PMC:7565482 / 7513-8460 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T31","span":{"begin":271,"end":281},"obj":"Body_part"},{"id":"T32","span":{"begin":330,"end":341},"obj":"Body_part"},{"id":"T33","span":{"begin":405,"end":415},"obj":"Body_part"},{"id":"T34","span":{"begin":601,"end":611},"obj":"Body_part"},{"id":"T35","span":{"begin":744,"end":754},"obj":"Body_part"},{"id":"T36","span":{"begin":789,"end":798},"obj":"Body_part"}],"attributes":[{"id":"A31","pred":"fma_id","subj":"T31","obj":"http://purl.org/sig/ont/fma/fma82740"},{"id":"A32","pred":"fma_id","subj":"T32","obj":"http://purl.org/sig/ont/fma/fma82740"},{"id":"A33","pred":"fma_id","subj":"T33","obj":"http://purl.org/sig/ont/fma/fma82739"},{"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/fma82739"},{"id":"A36","pred":"fma_id","subj":"T36","obj":"http://purl.org/sig/ont/fma/fma82739"}],"text":"A total of 1731 full-length SARS-CoV-2 sequences were downloaded from NCBI (30 April 2020, txid2697049, minimum length = 29,000 bp) and aligned using MAFFT [44]. The alignment was visually inspected and curated using Genbank NC_045512.2 as a coordinate reference [45]. A nucleotide consensus sequence was generated by keeping all nucleotides present in at least 25% of the sequences in the alignment. The amino acid consensus sequence was then created by using NC_045512.2 annotated Open Reading Frames (ORFs) plus additional ORFs described in Finkel et al. [46] using the Biostrings R package. Mixed nucleotide positions were either resolved if they were synonymous or flagged for downstream analysis. Positional entropy was calculated at the amino acid level both as the standard and 22-aminoacid-normalized Shannon entropy for every ORF using Bio3d R package on the alignment [47], and afterward, the mean OLP normalized entropy was calculated."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T34","span":{"begin":28,"end":36},"obj":"Disease"}],"attributes":[{"id":"A34","pred":"mondo_id","subj":"T34","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"A total of 1731 full-length SARS-CoV-2 sequences were downloaded from NCBI (30 April 2020, txid2697049, minimum length = 29,000 bp) and aligned using MAFFT [44]. The alignment was visually inspected and curated using Genbank NC_045512.2 as a coordinate reference [45]. A nucleotide consensus sequence was generated by keeping all nucleotides present in at least 25% of the sequences in the alignment. The amino acid consensus sequence was then created by using NC_045512.2 annotated Open Reading Frames (ORFs) plus additional ORFs described in Finkel et al. [46] using the Biostrings R package. Mixed nucleotide positions were either resolved if they were synonymous or flagged for downstream analysis. Positional entropy was calculated at the amino acid level both as the standard and 22-aminoacid-normalized Shannon entropy for every ORF using Bio3d R package on the alignment [47], and afterward, the mean OLP normalized entropy was calculated."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T61","span":{"begin":0,"end":1},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T62","span":{"begin":240,"end":241},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T63","span":{"begin":264,"end":266},"obj":"http://purl.obolibrary.org/obo/CLO_0053799"},{"id":"T64","span":{"begin":269,"end":270},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T65","span":{"begin":786,"end":788},"obj":"http://purl.obolibrary.org/obo/CLO_0050507"}],"text":"A total of 1731 full-length SARS-CoV-2 sequences were downloaded from NCBI (30 April 2020, txid2697049, minimum length = 29,000 bp) and aligned using MAFFT [44]. The alignment was visually inspected and curated using Genbank NC_045512.2 as a coordinate reference [45]. A nucleotide consensus sequence was generated by keeping all nucleotides present in at least 25% of the sequences in the alignment. The amino acid consensus sequence was then created by using NC_045512.2 annotated Open Reading Frames (ORFs) plus additional ORFs described in Finkel et al. [46] using the Biostrings R package. Mixed nucleotide positions were either resolved if they were synonymous or flagged for downstream analysis. Positional entropy was calculated at the amino acid level both as the standard and 22-aminoacid-normalized Shannon entropy for every ORF using Bio3d R package on the alignment [47], and afterward, the mean OLP normalized entropy was calculated."}

{"project":"LitCovid-PubTator","denotations":[{"id":"97","span":{"begin":28,"end":38},"obj":"Species"}],"attributes":[{"id":"A97","pred":"tao:has_database_id","subj":"97","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":"A total of 1731 full-length SARS-CoV-2 sequences were downloaded from NCBI (30 April 2020, txid2697049, minimum length = 29,000 bp) and aligned using MAFFT [44]. The alignment was visually inspected and curated using Genbank NC_045512.2 as a coordinate reference [45]. A nucleotide consensus sequence was generated by keeping all nucleotides present in at least 25% of the sequences in the alignment. The amino acid consensus sequence was then created by using NC_045512.2 annotated Open Reading Frames (ORFs) plus additional ORFs described in Finkel et al. [46] using the Biostrings R package. Mixed nucleotide positions were either resolved if they were synonymous or flagged for downstream analysis. Positional entropy was calculated at the amino acid level both as the standard and 22-aminoacid-normalized Shannon entropy for every ORF using Bio3d R package on the alignment [47], and afterward, the mean OLP normalized entropy was calculated."}

{"project":"LitCovid-sentences","denotations":[{"id":"T43","span":{"begin":0,"end":161},"obj":"Sentence"},{"id":"T44","span":{"begin":162,"end":268},"obj":"Sentence"},{"id":"T45","span":{"begin":269,"end":400},"obj":"Sentence"},{"id":"T46","span":{"begin":401,"end":594},"obj":"Sentence"},{"id":"T47","span":{"begin":595,"end":702},"obj":"Sentence"},{"id":"T48","span":{"begin":703,"end":947},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"A total of 1731 full-length SARS-CoV-2 sequences were downloaded from NCBI (30 April 2020, txid2697049, minimum length = 29,000 bp) and aligned using MAFFT [44]. The alignment was visually inspected and curated using Genbank NC_045512.2 as a coordinate reference [45]. A nucleotide consensus sequence was generated by keeping all nucleotides present in at least 25% of the sequences in the alignment. The amino acid consensus sequence was then created by using NC_045512.2 annotated Open Reading Frames (ORFs) plus additional ORFs described in Finkel et al. [46] using the Biostrings R package. Mixed nucleotide positions were either resolved if they were synonymous or flagged for downstream analysis. Positional entropy was calculated at the amino acid level both as the standard and 22-aminoacid-normalized Shannon entropy for every ORF using Bio3d R package on the alignment [47], and afterward, the mean OLP normalized entropy was calculated."}