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LitCovid-PubTator

LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T31","span":{"begin":253,"end":259},"obj":"Body_part"},{"id":"T32","span":{"begin":395,"end":402},"obj":"Body_part"},{"id":"T33","span":{"begin":439,"end":449},"obj":"Body_part"},{"id":"T34","span":{"begin":570,"end":580},"obj":"Body_part"},{"id":"T35","span":{"begin":923,"end":930},"obj":"Body_part"},{"id":"T36","span":{"begin":1193,"end":1200},"obj":"Body_part"},{"id":"T37","span":{"begin":1520,"end":1526},"obj":"Body_part"}],"attributes":[{"id":"A31","pred":"fma_id","subj":"T31","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A32","pred":"fma_id","subj":"T32","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A33","pred":"fma_id","subj":"T33","obj":"http://purl.org/sig/ont/fma/fma82740"},{"id":"A34","pred":"fma_id","subj":"T34","obj":"http://purl.org/sig/ont/fma/fma82740"},{"id":"A35","pred":"fma_id","subj":"T35","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A36","pred":"fma_id","subj":"T36","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A37","pred":"fma_id","subj":"T37","obj":"http://purl.org/sig/ont/fma/fma84116"}],"text":"To date, seven pathogenic HCoVs (Fig. 2a, b) have been found:1,29 (i) 2019-nCoV/SARS-CoV-2, SARS-CoV, MERS-CoV, HCoV-OC43, and HCoV-HKU1 are β genera, and (ii) HCoV-NL63 and HCoV-229E are α genera. We performed the phylogenetic analyses using the whole-genome sequence data from 15 HCoVs to inspect the evolutionary relationship of 2019-nCoV/SARS-CoV-2 with other HCoVs. We found that the whole genomes of 2019-nCoV/SARS-CoV-2 had ~99.99% nucleotide sequence identity across three diagnosed patients (Supplementary Table S1). The 2019-nCoV/SARS-CoV-2 shares the highest nucleotide sequence identity (79.7%) with SARS-CoV among the six other known pathogenic HCoVs, revealing conserved evolutionary relationship between 2019-nCoV/SARS-CoV-2 and SARS-CoV (Fig. 2a).\nFig. 2 Phylogenetic analysis of coronaviruses.\na Phylogenetic tree of coronavirus (CoV). Phylogenetic algorithm analyzed evolutionary conservation among whole genomes of 15 coronaviruses. Red color highlights the recent emergent coronavirus, 2019-nCoV/SARS-CoV-2. Numbers on the branches indicate bootstrap support values. The scale shows the evolutionary distance computed using the p-distance method. b Schematic plot for HCoV genomes. The genus and host information of viruses was labeled on the left by different colors. Empty dark gray boxes represent accessory open reading frames (ORFs). c–e The 3D structures of SARS-CoV nsp12 (PDB ID: 6NUR) (c), spike (PDB ID: 6ACK) (d), and nucleocapsid (PDB ID: 2CJR) (e) shown were based on homology modeling. Genome information and phylogenetic analysis results are provided in Supplementary Tables S1 and S2."}

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T3","span":{"begin":1091,"end":1096},"obj":"Body_part"}],"attributes":[{"id":"A3","pred":"uberon_id","subj":"T3","obj":"http://purl.obolibrary.org/obo/UBERON_0002542"}],"text":"To date, seven pathogenic HCoVs (Fig. 2a, b) have been found:1,29 (i) 2019-nCoV/SARS-CoV-2, SARS-CoV, MERS-CoV, HCoV-OC43, and HCoV-HKU1 are β genera, and (ii) HCoV-NL63 and HCoV-229E are α genera. We performed the phylogenetic analyses using the whole-genome sequence data from 15 HCoVs to inspect the evolutionary relationship of 2019-nCoV/SARS-CoV-2 with other HCoVs. We found that the whole genomes of 2019-nCoV/SARS-CoV-2 had ~99.99% nucleotide sequence identity across three diagnosed patients (Supplementary Table S1). The 2019-nCoV/SARS-CoV-2 shares the highest nucleotide sequence identity (79.7%) with SARS-CoV among the six other known pathogenic HCoVs, revealing conserved evolutionary relationship between 2019-nCoV/SARS-CoV-2 and SARS-CoV (Fig. 2a).\nFig. 2 Phylogenetic analysis of coronaviruses.\na Phylogenetic tree of coronavirus (CoV). Phylogenetic algorithm analyzed evolutionary conservation among whole genomes of 15 coronaviruses. Red color highlights the recent emergent coronavirus, 2019-nCoV/SARS-CoV-2. Numbers on the branches indicate bootstrap support values. The scale shows the evolutionary distance computed using the p-distance method. b Schematic plot for HCoV genomes. The genus and host information of viruses was labeled on the left by different colors. Empty dark gray boxes represent accessory open reading frames (ORFs). c–e The 3D structures of SARS-CoV nsp12 (PDB ID: 6NUR) (c), spike (PDB ID: 6ACK) (d), and nucleocapsid (PDB ID: 2CJR) (e) shown were based on homology modeling. Genome information and phylogenetic analysis results are provided in Supplementary Tables S1 and S2."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T30","span":{"begin":80,"end":88},"obj":"Disease"},{"id":"T31","span":{"begin":92,"end":100},"obj":"Disease"},{"id":"T32","span":{"begin":342,"end":350},"obj":"Disease"},{"id":"T33","span":{"begin":416,"end":424},"obj":"Disease"},{"id":"T34","span":{"begin":540,"end":548},"obj":"Disease"},{"id":"T35","span":{"begin":612,"end":620},"obj":"Disease"},{"id":"T36","span":{"begin":729,"end":737},"obj":"Disease"},{"id":"T37","span":{"begin":744,"end":752},"obj":"Disease"},{"id":"T38","span":{"begin":1016,"end":1024},"obj":"Disease"},{"id":"T39","span":{"begin":1384,"end":1392},"obj":"Disease"}],"attributes":[{"id":"A30","pred":"mondo_id","subj":"T30","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A31","pred":"mondo_id","subj":"T31","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A32","pred":"mondo_id","subj":"T32","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A33","pred":"mondo_id","subj":"T33","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A34","pred":"mondo_id","subj":"T34","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A35","pred":"mondo_id","subj":"T35","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A36","pred":"mondo_id","subj":"T36","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A37","pred":"mondo_id","subj":"T37","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A38","pred":"mondo_id","subj":"T38","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A39","pred":"mondo_id","subj":"T39","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"To date, seven pathogenic HCoVs (Fig. 2a, b) have been found:1,29 (i) 2019-nCoV/SARS-CoV-2, SARS-CoV, MERS-CoV, HCoV-OC43, and HCoV-HKU1 are β genera, and (ii) HCoV-NL63 and HCoV-229E are α genera. We performed the phylogenetic analyses using the whole-genome sequence data from 15 HCoVs to inspect the evolutionary relationship of 2019-nCoV/SARS-CoV-2 with other HCoVs. We found that the whole genomes of 2019-nCoV/SARS-CoV-2 had ~99.99% nucleotide sequence identity across three diagnosed patients (Supplementary Table S1). The 2019-nCoV/SARS-CoV-2 shares the highest nucleotide sequence identity (79.7%) with SARS-CoV among the six other known pathogenic HCoVs, revealing conserved evolutionary relationship between 2019-nCoV/SARS-CoV-2 and SARS-CoV (Fig. 2a).\nFig. 2 Phylogenetic analysis of coronaviruses.\na Phylogenetic tree of coronavirus (CoV). Phylogenetic algorithm analyzed evolutionary conservation among whole genomes of 15 coronaviruses. Red color highlights the recent emergent coronavirus, 2019-nCoV/SARS-CoV-2. Numbers on the branches indicate bootstrap support values. The scale shows the evolutionary distance computed using the p-distance method. b Schematic plot for HCoV genomes. The genus and host information of viruses was labeled on the left by different colors. Empty dark gray boxes represent accessory open reading frames (ORFs). c–e The 3D structures of SARS-CoV nsp12 (PDB ID: 6NUR) (c), spike (PDB ID: 6ACK) (d), and nucleocapsid (PDB ID: 2CJR) (e) shown were based on homology modeling. Genome information and phylogenetic analysis results are provided in Supplementary Tables S1 and S2."}

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T59","span":{"begin":38,"end":40},"obj":"http://purl.obolibrary.org/obo/CLO_0001236"},{"id":"T60","span":{"begin":42,"end":43},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T61","span":{"begin":521,"end":523},"obj":"http://purl.obolibrary.org/obo/CLO_0050050"},{"id":"T62","span":{"begin":759,"end":761},"obj":"http://purl.obolibrary.org/obo/CLO_0001236"},{"id":"T63","span":{"begin":811,"end":812},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T64","span":{"begin":1167,"end":1168},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T65","span":{"begin":1236,"end":1243},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T66","span":{"begin":1248,"end":1255},"obj":"http://purl.obolibrary.org/obo/CLO_0007225"},{"id":"T67","span":{"begin":1610,"end":1612},"obj":"http://purl.obolibrary.org/obo/CLO_0050050"},{"id":"T68","span":{"begin":1617,"end":1619},"obj":"http://purl.obolibrary.org/obo/CLO_0008922"},{"id":"T69","span":{"begin":1617,"end":1619},"obj":"http://purl.obolibrary.org/obo/CLO_0050052"}],"text":"To date, seven pathogenic HCoVs (Fig. 2a, b) have been found:1,29 (i) 2019-nCoV/SARS-CoV-2, SARS-CoV, MERS-CoV, HCoV-OC43, and HCoV-HKU1 are β genera, and (ii) HCoV-NL63 and HCoV-229E are α genera. We performed the phylogenetic analyses using the whole-genome sequence data from 15 HCoVs to inspect the evolutionary relationship of 2019-nCoV/SARS-CoV-2 with other HCoVs. We found that the whole genomes of 2019-nCoV/SARS-CoV-2 had ~99.99% nucleotide sequence identity across three diagnosed patients (Supplementary Table S1). The 2019-nCoV/SARS-CoV-2 shares the highest nucleotide sequence identity (79.7%) with SARS-CoV among the six other known pathogenic HCoVs, revealing conserved evolutionary relationship between 2019-nCoV/SARS-CoV-2 and SARS-CoV (Fig. 2a).\nFig. 2 Phylogenetic analysis of coronaviruses.\na Phylogenetic tree of coronavirus (CoV). Phylogenetic algorithm analyzed evolutionary conservation among whole genomes of 15 coronaviruses. Red color highlights the recent emergent coronavirus, 2019-nCoV/SARS-CoV-2. Numbers on the branches indicate bootstrap support values. The scale shows the evolutionary distance computed using the p-distance method. b Schematic plot for HCoV genomes. The genus and host information of viruses was labeled on the left by different colors. Empty dark gray boxes represent accessory open reading frames (ORFs). c–e The 3D structures of SARS-CoV nsp12 (PDB ID: 6NUR) (c), spike (PDB ID: 6ACK) (d), and nucleocapsid (PDB ID: 2CJR) (e) shown were based on homology modeling. Genome information and phylogenetic analysis results are provided in Supplementary Tables S1 and S2."}

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T90","span":{"begin":439,"end":449},"obj":"Chemical"},{"id":"T91","span":{"begin":570,"end":580},"obj":"Chemical"},{"id":"T92","span":{"begin":1404,"end":1406},"obj":"Chemical"},{"id":"T93","span":{"begin":1430,"end":1432},"obj":"Chemical"},{"id":"T94","span":{"begin":1467,"end":1469},"obj":"Chemical"},{"id":"T95","span":{"begin":1617,"end":1619},"obj":"Chemical"}],"attributes":[{"id":"A90","pred":"chebi_id","subj":"T90","obj":"http://purl.obolibrary.org/obo/CHEBI_36976"},{"id":"A91","pred":"chebi_id","subj":"T91","obj":"http://purl.obolibrary.org/obo/CHEBI_36976"},{"id":"A92","pred":"chebi_id","subj":"T92","obj":"http://purl.obolibrary.org/obo/CHEBI_141439"},{"id":"A93","pred":"chebi_id","subj":"T93","obj":"http://purl.obolibrary.org/obo/CHEBI_141439"},{"id":"A94","pred":"chebi_id","subj":"T94","obj":"http://purl.obolibrary.org/obo/CHEBI_141439"},{"id":"A95","pred":"chebi_id","subj":"T95","obj":"http://purl.obolibrary.org/obo/CHEBI_29387"}],"text":"To date, seven pathogenic HCoVs (Fig. 2a, b) have been found:1,29 (i) 2019-nCoV/SARS-CoV-2, SARS-CoV, MERS-CoV, HCoV-OC43, and HCoV-HKU1 are β genera, and (ii) HCoV-NL63 and HCoV-229E are α genera. We performed the phylogenetic analyses using the whole-genome sequence data from 15 HCoVs to inspect the evolutionary relationship of 2019-nCoV/SARS-CoV-2 with other HCoVs. We found that the whole genomes of 2019-nCoV/SARS-CoV-2 had ~99.99% nucleotide sequence identity across three diagnosed patients (Supplementary Table S1). The 2019-nCoV/SARS-CoV-2 shares the highest nucleotide sequence identity (79.7%) with SARS-CoV among the six other known pathogenic HCoVs, revealing conserved evolutionary relationship between 2019-nCoV/SARS-CoV-2 and SARS-CoV (Fig. 2a).\nFig. 2 Phylogenetic analysis of coronaviruses.\na Phylogenetic tree of coronavirus (CoV). Phylogenetic algorithm analyzed evolutionary conservation among whole genomes of 15 coronaviruses. Red color highlights the recent emergent coronavirus, 2019-nCoV/SARS-CoV-2. Numbers on the branches indicate bootstrap support values. The scale shows the evolutionary distance computed using the p-distance method. b Schematic plot for HCoV genomes. The genus and host information of viruses was labeled on the left by different colors. Empty dark gray boxes represent accessory open reading frames (ORFs). c–e The 3D structures of SARS-CoV nsp12 (PDB ID: 6NUR) (c), spike (PDB ID: 6ACK) (d), and nucleocapsid (PDB ID: 2CJR) (e) shown were based on homology modeling. Genome information and phylogenetic analysis results are provided in Supplementary Tables S1 and S2."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T44","span":{"begin":0,"end":197},"obj":"Sentence"},{"id":"T45","span":{"begin":198,"end":370},"obj":"Sentence"},{"id":"T46","span":{"begin":371,"end":525},"obj":"Sentence"},{"id":"T47","span":{"begin":526,"end":763},"obj":"Sentence"},{"id":"T48","span":{"begin":764,"end":810},"obj":"Sentence"},{"id":"T49","span":{"begin":811,"end":852},"obj":"Sentence"},{"id":"T50","span":{"begin":853,"end":951},"obj":"Sentence"},{"id":"T51","span":{"begin":952,"end":1027},"obj":"Sentence"},{"id":"T52","span":{"begin":1028,"end":1086},"obj":"Sentence"},{"id":"T53","span":{"begin":1087,"end":1201},"obj":"Sentence"},{"id":"T54","span":{"begin":1202,"end":1288},"obj":"Sentence"},{"id":"T55","span":{"begin":1289,"end":1407},"obj":"Sentence"},{"id":"T56","span":{"begin":1408,"end":1433},"obj":"Sentence"},{"id":"T57","span":{"begin":1434,"end":1470},"obj":"Sentence"},{"id":"T58","span":{"begin":1471,"end":1519},"obj":"Sentence"},{"id":"T59","span":{"begin":1520,"end":1620},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"To date, seven pathogenic HCoVs (Fig. 2a, b) have been found:1,29 (i) 2019-nCoV/SARS-CoV-2, SARS-CoV, MERS-CoV, HCoV-OC43, and HCoV-HKU1 are β genera, and (ii) HCoV-NL63 and HCoV-229E are α genera. We performed the phylogenetic analyses using the whole-genome sequence data from 15 HCoVs to inspect the evolutionary relationship of 2019-nCoV/SARS-CoV-2 with other HCoVs. We found that the whole genomes of 2019-nCoV/SARS-CoV-2 had ~99.99% nucleotide sequence identity across three diagnosed patients (Supplementary Table S1). The 2019-nCoV/SARS-CoV-2 shares the highest nucleotide sequence identity (79.7%) with SARS-CoV among the six other known pathogenic HCoVs, revealing conserved evolutionary relationship between 2019-nCoV/SARS-CoV-2 and SARS-CoV (Fig. 2a).\nFig. 2 Phylogenetic analysis of coronaviruses.\na Phylogenetic tree of coronavirus (CoV). Phylogenetic algorithm analyzed evolutionary conservation among whole genomes of 15 coronaviruses. Red color highlights the recent emergent coronavirus, 2019-nCoV/SARS-CoV-2. Numbers on the branches indicate bootstrap support values. The scale shows the evolutionary distance computed using the p-distance method. b Schematic plot for HCoV genomes. The genus and host information of viruses was labeled on the left by different colors. Empty dark gray boxes represent accessory open reading frames (ORFs). c–e The 3D structures of SARS-CoV nsp12 (PDB ID: 6NUR) (c), spike (PDB ID: 6ACK) (d), and nucleocapsid (PDB ID: 2CJR) (e) shown were based on homology modeling. Genome information and phylogenetic analysis results are provided in Supplementary Tables S1 and S2."}

2_test

{"project":"2_test","denotations":[{"id":"32194980-26868298-19614170","span":{"begin":61,"end":62},"obj":"26868298"},{"id":"32194980-27743750-19614171","span":{"begin":63,"end":65},"obj":"27743750"}],"text":"To date, seven pathogenic HCoVs (Fig. 2a, b) have been found:1,29 (i) 2019-nCoV/SARS-CoV-2, SARS-CoV, MERS-CoV, HCoV-OC43, and HCoV-HKU1 are β genera, and (ii) HCoV-NL63 and HCoV-229E are α genera. We performed the phylogenetic analyses using the whole-genome sequence data from 15 HCoVs to inspect the evolutionary relationship of 2019-nCoV/SARS-CoV-2 with other HCoVs. We found that the whole genomes of 2019-nCoV/SARS-CoV-2 had ~99.99% nucleotide sequence identity across three diagnosed patients (Supplementary Table S1). The 2019-nCoV/SARS-CoV-2 shares the highest nucleotide sequence identity (79.7%) with SARS-CoV among the six other known pathogenic HCoVs, revealing conserved evolutionary relationship between 2019-nCoV/SARS-CoV-2 and SARS-CoV (Fig. 2a).\nFig. 2 Phylogenetic analysis of coronaviruses.\na Phylogenetic tree of coronavirus (CoV). Phylogenetic algorithm analyzed evolutionary conservation among whole genomes of 15 coronaviruses. Red color highlights the recent emergent coronavirus, 2019-nCoV/SARS-CoV-2. Numbers on the branches indicate bootstrap support values. The scale shows the evolutionary distance computed using the p-distance method. b Schematic plot for HCoV genomes. The genus and host information of viruses was labeled on the left by different colors. Empty dark gray boxes represent accessory open reading frames (ORFs). c–e The 3D structures of SARS-CoV nsp12 (PDB ID: 6NUR) (c), spike (PDB ID: 6ACK) (d), and nucleocapsid (PDB ID: 2CJR) (e) shown were based on homology modeling. Genome information and phylogenetic analysis results are provided in Supplementary Tables S1 and S2."}

PMC:7073332 / 8564-10184 JSONTXT

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PMC:7073332 / 8564-10184 JSON TXT