PMC:6988269 / 8901-10011 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T26","span":{"begin":774,"end":780},"obj":"Body_part"}],"attributes":[{"id":"A26","pred":"fma_id","subj":"T26","obj":"http://purl.org/sig/ont/fma/fma84116"}],"text":"Before public release of virus sequences from cases of 2019-nCoV, we relied on social media reports announcing detection of a SARS-like virus. We thus assumed that a SARS-related CoV is involved in the outbreak. We downloaded all complete and partial (if \u003e 400 nt) SARS-related virus sequences available in GenBank by 1 January 2020. The list (n = 729 entries) was manually checked and artificial sequences (laboratory-derived, synthetic, etc), as well as sequence duplicates were removed, resulting in a final list of 375 sequences. These sequences were aligned and the alignment was used for assay design (Supplementary Figure S1). Upon release of the first 2019-nCoV sequence at virological.org, three assays were selected based on how well they matched to the 2019-nCoV genome (Figure 1). The alignment was complemented by additional sequences released independently on GISAID (https://www.gisaid.org), confirming the good matching of selected primers to all sequences. Alignments of primer binding domains with 2019-nCoV, SARS-CoV as well as selected bat-associated SARS-related CoV are shown in Figure 2."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T22","span":{"begin":126,"end":130},"obj":"Disease"},{"id":"T23","span":{"begin":166,"end":170},"obj":"Disease"},{"id":"T24","span":{"begin":265,"end":269},"obj":"Disease"},{"id":"T25","span":{"begin":1027,"end":1035},"obj":"Disease"},{"id":"T26","span":{"begin":1027,"end":1031},"obj":"Disease"},{"id":"T27","span":{"begin":1071,"end":1075},"obj":"Disease"}],"attributes":[{"id":"A22","pred":"mondo_id","subj":"T22","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A23","pred":"mondo_id","subj":"T23","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A24","pred":"mondo_id","subj":"T24","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A25","pred":"mondo_id","subj":"T25","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A26","pred":"mondo_id","subj":"T26","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A27","pred":"mondo_id","subj":"T27","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"Before public release of virus sequences from cases of 2019-nCoV, we relied on social media reports announcing detection of a SARS-like virus. We thus assumed that a SARS-related CoV is involved in the outbreak. We downloaded all complete and partial (if \u003e 400 nt) SARS-related virus sequences available in GenBank by 1 January 2020. The list (n = 729 entries) was manually checked and artificial sequences (laboratory-derived, synthetic, etc), as well as sequence duplicates were removed, resulting in a final list of 375 sequences. These sequences were aligned and the alignment was used for assay design (Supplementary Figure S1). Upon release of the first 2019-nCoV sequence at virological.org, three assays were selected based on how well they matched to the 2019-nCoV genome (Figure 1). The alignment was complemented by additional sequences released independently on GISAID (https://www.gisaid.org), confirming the good matching of selected primers to all sequences. Alignments of primer binding domains with 2019-nCoV, SARS-CoV as well as selected bat-associated SARS-related CoV are shown in Figure 2."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T77","span":{"begin":25,"end":30},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T78","span":{"begin":124,"end":125},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T79","span":{"begin":136,"end":141},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T80","span":{"begin":164,"end":165},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T81","span":{"begin":278,"end":283},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T82","span":{"begin":503,"end":504},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T83","span":{"begin":629,"end":631},"obj":"http://purl.obolibrary.org/obo/CLO_0050050"},{"id":"T84","span":{"begin":1056,"end":1059},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9397"}],"text":"Before public release of virus sequences from cases of 2019-nCoV, we relied on social media reports announcing detection of a SARS-like virus. We thus assumed that a SARS-related CoV is involved in the outbreak. We downloaded all complete and partial (if \u003e 400 nt) SARS-related virus sequences available in GenBank by 1 January 2020. The list (n = 729 entries) was manually checked and artificial sequences (laboratory-derived, synthetic, etc), as well as sequence duplicates were removed, resulting in a final list of 375 sequences. These sequences were aligned and the alignment was used for assay design (Supplementary Figure S1). Upon release of the first 2019-nCoV sequence at virological.org, three assays were selected based on how well they matched to the 2019-nCoV genome (Figure 1). The alignment was complemented by additional sequences released independently on GISAID (https://www.gisaid.org), confirming the good matching of selected primers to all sequences. Alignments of primer binding domains with 2019-nCoV, SARS-CoV as well as selected bat-associated SARS-related CoV are shown in Figure 2."}

{"project":"LitCovid-sentences","denotations":[{"id":"T73","span":{"begin":0,"end":142},"obj":"Sentence"},{"id":"T74","span":{"begin":143,"end":211},"obj":"Sentence"},{"id":"T75","span":{"begin":212,"end":333},"obj":"Sentence"},{"id":"T76","span":{"begin":334,"end":533},"obj":"Sentence"},{"id":"T77","span":{"begin":534,"end":633},"obj":"Sentence"},{"id":"T78","span":{"begin":634,"end":792},"obj":"Sentence"},{"id":"T79","span":{"begin":793,"end":973},"obj":"Sentence"},{"id":"T80","span":{"begin":974,"end":1110},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Before public release of virus sequences from cases of 2019-nCoV, we relied on social media reports announcing detection of a SARS-like virus. We thus assumed that a SARS-related CoV is involved in the outbreak. We downloaded all complete and partial (if \u003e 400 nt) SARS-related virus sequences available in GenBank by 1 January 2020. The list (n = 729 entries) was manually checked and artificial sequences (laboratory-derived, synthetic, etc), as well as sequence duplicates were removed, resulting in a final list of 375 sequences. These sequences were aligned and the alignment was used for assay design (Supplementary Figure S1). Upon release of the first 2019-nCoV sequence at virological.org, three assays were selected based on how well they matched to the 2019-nCoV genome (Figure 1). The alignment was complemented by additional sequences released independently on GISAID (https://www.gisaid.org), confirming the good matching of selected primers to all sequences. Alignments of primer binding domains with 2019-nCoV, SARS-CoV as well as selected bat-associated SARS-related CoV are shown in Figure 2."}

{"project":"LitCovid-PubTator","denotations":[{"id":"170","span":{"begin":55,"end":64},"obj":"Species"},{"id":"171","span":{"begin":166,"end":182},"obj":"Species"},{"id":"172","span":{"begin":265,"end":283},"obj":"Species"},{"id":"173","span":{"begin":386,"end":406},"obj":"Species"},{"id":"174","span":{"begin":660,"end":669},"obj":"Species"},{"id":"175","span":{"begin":764,"end":773},"obj":"Species"},{"id":"176","span":{"begin":1016,"end":1025},"obj":"Species"},{"id":"177","span":{"begin":1027,"end":1035},"obj":"Species"},{"id":"178","span":{"begin":1071,"end":1087},"obj":"Species"},{"id":"179","span":{"begin":428,"end":437},"obj":"Species"}],"attributes":[{"id":"A170","pred":"tao:has_database_id","subj":"170","obj":"Tax:2697049"},{"id":"A171","pred":"tao:has_database_id","subj":"171","obj":"Tax:694009"},{"id":"A172","pred":"tao:has_database_id","subj":"172","obj":"Tax:694009"},{"id":"A173","pred":"tao:has_database_id","subj":"173","obj":"Tax:81077"},{"id":"A174","pred":"tao:has_database_id","subj":"174","obj":"Tax:2697049"},{"id":"A175","pred":"tao:has_database_id","subj":"175","obj":"Tax:2697049"},{"id":"A176","pred":"tao:has_database_id","subj":"176","obj":"Tax:2697049"},{"id":"A177","pred":"tao:has_database_id","subj":"177","obj":"Tax:694009"},{"id":"A178","pred":"tao:has_database_id","subj":"178","obj":"Tax:694009"},{"id":"A179","pred":"tao:has_database_id","subj":"179","obj":"Tax:2086595"}],"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":"Before public release of virus sequences from cases of 2019-nCoV, we relied on social media reports announcing detection of a SARS-like virus. We thus assumed that a SARS-related CoV is involved in the outbreak. We downloaded all complete and partial (if \u003e 400 nt) SARS-related virus sequences available in GenBank by 1 January 2020. The list (n = 729 entries) was manually checked and artificial sequences (laboratory-derived, synthetic, etc), as well as sequence duplicates were removed, resulting in a final list of 375 sequences. These sequences were aligned and the alignment was used for assay design (Supplementary Figure S1). Upon release of the first 2019-nCoV sequence at virological.org, three assays were selected based on how well they matched to the 2019-nCoV genome (Figure 1). The alignment was complemented by additional sequences released independently on GISAID (https://www.gisaid.org), confirming the good matching of selected primers to all sequences. Alignments of primer binding domains with 2019-nCoV, SARS-CoV as well as selected bat-associated SARS-related CoV are shown in Figure 2."}