PMC:7565482 / 11934-12652 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T54","span":{"begin":126,"end":136},"obj":"Body_part"},{"id":"T55","span":{"begin":168,"end":175},"obj":"Body_part"},{"id":"T56","span":{"begin":200,"end":206},"obj":"Body_part"},{"id":"T57","span":{"begin":207,"end":217},"obj":"Body_part"},{"id":"T58","span":{"begin":384,"end":395},"obj":"Body_part"},{"id":"T59","span":{"begin":568,"end":575},"obj":"Body_part"},{"id":"T60","span":{"begin":576,"end":588},"obj":"Body_part"}],"attributes":[{"id":"A54","pred":"fma_id","subj":"T54","obj":"http://purl.org/sig/ont/fma/fma82740"},{"id":"A55","pred":"fma_id","subj":"T55","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A56","pred":"fma_id","subj":"T56","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A57","pred":"fma_id","subj":"T57","obj":"http://purl.org/sig/ont/fma/fma82740"},{"id":"A58","pred":"fma_id","subj":"T58","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A59","pred":"fma_id","subj":"T59","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A60","pred":"fma_id","subj":"T60","obj":"http://purl.org/sig/ont/fma/fma62925"}],"text":"3.1. Open Reading Frames and Sequence Isolates for CoV-2-Cons Sequence Creation\nFor creation of the CoV-2 Consensus sequence, nucleotide sequences from 1731 SARS-CoV-2 genomes were aligned and a full genome nucleotide consensus was created, 23 open reading frames (ORF) were then located in the alignment using the NC_045512.2 and the Finkel et al. [46] coordinates and translated to amino acids. Of the 23 ORF, 12 were canonical ORF as annotated in NC_045512.2 and 11 in alternative reading frames described by Finkel et al. [46] (Table 1). In addition, the membrane protein glycoprotein (M), is completely embedded inside an extended ORF (exORFM) without any frameshifts and was not used for separate OLP set design."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T40","span":{"begin":157,"end":165},"obj":"Disease"}],"attributes":[{"id":"A40","pred":"mondo_id","subj":"T40","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"3.1. Open Reading Frames and Sequence Isolates for CoV-2-Cons Sequence Creation\nFor creation of the CoV-2 Consensus sequence, nucleotide sequences from 1731 SARS-CoV-2 genomes were aligned and a full genome nucleotide consensus was created, 23 open reading frames (ORF) were then located in the alignment using the NC_045512.2 and the Finkel et al. [46] coordinates and translated to amino acids. Of the 23 ORF, 12 were canonical ORF as annotated in NC_045512.2 and 11 in alternative reading frames described by Finkel et al. [46] (Table 1). In addition, the membrane protein glycoprotein (M), is completely embedded inside an extended ORF (exORFM) without any frameshifts and was not used for separate OLP set design."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T95","span":{"begin":193,"end":194},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T96","span":{"begin":466,"end":468},"obj":"http://purl.obolibrary.org/obo/CLO_0053733"},{"id":"T97","span":{"begin":559,"end":567},"obj":"http://purl.obolibrary.org/obo/UBERON_0000158"}],"text":"3.1. Open Reading Frames and Sequence Isolates for CoV-2-Cons Sequence Creation\nFor creation of the CoV-2 Consensus sequence, nucleotide sequences from 1731 SARS-CoV-2 genomes were aligned and a full genome nucleotide consensus was created, 23 open reading frames (ORF) were then located in the alignment using the NC_045512.2 and the Finkel et al. [46] coordinates and translated to amino acids. Of the 23 ORF, 12 were canonical ORF as annotated in NC_045512.2 and 11 in alternative reading frames described by Finkel et al. [46] (Table 1). In addition, the membrane protein glycoprotein (M), is completely embedded inside an extended ORF (exORFM) without any frameshifts and was not used for separate OLP set design."}

{"project":"LitCovid-PubTator","denotations":[{"id":"149","span":{"begin":51,"end":56},"obj":"Species"},{"id":"153","span":{"begin":590,"end":591},"obj":"Gene"},{"id":"154","span":{"begin":100,"end":105},"obj":"Species"},{"id":"155","span":{"begin":157,"end":167},"obj":"Species"}],"attributes":[{"id":"A149","pred":"tao:has_database_id","subj":"149","obj":"Tax:2697049"},{"id":"A153","pred":"tao:has_database_id","subj":"153","obj":"Gene:43740571"},{"id":"A154","pred":"tao:has_database_id","subj":"154","obj":"Tax:2697049"},{"id":"A155","pred":"tao:has_database_id","subj":"155","obj":"Tax:2697049"}],"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":"3.1. Open Reading Frames and Sequence Isolates for CoV-2-Cons Sequence Creation\nFor creation of the CoV-2 Consensus sequence, nucleotide sequences from 1731 SARS-CoV-2 genomes were aligned and a full genome nucleotide consensus was created, 23 open reading frames (ORF) were then located in the alignment using the NC_045512.2 and the Finkel et al. [46] coordinates and translated to amino acids. Of the 23 ORF, 12 were canonical ORF as annotated in NC_045512.2 and 11 in alternative reading frames described by Finkel et al. [46] (Table 1). In addition, the membrane protein glycoprotein (M), is completely embedded inside an extended ORF (exORFM) without any frameshifts and was not used for separate OLP set design."}

{"project":"LitCovid-sentences","denotations":[{"id":"T77","span":{"begin":0,"end":4},"obj":"Sentence"},{"id":"T78","span":{"begin":5,"end":79},"obj":"Sentence"},{"id":"T79","span":{"begin":80,"end":396},"obj":"Sentence"},{"id":"T80","span":{"begin":397,"end":541},"obj":"Sentence"},{"id":"T81","span":{"begin":542,"end":718},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"3.1. Open Reading Frames and Sequence Isolates for CoV-2-Cons Sequence Creation\nFor creation of the CoV-2 Consensus sequence, nucleotide sequences from 1731 SARS-CoV-2 genomes were aligned and a full genome nucleotide consensus was created, 23 open reading frames (ORF) were then located in the alignment using the NC_045512.2 and the Finkel et al. [46] coordinates and translated to amino acids. Of the 23 ORF, 12 were canonical ORF as annotated in NC_045512.2 and 11 in alternative reading frames described by Finkel et al. [46] (Table 1). In addition, the membrane protein glycoprotein (M), is completely embedded inside an extended ORF (exORFM) without any frameshifts and was not used for separate OLP set design."}