PMC:7033720 / 3598-4574 JSONTXT

{"project":"LitCovid-PubTator","denotations":[{"id":"68","span":{"begin":68,"end":76},"obj":"Species"},{"id":"69","span":{"begin":90,"end":99},"obj":"Disease"},{"id":"72","span":{"begin":618,"end":627},"obj":"Species"},{"id":"73","span":{"begin":660,"end":663},"obj":"Species"}],"attributes":[{"id":"A68","pred":"tao:has_database_id","subj":"68","obj":"Tax:9606"},{"id":"A69","pred":"tao:has_database_id","subj":"69","obj":"MESH:D011014"},{"id":"A72","pred":"tao:has_database_id","subj":"72","obj":"Tax:2697049"},{"id":"A73","pred":"tao:has_database_id","subj":"73","obj":"Tax:11118"}],"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":"Sequence of events\n2nd January 2020. Obtained BALF samples from two patients with unusual pneumonia.\n3rd January 2020. Performed SARS-specific RT-PCR assay, yielded partial RdRp fragment, and revealed potential pathogen.\n4th January 2020. Extended RdRp fragments and obtained more genome fragments, and started mNGS RNA library preparation\n5th January 2020. Completed mNGS RNA library preparation.\n6th January 2020. Started mNGS sequencing on Miseq platform.\n7th January 2020. Received sequencing data, started pathogen identification pipeline, obtained virus genome, corrected the genome end with mapping, identified 2019-nCoV as sole pathogen, and the final CoV genome was 29,881 nt.\n8th January 2020. Performed genome comparisons and evolutionary analyses.\nSince 3rd January 2020, instant progress reports have been sent to Chinese Center for Disease Control and Prevention (CDC), keeping pace with every advancement we made in pathogen identification and characterization."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T19","span":{"begin":281,"end":287},"obj":"Body_part"},{"id":"T20","span":{"begin":316,"end":319},"obj":"Body_part"},{"id":"T21","span":{"begin":373,"end":376},"obj":"Body_part"},{"id":"T22","span":{"begin":560,"end":566},"obj":"Body_part"},{"id":"T23","span":{"begin":582,"end":588},"obj":"Body_part"},{"id":"T24","span":{"begin":631,"end":635},"obj":"Body_part"},{"id":"T25","span":{"begin":664,"end":670},"obj":"Body_part"},{"id":"T26","span":{"begin":714,"end":720},"obj":"Body_part"}],"attributes":[{"id":"A19","pred":"fma_id","subj":"T19","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A20","pred":"fma_id","subj":"T20","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A21","pred":"fma_id","subj":"T21","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A22","pred":"fma_id","subj":"T22","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A23","pred":"fma_id","subj":"T23","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A24","pred":"fma_id","subj":"T24","obj":"http://purl.org/sig/ont/fma/fma25000"},{"id":"A25","pred":"fma_id","subj":"T25","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A26","pred":"fma_id","subj":"T26","obj":"http://purl.org/sig/ont/fma/fma84116"}],"text":"Sequence of events\n2nd January 2020. Obtained BALF samples from two patients with unusual pneumonia.\n3rd January 2020. Performed SARS-specific RT-PCR assay, yielded partial RdRp fragment, and revealed potential pathogen.\n4th January 2020. Extended RdRp fragments and obtained more genome fragments, and started mNGS RNA library preparation\n5th January 2020. Completed mNGS RNA library preparation.\n6th January 2020. Started mNGS sequencing on Miseq platform.\n7th January 2020. Received sequencing data, started pathogen identification pipeline, obtained virus genome, corrected the genome end with mapping, identified 2019-nCoV as sole pathogen, and the final CoV genome was 29,881 nt.\n8th January 2020. Performed genome comparisons and evolutionary analyses.\nSince 3rd January 2020, instant progress reports have been sent to Chinese Center for Disease Control and Prevention (CDC), keeping pace with every advancement we made in pathogen identification and characterization."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T7","span":{"begin":90,"end":99},"obj":"Disease"},{"id":"T8","span":{"begin":129,"end":133},"obj":"Disease"}],"attributes":[{"id":"A7","pred":"mondo_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/MONDO_0005249"},{"id":"A8","pred":"mondo_id","subj":"T8","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"Sequence of events\n2nd January 2020. Obtained BALF samples from two patients with unusual pneumonia.\n3rd January 2020. Performed SARS-specific RT-PCR assay, yielded partial RdRp fragment, and revealed potential pathogen.\n4th January 2020. Extended RdRp fragments and obtained more genome fragments, and started mNGS RNA library preparation\n5th January 2020. Completed mNGS RNA library preparation.\n6th January 2020. Started mNGS sequencing on Miseq platform.\n7th January 2020. Received sequencing data, started pathogen identification pipeline, obtained virus genome, corrected the genome end with mapping, identified 2019-nCoV as sole pathogen, and the final CoV genome was 29,881 nt.\n8th January 2020. Performed genome comparisons and evolutionary analyses.\nSince 3rd January 2020, instant progress reports have been sent to Chinese Center for Disease Control and Prevention (CDC), keeping pace with every advancement we made in pathogen identification and characterization."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T34","span":{"begin":554,"end":559},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T35","span":{"begin":878,"end":881},"obj":"http://purl.obolibrary.org/obo/CL_0000990"}],"text":"Sequence of events\n2nd January 2020. Obtained BALF samples from two patients with unusual pneumonia.\n3rd January 2020. Performed SARS-specific RT-PCR assay, yielded partial RdRp fragment, and revealed potential pathogen.\n4th January 2020. Extended RdRp fragments and obtained more genome fragments, and started mNGS RNA library preparation\n5th January 2020. Completed mNGS RNA library preparation.\n6th January 2020. Started mNGS sequencing on Miseq platform.\n7th January 2020. Received sequencing data, started pathogen identification pipeline, obtained virus genome, corrected the genome end with mapping, identified 2019-nCoV as sole pathogen, and the final CoV genome was 29,881 nt.\n8th January 2020. Performed genome comparisons and evolutionary analyses.\nSince 3rd January 2020, instant progress reports have been sent to Chinese Center for Disease Control and Prevention (CDC), keeping pace with every advancement we made in pathogen identification and characterization."}

{"project":"LitCovid-PD-HP","denotations":[{"id":"T6","span":{"begin":90,"end":99},"obj":"Phenotype"}],"attributes":[{"id":"A6","pred":"hp_id","subj":"T6","obj":"http://purl.obolibrary.org/obo/HP_0002090"}],"text":"Sequence of events\n2nd January 2020. Obtained BALF samples from two patients with unusual pneumonia.\n3rd January 2020. Performed SARS-specific RT-PCR assay, yielded partial RdRp fragment, and revealed potential pathogen.\n4th January 2020. Extended RdRp fragments and obtained more genome fragments, and started mNGS RNA library preparation\n5th January 2020. Completed mNGS RNA library preparation.\n6th January 2020. Started mNGS sequencing on Miseq platform.\n7th January 2020. Received sequencing data, started pathogen identification pipeline, obtained virus genome, corrected the genome end with mapping, identified 2019-nCoV as sole pathogen, and the final CoV genome was 29,881 nt.\n8th January 2020. Performed genome comparisons and evolutionary analyses.\nSince 3rd January 2020, instant progress reports have been sent to Chinese Center for Disease Control and Prevention (CDC), keeping pace with every advancement we made in pathogen identification and characterization."}

{"project":"LitCovid-sentences","denotations":[{"id":"T29","span":{"begin":0,"end":18},"obj":"Sentence"},{"id":"T30","span":{"begin":19,"end":36},"obj":"Sentence"},{"id":"T31","span":{"begin":37,"end":100},"obj":"Sentence"},{"id":"T32","span":{"begin":101,"end":118},"obj":"Sentence"},{"id":"T33","span":{"begin":119,"end":220},"obj":"Sentence"},{"id":"T34","span":{"begin":221,"end":238},"obj":"Sentence"},{"id":"T35","span":{"begin":239,"end":339},"obj":"Sentence"},{"id":"T36","span":{"begin":340,"end":357},"obj":"Sentence"},{"id":"T37","span":{"begin":358,"end":397},"obj":"Sentence"},{"id":"T38","span":{"begin":398,"end":415},"obj":"Sentence"},{"id":"T39","span":{"begin":416,"end":458},"obj":"Sentence"},{"id":"T40","span":{"begin":459,"end":476},"obj":"Sentence"},{"id":"T41","span":{"begin":477,"end":685},"obj":"Sentence"},{"id":"T42","span":{"begin":686,"end":703},"obj":"Sentence"},{"id":"T43","span":{"begin":704,"end":759},"obj":"Sentence"},{"id":"T44","span":{"begin":760,"end":976},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Sequence of events\n2nd January 2020. Obtained BALF samples from two patients with unusual pneumonia.\n3rd January 2020. Performed SARS-specific RT-PCR assay, yielded partial RdRp fragment, and revealed potential pathogen.\n4th January 2020. Extended RdRp fragments and obtained more genome fragments, and started mNGS RNA library preparation\n5th January 2020. Completed mNGS RNA library preparation.\n6th January 2020. Started mNGS sequencing on Miseq platform.\n7th January 2020. Received sequencing data, started pathogen identification pipeline, obtained virus genome, corrected the genome end with mapping, identified 2019-nCoV as sole pathogen, and the final CoV genome was 29,881 nt.\n8th January 2020. Performed genome comparisons and evolutionary analyses.\nSince 3rd January 2020, instant progress reports have been sent to Chinese Center for Disease Control and Prevention (CDC), keeping pace with every advancement we made in pathogen identification and characterization."}