PMC:7565482 / 15716-16487 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T77","span":{"begin":74,"end":84},"obj":"Body_part"},{"id":"T78","span":{"begin":120,"end":126},"obj":"Body_part"},{"id":"T79","span":{"begin":138,"end":149},"obj":"Body_part"},{"id":"T80","span":{"begin":252,"end":255},"obj":"Body_part"},{"id":"T81","span":{"begin":295,"end":303},"obj":"Body_part"},{"id":"T82","span":{"begin":446,"end":450},"obj":"Body_part"}],"attributes":[{"id":"A77","pred":"fma_id","subj":"T77","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A78","pred":"fma_id","subj":"T78","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A79","pred":"fma_id","subj":"T79","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A80","pred":"fma_id","subj":"T80","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A81","pred":"fma_id","subj":"T81","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A82","pred":"fma_id","subj":"T82","obj":"http://purl.org/sig/ont/fma/fma68646"}],"text":"Based on the SARS-CoV-2 alignment used to design the consensus, only nine amino acid positions in the entire SARS-CoV-2 genome showed two amino acids present in at least 25% of the sequences (Figure 2). Three of them were located in ORF1ab, one in the RNA polymerase and two in the Helicase sub-proteins. None of them were located close enough to each other to affect the same OLP. Still, the synthesis of a single consensus peptide could miss T cell responses in individuals exposed to the virus with the subdominant sequence variant. To prevent missing responses, a small number of additional OLP containing each of the variants were generated to cover the variability of these OLP, creating an additional set of 31 different variant OLP in the 15–11 OLP set (Table 2)."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T43","span":{"begin":13,"end":21},"obj":"Disease"},{"id":"T44","span":{"begin":109,"end":117},"obj":"Disease"}],"attributes":[{"id":"A43","pred":"mondo_id","subj":"T43","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A44","pred":"mondo_id","subj":"T44","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"Based on the SARS-CoV-2 alignment used to design the consensus, only nine amino acid positions in the entire SARS-CoV-2 genome showed two amino acids present in at least 25% of the sequences (Figure 2). Three of them were located in ORF1ab, one in the RNA polymerase and two in the Helicase sub-proteins. None of them were located close enough to each other to affect the same OLP. Still, the synthesis of a single consensus peptide could miss T cell responses in individuals exposed to the virus with the subdominant sequence variant. To prevent missing responses, a small number of additional OLP containing each of the variants were generated to cover the variability of these OLP, creating an additional set of 31 different variant OLP in the 15–11 OLP set (Table 2)."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T132","span":{"begin":406,"end":407},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T133","span":{"begin":425,"end":432},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T134","span":{"begin":444,"end":450},"obj":"http://purl.obolibrary.org/obo/CL_0000084"},{"id":"T135","span":{"begin":491,"end":496},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T136","span":{"begin":566,"end":567},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T137","span":{"begin":750,"end":752},"obj":"http://purl.obolibrary.org/obo/CLO_0053733"}],"text":"Based on the SARS-CoV-2 alignment used to design the consensus, only nine amino acid positions in the entire SARS-CoV-2 genome showed two amino acids present in at least 25% of the sequences (Figure 2). Three of them were located in ORF1ab, one in the RNA polymerase and two in the Helicase sub-proteins. None of them were located close enough to each other to affect the same OLP. Still, the synthesis of a single consensus peptide could miss T cell responses in individuals exposed to the virus with the subdominant sequence variant. To prevent missing responses, a small number of additional OLP containing each of the variants were generated to cover the variability of these OLP, creating an additional set of 31 different variant OLP in the 15–11 OLP set (Table 2)."}

{"project":"LitCovid-PubTator","denotations":[{"id":"178","span":{"begin":233,"end":239},"obj":"Gene"},{"id":"179","span":{"begin":282,"end":290},"obj":"Gene"},{"id":"180","span":{"begin":13,"end":23},"obj":"Species"},{"id":"181","span":{"begin":109,"end":119},"obj":"Species"}],"attributes":[{"id":"A178","pred":"tao:has_database_id","subj":"178","obj":"Gene:43740578"},{"id":"A179","pred":"tao:has_database_id","subj":"179","obj":"Gene:164045"},{"id":"A180","pred":"tao:has_database_id","subj":"180","obj":"Tax:2697049"},{"id":"A181","pred":"tao:has_database_id","subj":"181","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":"Based on the SARS-CoV-2 alignment used to design the consensus, only nine amino acid positions in the entire SARS-CoV-2 genome showed two amino acids present in at least 25% of the sequences (Figure 2). Three of them were located in ORF1ab, one in the RNA polymerase and two in the Helicase sub-proteins. None of them were located close enough to each other to affect the same OLP. Still, the synthesis of a single consensus peptide could miss T cell responses in individuals exposed to the virus with the subdominant sequence variant. To prevent missing responses, a small number of additional OLP containing each of the variants were generated to cover the variability of these OLP, creating an additional set of 31 different variant OLP in the 15–11 OLP set (Table 2)."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T15","span":{"begin":393,"end":402},"obj":"http://purl.obolibrary.org/obo/GO_0009058"}],"text":"Based on the SARS-CoV-2 alignment used to design the consensus, only nine amino acid positions in the entire SARS-CoV-2 genome showed two amino acids present in at least 25% of the sequences (Figure 2). Three of them were located in ORF1ab, one in the RNA polymerase and two in the Helicase sub-proteins. None of them were located close enough to each other to affect the same OLP. Still, the synthesis of a single consensus peptide could miss T cell responses in individuals exposed to the virus with the subdominant sequence variant. To prevent missing responses, a small number of additional OLP containing each of the variants were generated to cover the variability of these OLP, creating an additional set of 31 different variant OLP in the 15–11 OLP set (Table 2)."}

{"project":"LitCovid-sentences","denotations":[{"id":"T108","span":{"begin":0,"end":202},"obj":"Sentence"},{"id":"T109","span":{"begin":203,"end":304},"obj":"Sentence"},{"id":"T110","span":{"begin":305,"end":381},"obj":"Sentence"},{"id":"T111","span":{"begin":382,"end":535},"obj":"Sentence"},{"id":"T112","span":{"begin":536,"end":771},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Based on the SARS-CoV-2 alignment used to design the consensus, only nine amino acid positions in the entire SARS-CoV-2 genome showed two amino acids present in at least 25% of the sequences (Figure 2). Three of them were located in ORF1ab, one in the RNA polymerase and two in the Helicase sub-proteins. None of them were located close enough to each other to affect the same OLP. Still, the synthesis of a single consensus peptide could miss T cell responses in individuals exposed to the virus with the subdominant sequence variant. To prevent missing responses, a small number of additional OLP containing each of the variants were generated to cover the variability of these OLP, creating an additional set of 31 different variant OLP in the 15–11 OLP set (Table 2)."}