PMC:7307149 / 22891-24528 JSON TXT

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LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T151","span":{"begin":306,"end":316},"obj":"Body_part"},{"id":"T152","span":{"begin":1017,"end":1028},"obj":"Body_part"},{"id":"T153","span":{"begin":1271,"end":1281},"obj":"Body_part"}],"attributes":[{"id":"A151","pred":"fma_id","subj":"T151","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A152","pred":"fma_id","subj":"T152","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A153","pred":"fma_id","subj":"T153","obj":"http://purl.org/sig/ont/fma/fma82739"}],"text":"Aligned sequences were imported into Jalview v. 2.1.1 (71) with automated generation of the following alignment annotations: (i) sequence consensus, calculated as the percentage of the modal residue per column; (ii) sequence conservation (0 to 11), measured as a numerical index reflecting conservation of amino acid physicochemical properties in the alignment; (iii) alignment quality (0 to 1), measured as a normalized sum of BLOSUM62 ratios for all residues at each position; and (iv) occupancy, calculated as the number of aligned residues (not including gaps) for each position. In all cases, sequence conservation was assessed for each of the following three groups: only human-infecting coronavirus sequences (n = 7), all betacoronavirus sequences (n = 16), and all alpha- and betacoronavirus sequences combined (n = 34). Aligned SARS-CoV-2 sequences and all annotations were manually exported for subsequent analysis. Conserved human coronavirus peptides were defined as those with a length of ≥8 consecutive amino acids, each showing agreement with SARS-CoV-2 sequences and ≥4 other human coronavirus sequences with the consensus sequence (Table S2). For each of these conserved peptides, we also assessed the component number of 8- to 12-mers sharing identical amino acid sequence between SARS-CoV-2 and each of the four other common human coronaviruses (i.e., OC43, HKU1, NL63, and 229E) (Table S3). For all peptides, human, beta, and combined conservation scores were obtained using a custom R v.3.6.2 script representing mean sequence conservation (minus gap penalties where relevant) (see https://github.com/pdxgx/covid19)."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T96","span":{"begin":837,"end":845},"obj":"Disease"},{"id":"T97","span":{"begin":1058,"end":1066},"obj":"Disease"},{"id":"T98","span":{"begin":1299,"end":1307},"obj":"Disease"}],"attributes":[{"id":"A96","pred":"mondo_id","subj":"T96","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A97","pred":"mondo_id","subj":"T97","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A98","pred":"mondo_id","subj":"T98","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"Aligned sequences were imported into Jalview v. 2.1.1 (71) with automated generation of the following alignment annotations: (i) sequence consensus, calculated as the percentage of the modal residue per column; (ii) sequence conservation (0 to 11), measured as a numerical index reflecting conservation of amino acid physicochemical properties in the alignment; (iii) alignment quality (0 to 1), measured as a normalized sum of BLOSUM62 ratios for all residues at each position; and (iv) occupancy, calculated as the number of aligned residues (not including gaps) for each position. In all cases, sequence conservation was assessed for each of the following three groups: only human-infecting coronavirus sequences (n = 7), all betacoronavirus sequences (n = 16), and all alpha- and betacoronavirus sequences combined (n = 34). Aligned SARS-CoV-2 sequences and all annotations were manually exported for subsequent analysis. Conserved human coronavirus peptides were defined as those with a length of ≥8 consecutive amino acids, each showing agreement with SARS-CoV-2 sequences and ≥4 other human coronavirus sequences with the consensus sequence (Table S2). For each of these conserved peptides, we also assessed the component number of 8- to 12-mers sharing identical amino acid sequence between SARS-CoV-2 and each of the four other common human coronaviruses (i.e., OC43, HKU1, NL63, and 229E) (Table S3). For all peptides, human, beta, and combined conservation scores were obtained using a custom R v.3.6.2 script representing mean sequence conservation (minus gap penalties where relevant) (see https://github.com/pdxgx/covid19)."}

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T226","span":{"begin":55,"end":57},"obj":"http://purl.obolibrary.org/obo/CLO_0054055"},{"id":"T227","span":{"begin":244,"end":246},"obj":"http://purl.obolibrary.org/obo/CLO_0053733"},{"id":"T228","span":{"begin":261,"end":262},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T229","span":{"begin":408,"end":409},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T230","span":{"begin":678,"end":683},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T231","span":{"begin":824,"end":826},"obj":"http://purl.obolibrary.org/obo/CLO_0001302"},{"id":"T232","span":{"begin":936,"end":941},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T233","span":{"begin":954,"end":962},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T234","span":{"begin":990,"end":991},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T235","span":{"begin":1092,"end":1097},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T236","span":{"begin":1155,"end":1157},"obj":"http://purl.obolibrary.org/obo/CLO_0008922"},{"id":"T237","span":{"begin":1155,"end":1157},"obj":"http://purl.obolibrary.org/obo/CLO_0050052"},{"id":"T238","span":{"begin":1188,"end":1196},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T239","span":{"begin":1344,"end":1349},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T240","span":{"begin":1419,"end":1427},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T241","span":{"begin":1429,"end":1434},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T242","span":{"begin":1495,"end":1496},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"Aligned sequences were imported into Jalview v. 2.1.1 (71) with automated generation of the following alignment annotations: (i) sequence consensus, calculated as the percentage of the modal residue per column; (ii) sequence conservation (0 to 11), measured as a numerical index reflecting conservation of amino acid physicochemical properties in the alignment; (iii) alignment quality (0 to 1), measured as a normalized sum of BLOSUM62 ratios for all residues at each position; and (iv) occupancy, calculated as the number of aligned residues (not including gaps) for each position. In all cases, sequence conservation was assessed for each of the following three groups: only human-infecting coronavirus sequences (n = 7), all betacoronavirus sequences (n = 16), and all alpha- and betacoronavirus sequences combined (n = 34). Aligned SARS-CoV-2 sequences and all annotations were manually exported for subsequent analysis. Conserved human coronavirus peptides were defined as those with a length of ≥8 consecutive amino acids, each showing agreement with SARS-CoV-2 sequences and ≥4 other human coronavirus sequences with the consensus sequence (Table S2). For each of these conserved peptides, we also assessed the component number of 8- to 12-mers sharing identical amino acid sequence between SARS-CoV-2 and each of the four other common human coronaviruses (i.e., OC43, HKU1, NL63, and 229E) (Table S3). For all peptides, human, beta, and combined conservation scores were obtained using a custom R v.3.6.2 script representing mean sequence conservation (minus gap penalties where relevant) (see https://github.com/pdxgx/covid19)."}

LitCovid-PD-CHEBI

LitCovid-PubTator

{"project":"LitCovid-PubTator","denotations":[{"id":"107","span":{"begin":1299,"end":1309},"obj":"Species"},{"id":"418","span":{"begin":678,"end":683},"obj":"Species"},{"id":"419","span":{"begin":694,"end":705},"obj":"Species"},{"id":"420","span":{"begin":729,"end":744},"obj":"Species"},{"id":"421","span":{"begin":784,"end":799},"obj":"Species"},{"id":"422","span":{"begin":837,"end":847},"obj":"Species"},{"id":"423","span":{"begin":936,"end":953},"obj":"Species"},{"id":"424","span":{"begin":1058,"end":1068},"obj":"Species"},{"id":"425","span":{"begin":1092,"end":1109},"obj":"Species"},{"id":"427","span":{"begin":1344,"end":1349},"obj":"Species"},{"id":"428","span":{"begin":1350,"end":1363},"obj":"Species"},{"id":"429","span":{"begin":1429,"end":1434},"obj":"Species"}],"attributes":[{"id":"A107","pred":"tao:has_database_id","subj":"107","obj":"Tax:2697049"},{"id":"A418","pred":"tao:has_database_id","subj":"418","obj":"Tax:9606"},{"id":"A419","pred":"tao:has_database_id","subj":"419","obj":"Tax:11118"},{"id":"A420","pred":"tao:has_database_id","subj":"420","obj":"Tax:694002"},{"id":"A421","pred":"tao:has_database_id","subj":"421","obj":"Tax:694002"},{"id":"A422","pred":"tao:has_database_id","subj":"422","obj":"Tax:2697049"},{"id":"A423","pred":"tao:has_database_id","subj":"423","obj":"Tax:694448"},{"id":"A424","pred":"tao:has_database_id","subj":"424","obj":"Tax:2697049"},{"id":"A425","pred":"tao:has_database_id","subj":"425","obj":"Tax:694448"},{"id":"A427","pred":"tao:has_database_id","subj":"427","obj":"Tax:9606"},{"id":"A428","pred":"tao:has_database_id","subj":"428","obj":"Tax:11118"},{"id":"A429","pred":"tao:has_database_id","subj":"429","obj":"Tax:9606"}],"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":"Aligned sequences were imported into Jalview v. 2.1.1 (71) with automated generation of the following alignment annotations: (i) sequence consensus, calculated as the percentage of the modal residue per column; (ii) sequence conservation (0 to 11), measured as a numerical index reflecting conservation of amino acid physicochemical properties in the alignment; (iii) alignment quality (0 to 1), measured as a normalized sum of BLOSUM62 ratios for all residues at each position; and (iv) occupancy, calculated as the number of aligned residues (not including gaps) for each position. In all cases, sequence conservation was assessed for each of the following three groups: only human-infecting coronavirus sequences (n = 7), all betacoronavirus sequences (n = 16), and all alpha- and betacoronavirus sequences combined (n = 34). Aligned SARS-CoV-2 sequences and all annotations were manually exported for subsequent analysis. Conserved human coronavirus peptides were defined as those with a length of ≥8 consecutive amino acids, each showing agreement with SARS-CoV-2 sequences and ≥4 other human coronavirus sequences with the consensus sequence (Table S2). For each of these conserved peptides, we also assessed the component number of 8- to 12-mers sharing identical amino acid sequence between SARS-CoV-2 and each of the four other common human coronaviruses (i.e., OC43, HKU1, NL63, and 229E) (Table S3). For all peptides, human, beta, and combined conservation scores were obtained using a custom R v.3.6.2 script representing mean sequence conservation (minus gap penalties where relevant) (see https://github.com/pdxgx/covid19)."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T122","span":{"begin":0,"end":47},"obj":"Sentence"},{"id":"T123","span":{"begin":48,"end":583},"obj":"Sentence"},{"id":"T124","span":{"begin":584,"end":828},"obj":"Sentence"},{"id":"T125","span":{"begin":829,"end":925},"obj":"Sentence"},{"id":"T126","span":{"begin":926,"end":1159},"obj":"Sentence"},{"id":"T127","span":{"begin":1160,"end":1410},"obj":"Sentence"},{"id":"T128","span":{"begin":1411,"end":1637},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Aligned sequences were imported into Jalview v. 2.1.1 (71) with automated generation of the following alignment annotations: (i) sequence consensus, calculated as the percentage of the modal residue per column; (ii) sequence conservation (0 to 11), measured as a numerical index reflecting conservation of amino acid physicochemical properties in the alignment; (iii) alignment quality (0 to 1), measured as a normalized sum of BLOSUM62 ratios for all residues at each position; and (iv) occupancy, calculated as the number of aligned residues (not including gaps) for each position. In all cases, sequence conservation was assessed for each of the following three groups: only human-infecting coronavirus sequences (n = 7), all betacoronavirus sequences (n = 16), and all alpha- and betacoronavirus sequences combined (n = 34). Aligned SARS-CoV-2 sequences and all annotations were manually exported for subsequent analysis. Conserved human coronavirus peptides were defined as those with a length of ≥8 consecutive amino acids, each showing agreement with SARS-CoV-2 sequences and ≥4 other human coronavirus sequences with the consensus sequence (Table S2). For each of these conserved peptides, we also assessed the component number of 8- to 12-mers sharing identical amino acid sequence between SARS-CoV-2 and each of the four other common human coronaviruses (i.e., OC43, HKU1, NL63, and 229E) (Table S3). For all peptides, human, beta, and combined conservation scores were obtained using a custom R v.3.6.2 script representing mean sequence conservation (minus gap penalties where relevant) (see https://github.com/pdxgx/covid19)."}

2_test

{"project":"2_test","denotations":[{"id":"32303592-19151095-65501649","span":{"begin":55,"end":57},"obj":"19151095"}],"text":"Aligned sequences were imported into Jalview v. 2.1.1 (71) with automated generation of the following alignment annotations: (i) sequence consensus, calculated as the percentage of the modal residue per column; (ii) sequence conservation (0 to 11), measured as a numerical index reflecting conservation of amino acid physicochemical properties in the alignment; (iii) alignment quality (0 to 1), measured as a normalized sum of BLOSUM62 ratios for all residues at each position; and (iv) occupancy, calculated as the number of aligned residues (not including gaps) for each position. In all cases, sequence conservation was assessed for each of the following three groups: only human-infecting coronavirus sequences (n = 7), all betacoronavirus sequences (n = 16), and all alpha- and betacoronavirus sequences combined (n = 34). Aligned SARS-CoV-2 sequences and all annotations were manually exported for subsequent analysis. Conserved human coronavirus peptides were defined as those with a length of ≥8 consecutive amino acids, each showing agreement with SARS-CoV-2 sequences and ≥4 other human coronavirus sequences with the consensus sequence (Table S2). For each of these conserved peptides, we also assessed the component number of 8- to 12-mers sharing identical amino acid sequence between SARS-CoV-2 and each of the four other common human coronaviruses (i.e., OC43, HKU1, NL63, and 229E) (Table S3). For all peptides, human, beta, and combined conservation scores were obtained using a custom R v.3.6.2 script representing mean sequence conservation (minus gap penalties where relevant) (see https://github.com/pdxgx/covid19)."}