"Species"},{"id":"95","span":{"begin":685,"end":703},"obj":"Species"},{"id":"96","span":{"begin":775,"end":784},"obj":"Species"},{"id":"97","span":{"begin":832,"end":858},"obj":"Species"},{"id":"98","span":{"begin":1105,"end":1110},"obj":"Species"},{"id":"99","span":{"begin":1153,"end":1162},"obj":"Species"},{"id":"100","span":{"begin":1278,"end":1293},"obj":"Species"},{"id":"101","span":{"begin":34,"end":43},"obj":"Disease"},{"id":"102","span":{"begin":336,"end":355},"obj":"Disease"},{"id":"103","span":{"begin":1474,"end":1483},"obj":"Disease"}],"attributes":[{"id":"A58","pred":"tao:has_database_id","subj":"58","obj":"Gene:570"},{"id":"A59","pred":"tao:has_database_id","subj":"59","obj":"Gene:570"},{"id":"A60","pred":"tao:has_database_id","subj":"60","obj":"Gene:112935892"},{"id":"A61","pred":"tao:has_database_id","subj":"61","obj":"Gene:25085"},{"id":"A62","pred":"tao:has_database_id","subj":"62","obj":"Gene:25085"},{"id":"A63","pred":"tao:has_database_id","subj":"63","obj":"Gene:25085"},{"id":"A64","pred":"tao:has_database_id","subj":"64","obj":"Gene:25085"},{"id":"A65","pred":"tao:has_database_id","subj":"65","obj":"Gene:25085"},{"id":"A66","pred":"tao:has_database_id","subj":"66","obj":"Gene:25085"},{"id":"A67","pred":"tao:has_database_id","subj":"67","obj":"Gene:25085"},{"id":"A68","pred":"tao:has_database_id","subj":"68","obj":"Gene:25085"},{"id":"A69","pred":"tao:has_database_id","subj":"69","obj":"Gene:25085"},{"id":"A70","pred":"tao:has_database_id","subj":"70","obj":"Gene:25085"},{"id":"A71","pred":"tao:has_database_id","subj":"71","obj":"Gene:25085"},{"id":"A72","pred":"tao:has_database_id","subj":"72","obj":"Gene:6999"},{"id":"A73","pred":"tao:has_database_id","subj":"73","obj":"Gene:43740568"},{"id":"A74","pred":"tao:has_database_id","subj":"74","obj":"Gene:43740568"},{"id":"A75","pred":"tao:has_database_id","subj":"75","obj":"Gene:6301"},{"id":"A76","pred":"tao:has_database_id","subj":"76","obj":"Gene:6301"},{"id":"A77","pred":"tao:has_database_id","subj":"77","obj":"Gene:43740577"},{"id":"A78","pred":"tao:has_database_id","subj":"78","obj":"Gene:6688"},{"id":"A79","pred":"tao:has_database_id","subj":"79","obj":"Gene:6688"},{"id":"A80","pred":"tao:has_database_id","subj":"80","obj":"Gene:6688"},{"id":"A81","pred":"tao:has_database_id","subj":"81","obj":"Gene:6688"},{"id":"A82","pred":"tao:has_database_id","subj":"82","obj":"Gene:6688"},{"id":"A83","pred":"tao:has_database_id","subj":"83","obj":"Gene:6688"},{"id":"A84","pred":"tao:has_database_id","subj":"84","obj":"Gene:6688"},{"id":"A85","pred":"tao:has_database_id","subj":"85","obj":"Gene:6688"},{"id":"A86","pred":"tao:has_database_id","subj":"86","obj":"Gene:6688"},{"id":"A87","pred":"tao:has_database_id","subj":"87","obj":"Gene:6688"},{"id":"A88","pred":"tao:has_database_id","subj":"88","obj":"Tax:2697049"},{"id":"A89","pred":"tao:has_database_id","subj":"89","obj":"Tax:2697049"},{"id":"A90","pred":"tao:has_database_id","subj":"90","obj":"Tax:2697049"},{"id":"A91","pred":"tao:has_database_id","subj":"91","obj":"Tax:9606"},{"id":"A92","pred":"tao:has_database_id","subj":"92","obj":"Tax:11118"},{"id":"A93","pred":"tao:has_database_id","subj":"93","obj":"Tax:2697049"},{"id":"A94","pred":"tao:has_database_id","subj":"94","obj":"Tax:694009"},{"id":"A95","pred":"tao:has_database_id","subj":"95","obj":"Tax:694009"},{"id":"A96","pred":"tao:has_database_id","subj":"96","obj":"Tax:2697049"},{"id":"A97","pred":"tao:has_database_id","subj":"97","obj":"Tax:694009"},{"id":"A98","pred":"tao:has_database_id","subj":"98","obj":"Tax:9838"},{"id":"A99","pred":"tao:has_database_id","subj":"99","obj":"Tax:2697049"},{"id":"A100","pred":"tao:has_database_id","subj":"100","obj":"Tax:694002"},{"id":"A101","pred":"tao:has_database_id","subj":"101","obj":"MESH:D011014"},{"id":"A102","pred":"tao:has_database_id","subj":"102","obj":"MESH:C000657245"},{"id":"A103","pred":"tao:has_database_id","subj":"103","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":"A mysterious outbreak of atypical pneumonia in late 2019 was traced to a seafood wholesale market in Wuhan of China. Within a few weeks, a novel coronavirus tentatively named as 2019 novel coronavirus (2019-nCoV) was announced by the World Health Organization. We performed bioinformatics analysis on a virus genome from a patient with 2019-nCoV infection and compared it with other related coronavirus genomes. Overall, the genome of 2019-nCoV has 89% nucleotide identity with bat SARS-like-CoVZXC21 and 82% with that of human SARS-CoV. The phylogenetic trees of their orf1a/b, Spike, Envelope, Membrane and Nucleoprotein also clustered closely with those of the bat, civet and human SARS coronaviruses. However, the external subdomain of Spike’s receptor binding domain of 2019-nCoV shares only 40% amino acid identity with other SARS-related coronaviruses. Remarkably, its orf3b encodes a completely novel short protein. Furthermore, its new orf8 likely encodes a secreted protein with an alpha-helix, following with a beta-sheet(s) containing six strands. Learning from the roles of civet in SARS and camel in MERS, hunting for the animal source of 2019-nCoV and its more ancestral virus would be important for understanding the origin and evolution of this novel lineage B betacoronavirus. These findings provide the basis for starting further studies on the pathogenesis, and optimizing the design of diagnostic, antiviral and vaccination strategies for this emerging infection."}

    LitCovid-PD-FMA-UBERON

    {"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T1","span":{"begin":309,"end":315},"obj":"Body_part"},{"id":"T2","span":{"begin":403,"end":410},"obj":"Body_part"},{"id":"T3","span":{"begin":425,"end":431},"obj":"Body_part"},{"id":"T4","span":{"begin":453,"end":463},"obj":"Body_part"},{"id":"T5","span":{"begin":801,"end":811},"obj":"Body_part"},{"id":"T6","span":{"begin":915,"end":922},"obj":"Body_part"},{"id":"T7","span":{"begin":976,"end":983},"obj":"Body_part"},{"id":"T8","span":{"begin":998,"end":1003},"obj":"Body_part"}],"attributes":[{"id":"A1","pred":"fma_id","subj":"T1","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A2","pred":"fma_id","subj":"T2","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A3","pred":"fma_id","subj":"T3","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A4","pred":"fma_id","subj":"T4","obj":"http://purl.org/sig/ont/fma/fma82740"},{"id":"A5","pred":"fma_id","subj":"T5","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A6","pred":"fma_id","subj":"T6","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A7","pred":"fma_id","subj":"T7","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A8","pred":"fma_id","subj":"T8","obj":"http://purl.org/sig/ont/fma/fma60992"}],"text":"A mysterious outbreak of atypical pneumonia in late 2019 was traced to a seafood wholesale market in Wuhan of China. Within a few weeks, a novel coronavirus tentatively named as 2019 novel coronavirus (2019-nCoV) was announced by the World Health Organization. We performed bioinformatics analysis on a virus genome from a patient with 2019-nCoV infection and compared it with other related coronavirus genomes. Overall, the genome of 2019-nCoV has 89% nucleotide identity with bat SARS-like-CoVZXC21 and 82% with that of human SARS-CoV. The phylogenetic trees of their orf1a/b, Spike, Envelope, Membrane and Nucleoprotein also clustered closely with those of the bat, civet and human SARS coronaviruses. However, the external subdomain of Spike’s receptor binding domain of 2019-nCoV shares only 40% amino acid identity with other SARS-related coronaviruses. Remarkably, its orf3b encodes a completely novel short protein. Furthermore, its new orf8 likely encodes a secreted protein with an alpha-helix, following with a beta-sheet(s) containing six strands. Learning from the roles of civet in SARS and camel in MERS, hunting for the animal source of 2019-nCoV and its more ancestral virus would be important for understanding the origin and evolution of this novel lineage B betacoronavirus. These findings provide the basis for starting further studies on the pathogenesis, and optimizing the design of diagnostic, antiviral and vaccination strategies for this emerging infection."}

    LitCovid-PD-UBERON

    {"project":"LitCovid-PD-UBERON","denotations":[{"id":"T1","span":{"begin":998,"end":1003},"obj":"Body_part"}],"attributes":[{"id":"A1","pred":"uberon_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/UBERON_0002488"}],"text":"A mysterious outbreak of atypical pneumonia in late 2019 was traced to a seafood wholesale market in Wuhan of China. Within a few weeks, a novel coronavirus tentatively named as 2019 novel coronavirus (2019-nCoV) was announced by the World Health Organization. We performed bioinformatics analysis on a virus genome from a patient with 2019-nCoV infection and compared it with other related coronavirus genomes. Overall, the genome of 2019-nCoV has 89% nucleotide identity with bat SARS-like-CoVZXC21 and 82% with that of human SARS-CoV. The phylogenetic trees of their orf1a/b, Spike, Envelope, Membrane and Nucleoprotein also clustered closely with those of the bat, civet and human SARS coronaviruses. However, the external subdomain of Spike’s receptor binding domain of 2019-nCoV shares only 40% amino acid identity with other SARS-related coronaviruses. Remarkably, its orf3b encodes a completely novel short protein. Furthermore, its new orf8 likely encodes a secreted protein with an alpha-helix, following with a beta-sheet(s) containing six strands. Learning from the roles of civet in SARS and camel in MERS, hunting for the animal source of 2019-nCoV and its more ancestral virus would be important for understanding the origin and evolution of this novel lineage B betacoronavirus. These findings provide the basis for starting further studies on the pathogenesis, and optimizing the design of diagnostic, antiviral and vaccination strategies for this emerging infection."}

    LitCovid-PD-HP

    {"project":"LitCovid-PD-HP","denotations":[{"id":"T2","span":{"begin":34,"end":43},"obj":"Phenotype"}],"attributes":[{"id":"A2","pred":"hp_id","subj":"T2","obj":"http://purl.obolibrary.org/obo/HP_0002090"}],"text":"A mysterious outbreak of atypical pneumonia in late 2019 was traced to a seafood wholesale market in Wuhan of China. Within a few weeks, a novel coronavirus tentatively named as 2019 novel coronavirus (2019-nCoV) was announced by the World Health Organization. We performed bioinformatics analysis on a virus genome from a patient with 2019-nCoV infection and compared it with other related coronavirus genomes. Overall, the genome of 2019-nCoV has 89% nucleotide identity with bat SARS-like-CoVZXC21 and 82% with that of human SARS-CoV. The phylogenetic trees of their orf1a/b, Spike, Envelope, Membrane and Nucleoprotein also clustered closely with those of the bat, civet and human SARS coronaviruses. However, the external subdomain of Spike’s receptor binding domain of 2019-nCoV shares only 40% amino acid identity with other SARS-related coronaviruses. Remarkably, its orf3b encodes a completely novel short protein. Furthermore, its new orf8 likely encodes a secreted protein with an alpha-helix, following with a beta-sheet(s) containing six strands. Learning from the roles of civet in SARS and camel in MERS, hunting for the animal source of 2019-nCoV and its more ancestral virus would be important for understanding the origin and evolution of this novel lineage B betacoronavirus. These findings provide the basis for starting further studies on the pathogenesis, and optimizing the design of diagnostic, antiviral and vaccination strategies for this emerging infection."}

    LitCovid-PD-MONDO

    {"project":"LitCovid-PD-MONDO","denotations":[{"id":"T3","span":{"begin":34,"end":43},"obj":"Disease"},{"id":"T4","span":{"begin":336,"end":355},"obj":"Disease"},{"id":"T5","span":{"begin":346,"end":355},"obj":"Disease"},{"id":"T6","span":{"begin":482,"end":486},"obj":"Disease"},{"id":"T7","span":{"begin":528,"end":536},"obj":"Disease"},{"id":"T8","span":{"begin":685,"end":689},"obj":"Disease"},{"id":"T9","span":{"begin":832,"end":836},"obj":"Disease"},{"id":"T10","span":{"begin":1096,"end":1100},"obj":"Disease"},{"id":"T11","span":{"begin":1474,"end":1483},"obj":"Disease"}],"attributes":[{"id":"A3","pred":"mondo_id","subj":"T3","obj":"http://purl.obolibrary.org/obo/MONDO_0005249"},{"id":"A4","pred":"mondo_id","subj":"T4","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A5","pred":"mondo_id","subj":"T5","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A6","pred":"mondo_id","subj":"T6","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A7","pred":"mondo_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A8","pred":"mondo_id","subj":"T8","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A9","pred":"mondo_id","subj":"T9","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A10","pred":"mondo_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A11","pred":"mondo_id","subj":"T11","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"}],"text":"A mysterious outbreak of atypical pneumonia in late 2019 was traced to a seafood wholesale market in Wuhan of China. Within a few weeks, a novel coronavirus tentatively named as 2019 novel coronavirus (2019-nCoV) was announced by the World Health Organization. We performed bioinformatics analysis on a virus genome from a patient with 2019-nCoV infection and compared it with other related coronavirus genomes. Overall, the genome of 2019-nCoV has 89% nucleotide identity with bat SARS-like-CoVZXC21 and 82% with that of human SARS-CoV. The phylogenetic trees of their orf1a/b, Spike, Envelope, Membrane and Nucleoprotein also clustered closely with those of the bat, civet and human SARS coronaviruses. However, the external subdomain of Spike’s receptor binding domain of 2019-nCoV shares only 40% amino acid identity with other SARS-related coronaviruses. Remarkably, its orf3b encodes a completely novel short protein. Furthermore, its new orf8 likely encodes a secreted protein with an alpha-helix, following with a beta-sheet(s) containing six strands. Learning from the roles of civet in SARS and camel in MERS, hunting for the animal source of 2019-nCoV and its more ancestral virus would be important for understanding the origin and evolution of this novel lineage B betacoronavirus. These findings provide the basis for starting further studies on the pathogenesis, and optimizing the design of diagnostic, antiviral and vaccination strategies for this emerging infection."}

    LitCovid-PD-CLO

    {"project":"LitCovid-PD-CLO","denotations":[{"id":"T3","span":{"begin":0,"end":1},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T4","span":{"begin":71,"end":72},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T5","span":{"begin":124,"end":125},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T6","span":{"begin":137,"end":138},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T7","span":{"begin":247,"end":259},"obj":"http://purl.obolibrary.org/obo/OBI_0000245"},{"id":"T8","span":{"begin":301,"end":302},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T9","span":{"begin":303,"end":308},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T10","span":{"begin":321,"end":322},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T11","span":{"begin":445,"end":448},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T12","span":{"begin":478,"end":481},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9397"},{"id":"T13","span":{"begin":522,"end":527},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T14","span":{"begin":576,"end":577},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T15","span":{"begin":596,"end":604},"obj":"http://purl.obolibrary.org/obo/UBERON_0000158"},{"id":"T16","span":{"begin":664,"end":667},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9397"},{"id":"T17","span":{"begin":679,"end":684},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T18","span":{"begin":890,"end":891},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T19","span":{"begin":965,"end":966},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T20","span":{"begin":1020,"end":1021},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T21","span":{"begin":1105,"end":1110},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9837"},{"id":"T22","span":{"begin":1136,"end":1142},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_33208"},{"id":"T23","span":{"begin":1186,"end":1191},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T24","span":{"begin":1276,"end":1277},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"}],"text":"A mysterious outbreak of atypical pneumonia in late 2019 was traced to a seafood wholesale market in Wuhan of China. Within a few weeks, a novel coronavirus tentatively named as 2019 novel coronavirus (2019-nCoV) was announced by the World Health Organization. We performed bioinformatics analysis on a virus genome from a patient with 2019-nCoV infection and compared it with other related coronavirus genomes. Overall, the genome of 2019-nCoV has 89% nucleotide identity with bat SARS-like-CoVZXC21 and 82% with that of human SARS-CoV. The phylogenetic trees of their orf1a/b, Spike, Envelope, Membrane and Nucleoprotein also clustered closely with those of the bat, civet and human SARS coronaviruses. However, the external subdomain of Spike’s receptor binding domain of 2019-nCoV shares only 40% amino acid identity with other SARS-related coronaviruses. Remarkably, its orf3b encodes a completely novel short protein. Furthermore, its new orf8 likely encodes a secreted protein with an alpha-helix, following with a beta-sheet(s) containing six strands. Learning from the roles of civet in SARS and camel in MERS, hunting for the animal source of 2019-nCoV and its more ancestral virus would be important for understanding the origin and evolution of this novel lineage B betacoronavirus. These findings provide the basis for starting further studies on the pathogenesis, and optimizing the design of diagnostic, antiviral and vaccination strategies for this emerging infection."}

    LitCovid-PD-CHEBI

    {"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T3","span":{"begin":453,"end":463},"obj":"Chemical"},{"id":"T4","span":{"begin":801,"end":811},"obj":"Chemical"},{"id":"T5","span":{"begin":801,"end":806},"obj":"Chemical"},{"id":"T6","span":{"begin":807,"end":811},"obj":"Chemical"},{"id":"T7","span":{"begin":915,"end":922},"obj":"Chemical"},{"id":"T8","span":{"begin":976,"end":983},"obj":"Chemical"},{"id":"T9","span":{"begin":992,"end":997},"obj":"Chemical"},{"id":"T10","span":{"begin":1022,"end":1026},"obj":"Chemical"},{"id":"T11","span":{"begin":1419,"end":1428},"obj":"Chemical"}],"attributes":[{"id":"A3","pred":"chebi_id","subj":"T3","obj":"http://purl.obolibrary.org/obo/CHEBI_36976"},{"id":"A4","pred":"chebi_id","subj":"T4","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"},{"id":"A5","pred":"chebi_id","subj":"T5","obj":"http://purl.obolibrary.org/obo/CHEBI_46882"},{"id":"A6","pred":"chebi_id","subj":"T6","obj":"http://purl.obolibrary.org/obo/CHEBI_37527"},{"id":"A7","pred":"chebi_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A8","pred":"chebi_id","subj":"T8","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A9","pred":"chebi_id","subj":"T9","obj":"http://purl.obolibrary.org/obo/CHEBI_30216"},{"id":"A10","pred":"chebi_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/CHEBI_10545"},{"id":"A11","pred":"chebi_id","subj":"T11","obj":"http://purl.obolibrary.org/obo/CHEBI_22587"}],"text":"A mysterious outbreak of atypical pneumonia in late 2019 was traced to a seafood wholesale market in Wuhan of China. Within a few weeks, a novel coronavirus tentatively named as 2019 novel coronavirus (2019-nCoV) was announced by the World Health Organization. We performed bioinformatics analysis on a virus genome from a patient with 2019-nCoV infection and compared it with other related coronavirus genomes. Overall, the genome of 2019-nCoV has 89% nucleotide identity with bat SARS-like-CoVZXC21 and 82% with that of human SARS-CoV. The phylogenetic trees of their orf1a/b, Spike, Envelope, Membrane and Nucleoprotein also clustered closely with those of the bat, civet and human SARS coronaviruses. However, the external subdomain of Spike’s receptor binding domain of 2019-nCoV shares only 40% amino acid identity with other SARS-related coronaviruses. Remarkably, its orf3b encodes a completely novel short protein. Furthermore, its new orf8 likely encodes a secreted protein with an alpha-helix, following with a beta-sheet(s) containing six strands. Learning from the roles of civet in SARS and camel in MERS, hunting for the animal source of 2019-nCoV and its more ancestral virus would be important for understanding the origin and evolution of this novel lineage B betacoronavirus. These findings provide the basis for starting further studies on the pathogenesis, and optimizing the design of diagnostic, antiviral and vaccination strategies for this emerging infection."}

    LitCovid-PD-GO-BP

    {"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T1","span":{"begin":1060,"end":1068},"obj":"http://purl.obolibrary.org/obo/GO_0007612"},{"id":"T2","span":{"begin":1364,"end":1376},"obj":"http://purl.obolibrary.org/obo/GO_0009405"}],"text":"A mysterious outbreak of atypical pneumonia in late 2019 was traced to a seafood wholesale market in Wuhan of China. Within a few weeks, a novel coronavirus tentatively named as 2019 novel coronavirus (2019-nCoV) was announced by the World Health Organization. We performed bioinformatics analysis on a virus genome from a patient with 2019-nCoV infection and compared it with other related coronavirus genomes. Overall, the genome of 2019-nCoV has 89% nucleotide identity with bat SARS-like-CoVZXC21 and 82% with that of human SARS-CoV. The phylogenetic trees of their orf1a/b, Spike, Envelope, Membrane and Nucleoprotein also clustered closely with those of the bat, civet and human SARS coronaviruses. However, the external subdomain of Spike’s receptor binding domain of 2019-nCoV shares only 40% amino acid identity with other SARS-related coronaviruses. Remarkably, its orf3b encodes a completely novel short protein. Furthermore, its new orf8 likely encodes a secreted protein with an alpha-helix, following with a beta-sheet(s) containing six strands. Learning from the roles of civet in SARS and camel in MERS, hunting for the animal source of 2019-nCoV and its more ancestral virus would be important for understanding the origin and evolution of this novel lineage B betacoronavirus. These findings provide the basis for starting further studies on the pathogenesis, and optimizing the design of diagnostic, antiviral and vaccination strategies for this emerging infection."}

    LitCovid-sentences

    {"project":"LitCovid-sentences","denotations":[{"id":"T8","span":{"begin":0,"end":116},"obj":"Sentence"},{"id":"T9","span":{"begin":117,"end":260},"obj":"Sentence"},{"id":"T10","span":{"begin":261,"end":411},"obj":"Sentence"},{"id":"T11","span":{"begin":412,"end":537},"obj":"Sentence"},{"id":"T12","span":{"begin":538,"end":704},"obj":"Sentence"},{"id":"T13","span":{"begin":705,"end":859},"obj":"Sentence"},{"id":"T14","span":{"begin":860,"end":923},"obj":"Sentence"},{"id":"T15","span":{"begin":924,"end":1059},"obj":"Sentence"},{"id":"T16","span":{"begin":1060,"end":1294},"obj":"Sentence"},{"id":"T17","span":{"begin":1295,"end":1484},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"A mysterious outbreak of atypical pneumonia in late 2019 was traced to a seafood wholesale market in Wuhan of China. Within a few weeks, a novel coronavirus tentatively named as 2019 novel coronavirus (2019-nCoV) was announced by the World Health Organization. We performed bioinformatics analysis on a virus genome from a patient with 2019-nCoV infection and compared it with other related coronavirus genomes. Overall, the genome of 2019-nCoV has 89% nucleotide identity with bat SARS-like-CoVZXC21 and 82% with that of human SARS-CoV. The phylogenetic trees of their orf1a/b, Spike, Envelope, Membrane and Nucleoprotein also clustered closely with those of the bat, civet and human SARS coronaviruses. However, the external subdomain of Spike’s receptor binding domain of 2019-nCoV shares only 40% amino acid identity with other SARS-related coronaviruses. Remarkably, its orf3b encodes a completely novel short protein. Furthermore, its new orf8 likely encodes a secreted protein with an alpha-helix, following with a beta-sheet(s) containing six strands. Learning from the roles of civet in SARS and camel in MERS, hunting for the animal source of 2019-nCoV and its more ancestral virus would be important for understanding the origin and evolution of this novel lineage B betacoronavirus. These findings provide the basis for starting further studies on the pathogenesis, and optimizing the design of diagnostic, antiviral and vaccination strategies for this emerging infection."}