PMC:7565482 / 9946-11136 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T44","span":{"begin":79,"end":86},"obj":"Body_part"},{"id":"T45","span":{"begin":527,"end":535},"obj":"Body_part"},{"id":"T46","span":{"begin":641,"end":649},"obj":"Body_part"},{"id":"T47","span":{"begin":666,"end":672},"obj":"Body_part"},{"id":"T48","span":{"begin":897,"end":904},"obj":"Body_part"},{"id":"T49","span":{"begin":994,"end":1004},"obj":"Body_part"}],"attributes":[{"id":"A44","pred":"fma_id","subj":"T44","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A45","pred":"fma_id","subj":"T45","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A46","pred":"fma_id","subj":"T46","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A47","pred":"fma_id","subj":"T47","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A48","pred":"fma_id","subj":"T48","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A49","pred":"fma_id","subj":"T49","obj":"http://purl.org/sig/ont/fma/fma82739"}],"text":"2.3. Detection of Conserved Peptides Among Coronavirus\nIn an attempt to detect protein fragments that are conserved across a wide range of members of the coronavirus family, full-length consensus ORF from SARS-CoV-2 were aligned with other coronavirus sequences. Three alignments were performed based on different sequence selection criteria: (i) 50 reference sequences (RefSeq) with the lowest E-values resulting from a pBLAST search [51] using the ORF-specific consensus sequences (pan-coronavirus alignment) (ii) homologous proteins from 17 viruses representing the Betacoronavirus taxon (beta-coronavirus alignment) or, (iii) homologous proteins from the 7 full-genome sequenced human coronaviruses (including SARS-CoV, MERS-CoV, and common cold species OC43, NL63, 229E, HKU1, human-coronavirus alignment). Selected sequences were aligned using the MUSCLE algorithm in MEGA X [52]. Conserved protein fragments were identified using BioEdit with the following criteria: minimum length of 8 amino acid, maximum average entropy of 0.25, maximum entropy per position of 1 and limiting the search to 1 gap per segment. Sequence logos were generated for the aligned peptides on Weblogo [53]."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T36","span":{"begin":205,"end":213},"obj":"Disease"},{"id":"T37","span":{"begin":714,"end":722},"obj":"Disease"},{"id":"T38","span":{"begin":738,"end":749},"obj":"Disease"}],"attributes":[{"id":"A36","pred":"mondo_id","subj":"T36","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A37","pred":"mondo_id","subj":"T37","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A38","pred":"mondo_id","subj":"T38","obj":"http://purl.obolibrary.org/obo/MONDO_0005709"}],"text":"2.3. Detection of Conserved Peptides Among Coronavirus\nIn an attempt to detect protein fragments that are conserved across a wide range of members of the coronavirus family, full-length consensus ORF from SARS-CoV-2 were aligned with other coronavirus sequences. Three alignments were performed based on different sequence selection criteria: (i) 50 reference sequences (RefSeq) with the lowest E-values resulting from a pBLAST search [51] using the ORF-specific consensus sequences (pan-coronavirus alignment) (ii) homologous proteins from 17 viruses representing the Betacoronavirus taxon (beta-coronavirus alignment) or, (iii) homologous proteins from the 7 full-genome sequenced human coronaviruses (including SARS-CoV, MERS-CoV, and common cold species OC43, NL63, 229E, HKU1, human-coronavirus alignment). Selected sequences were aligned using the MUSCLE algorithm in MEGA X [52]. Conserved protein fragments were identified using BioEdit with the following criteria: minimum length of 8 amino acid, maximum average entropy of 0.25, maximum entropy per position of 1 and limiting the search to 1 gap per segment. Sequence logos were generated for the aligned peptides on Weblogo [53]."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T75","span":{"begin":28,"end":36},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T76","span":{"begin":123,"end":124},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T77","span":{"begin":419,"end":420},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T78","span":{"begin":484,"end":487},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9596"},{"id":"T79","span":{"begin":544,"end":551},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T80","span":{"begin":683,"end":688},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T81","span":{"begin":782,"end":787},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T82","span":{"begin":854,"end":860},"obj":"http://purl.obolibrary.org/obo/UBERON_0001630"},{"id":"T83","span":{"begin":854,"end":860},"obj":"http://purl.obolibrary.org/obo/UBERON_0005090"},{"id":"T84","span":{"begin":854,"end":860},"obj":"http://www.ebi.ac.uk/efo/EFO_0000801"},{"id":"T85","span":{"begin":854,"end":860},"obj":"http://www.ebi.ac.uk/efo/EFO_0001949"},{"id":"T86","span":{"begin":882,"end":884},"obj":"http://purl.obolibrary.org/obo/CLO_0001407"},{"id":"T87","span":{"begin":1102,"end":1109},"obj":"http://purl.obolibrary.org/obo/CLO_0003453"},{"id":"T88","span":{"begin":1165,"end":1173},"obj":"http://purl.obolibrary.org/obo/PR_000018263"}],"text":"2.3. Detection of Conserved Peptides Among Coronavirus\nIn an attempt to detect protein fragments that are conserved across a wide range of members of the coronavirus family, full-length consensus ORF from SARS-CoV-2 were aligned with other coronavirus sequences. Three alignments were performed based on different sequence selection criteria: (i) 50 reference sequences (RefSeq) with the lowest E-values resulting from a pBLAST search [51] using the ORF-specific consensus sequences (pan-coronavirus alignment) (ii) homologous proteins from 17 viruses representing the Betacoronavirus taxon (beta-coronavirus alignment) or, (iii) homologous proteins from the 7 full-genome sequenced human coronaviruses (including SARS-CoV, MERS-CoV, and common cold species OC43, NL63, 229E, HKU1, human-coronavirus alignment). Selected sequences were aligned using the MUSCLE algorithm in MEGA X [52]. Conserved protein fragments were identified using BioEdit with the following criteria: minimum length of 8 amino acid, maximum average entropy of 0.25, maximum entropy per position of 1 and limiting the search to 1 gap per segment. Sequence logos were generated for the aligned peptides on Weblogo [53]."}

{"project":"LitCovid-PubTator","denotations":[{"id":"118","span":{"begin":154,"end":165},"obj":"Species"},{"id":"119","span":{"begin":205,"end":215},"obj":"Species"},{"id":"120","span":{"begin":240,"end":251},"obj":"Species"},{"id":"121","span":{"begin":488,"end":499},"obj":"Species"},{"id":"122","span":{"begin":569,"end":584},"obj":"Species"},{"id":"123","span":{"begin":592,"end":608},"obj":"Species"},{"id":"124","span":{"begin":683,"end":688},"obj":"Species"},{"id":"125","span":{"begin":689,"end":702},"obj":"Species"},{"id":"126","span":{"begin":714,"end":722},"obj":"Species"},{"id":"127","span":{"begin":724,"end":732},"obj":"Species"},{"id":"128","span":{"begin":782,"end":799},"obj":"Species"},{"id":"129","span":{"begin":770,"end":774},"obj":"Species"},{"id":"130","span":{"begin":745,"end":749},"obj":"Disease"},{"id":"131","span":{"begin":776,"end":780},"obj":"CellLine"}],"attributes":[{"id":"A118","pred":"tao:has_database_id","subj":"118","obj":"Tax:11118"},{"id":"A119","pred":"tao:has_database_id","subj":"119","obj":"Tax:2697049"},{"id":"A120","pred":"tao:has_database_id","subj":"120","obj":"Tax:11118"},{"id":"A121","pred":"tao:has_database_id","subj":"121","obj":"Tax:11118"},{"id":"A122","pred":"tao:has_database_id","subj":"122","obj":"Tax:694002"},{"id":"A123","pred":"tao:has_database_id","subj":"123","obj":"Tax:694002"},{"id":"A124","pred":"tao:has_database_id","subj":"124","obj":"Tax:9606"},{"id":"A125","pred":"tao:has_database_id","subj":"125","obj":"Tax:11118"},{"id":"A126","pred":"tao:has_database_id","subj":"126","obj":"Tax:694009"},{"id":"A127","pred":"tao:has_database_id","subj":"127","obj":"Tax:1335626"},{"id":"A128","pred":"tao:has_database_id","subj":"128","obj":"Tax:694448"},{"id":"A129","pred":"tao:has_database_id","subj":"129","obj":"Tax:11137"},{"id":"A130","pred":"tao:has_database_id","subj":"130","obj":"MESH:D000067390"},{"id":"A131","pred":"tao:has_database_id","subj":"131","obj":"CVCL:B526"}],"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":"2.3. Detection of Conserved Peptides Among Coronavirus\nIn an attempt to detect protein fragments that are conserved across a wide range of members of the coronavirus family, full-length consensus ORF from SARS-CoV-2 were aligned with other coronavirus sequences. Three alignments were performed based on different sequence selection criteria: (i) 50 reference sequences (RefSeq) with the lowest E-values resulting from a pBLAST search [51] using the ORF-specific consensus sequences (pan-coronavirus alignment) (ii) homologous proteins from 17 viruses representing the Betacoronavirus taxon (beta-coronavirus alignment) or, (iii) homologous proteins from the 7 full-genome sequenced human coronaviruses (including SARS-CoV, MERS-CoV, and common cold species OC43, NL63, 229E, HKU1, human-coronavirus alignment). Selected sequences were aligned using the MUSCLE algorithm in MEGA X [52]. Conserved protein fragments were identified using BioEdit with the following criteria: minimum length of 8 amino acid, maximum average entropy of 0.25, maximum entropy per position of 1 and limiting the search to 1 gap per segment. Sequence logos were generated for the aligned peptides on Weblogo [53]."}

{"project":"LitCovid-sentences","denotations":[{"id":"T60","span":{"begin":0,"end":4},"obj":"Sentence"},{"id":"T61","span":{"begin":5,"end":54},"obj":"Sentence"},{"id":"T62","span":{"begin":55,"end":262},"obj":"Sentence"},{"id":"T63","span":{"begin":263,"end":811},"obj":"Sentence"},{"id":"T64","span":{"begin":812,"end":886},"obj":"Sentence"},{"id":"T65","span":{"begin":887,"end":1118},"obj":"Sentence"},{"id":"T66","span":{"begin":1119,"end":1190},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"2.3. Detection of Conserved Peptides Among Coronavirus\nIn an attempt to detect protein fragments that are conserved across a wide range of members of the coronavirus family, full-length consensus ORF from SARS-CoV-2 were aligned with other coronavirus sequences. Three alignments were performed based on different sequence selection criteria: (i) 50 reference sequences (RefSeq) with the lowest E-values resulting from a pBLAST search [51] using the ORF-specific consensus sequences (pan-coronavirus alignment) (ii) homologous proteins from 17 viruses representing the Betacoronavirus taxon (beta-coronavirus alignment) or, (iii) homologous proteins from the 7 full-genome sequenced human coronaviruses (including SARS-CoV, MERS-CoV, and common cold species OC43, NL63, 229E, HKU1, human-coronavirus alignment). Selected sequences were aligned using the MUSCLE algorithm in MEGA X [52]. Conserved protein fragments were identified using BioEdit with the following criteria: minimum length of 8 amino acid, maximum average entropy of 0.25, maximum entropy per position of 1 and limiting the search to 1 gap per segment. Sequence logos were generated for the aligned peptides on Weblogo [53]."}