PMC:7111504 / 2556-3440 JSONTXT

{"project":"LitCovid-PubTator","denotations":[{"id":"48","span":{"begin":840,"end":843},"obj":"Gene"},{"id":"49","span":{"begin":120,"end":129},"obj":"Species"},{"id":"50","span":{"begin":336,"end":389},"obj":"Species"},{"id":"51","span":{"begin":391,"end":399},"obj":"Species"},{"id":"52","span":{"begin":436,"end":445},"obj":"Species"},{"id":"53","span":{"begin":529,"end":538},"obj":"Species"},{"id":"54","span":{"begin":625,"end":629},"obj":"Species"},{"id":"55","span":{"begin":764,"end":771},"obj":"Species"}],"attributes":[{"id":"A48","pred":"tao:has_database_id","subj":"48","obj":"Gene:6962"},{"id":"A49","pred":"tao:has_database_id","subj":"49","obj":"Tax:2697049"},{"id":"A50","pred":"tao:has_database_id","subj":"50","obj":"Tax:694009"},{"id":"A51","pred":"tao:has_database_id","subj":"51","obj":"Tax:694009"},{"id":"A52","pred":"tao:has_database_id","subj":"52","obj":"Tax:2697049"},{"id":"A53","pred":"tao:has_database_id","subj":"53","obj":"Tax:2697049"},{"id":"A54","pred":"tao:has_database_id","subj":"54","obj":"Tax:2697049"},{"id":"A55","pred":"tao:has_database_id","subj":"55","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":"In this regard, we report our recent effort to computationally identify immunogenic and/or cross-reactive peptides from 2019-nCoV. We provide a detailed screen of candidate peptides based on comparison with immunogenic peptides deposited in the Immune Epitope Database and Analysis Resource (IEDB) database including those derived from Severe acute respiratory syndrome-related coronavirus (SARS CoV) along with de novo prediction from 2019-nCoV 9-mer peptides. Here, we found i) 28 SARS-derived peptides having exact matches in 2019-nCoV proteome previously characterized to be immunogenic by in vitro T cell assays, ii) 22 nCoV peptides having a high sequence similarity with immunogenic peptides but with a greater predicted immunogenicity score, and iii) 44 + 19 nCoV peptides predicted to be immunogenic by the iPred algorithm and 1G4 TCR positional weight matrices respectively."}

{"project":"LitCovid-PMC-OGER-BB","denotations":[{"id":"T32","span":{"begin":72,"end":83},"obj":"CHEBI:60816;CHEBI:60816"},{"id":"T33","span":{"begin":120,"end":129},"obj":"SP_7"},{"id":"T34","span":{"begin":207,"end":218},"obj":"CHEBI:60816;CHEBI:60816"},{"id":"T35","span":{"begin":252,"end":259},"obj":"BV_9"},{"id":"T36","span":{"begin":349,"end":360},"obj":"UBERON:0001004"},{"id":"T37","span":{"begin":378,"end":389},"obj":"NCBITaxon:11118"},{"id":"T38","span":{"begin":391,"end":399},"obj":"SP_10"},{"id":"T39","span":{"begin":436,"end":445},"obj":"SP_7"},{"id":"T40","span":{"begin":483,"end":487},"obj":"SP_10"},{"id":"T41","span":{"begin":529,"end":538},"obj":"SP_7"},{"id":"T42","span":{"begin":579,"end":590},"obj":"CHEBI:60816;CHEBI:60816"},{"id":"T43","span":{"begin":594,"end":602},"obj":"CL:0001034"},{"id":"T44","span":{"begin":603,"end":609},"obj":"CL:0000084;BV_23"},{"id":"T45","span":{"begin":610,"end":616},"obj":"BV_23"},{"id":"T46","span":{"begin":678,"end":689},"obj":"CHEBI:60816;CHEBI:60816"},{"id":"T47","span":{"begin":728,"end":742},"obj":"BV_15"},{"id":"T48","span":{"begin":797,"end":808},"obj":"CHEBI:60816;CHEBI:60816"},{"id":"T54000","span":{"begin":72,"end":83},"obj":"CHEBI:60816;CHEBI:60816"},{"id":"T55605","span":{"begin":120,"end":129},"obj":"SP_7"},{"id":"T59948","span":{"begin":207,"end":218},"obj":"CHEBI:60816;CHEBI:60816"},{"id":"T85994","span":{"begin":252,"end":259},"obj":"BV_9"},{"id":"T37622","span":{"begin":349,"end":360},"obj":"UBERON:0001004"},{"id":"T60436","span":{"begin":378,"end":389},"obj":"NCBITaxon:11118"},{"id":"T19609","span":{"begin":391,"end":399},"obj":"SP_10"},{"id":"T53947","span":{"begin":436,"end":445},"obj":"SP_7"},{"id":"T59966","span":{"begin":483,"end":487},"obj":"SP_10"},{"id":"T58907","span":{"begin":529,"end":538},"obj":"SP_7"},{"id":"T79712","span":{"begin":579,"end":590},"obj":"CHEBI:60816;CHEBI:60816"},{"id":"T51170","span":{"begin":594,"end":602},"obj":"CL:0001034"},{"id":"T50252","span":{"begin":603,"end":609},"obj":"CL:0000084;BV_23"},{"id":"T88075","span":{"begin":610,"end":616},"obj":"BV_23"},{"id":"T93294","span":{"begin":678,"end":689},"obj":"CHEBI:60816;CHEBI:60816"},{"id":"T3928","span":{"begin":728,"end":742},"obj":"BV_15"},{"id":"T65499","span":{"begin":797,"end":808},"obj":"CHEBI:60816;CHEBI:60816"}],"text":"In this regard, we report our recent effort to computationally identify immunogenic and/or cross-reactive peptides from 2019-nCoV. We provide a detailed screen of candidate peptides based on comparison with immunogenic peptides deposited in the Immune Epitope Database and Analysis Resource (IEDB) database including those derived from Severe acute respiratory syndrome-related coronavirus (SARS CoV) along with de novo prediction from 2019-nCoV 9-mer peptides. Here, we found i) 28 SARS-derived peptides having exact matches in 2019-nCoV proteome previously characterized to be immunogenic by in vitro T cell assays, ii) 22 nCoV peptides having a high sequence similarity with immunogenic peptides but with a greater predicted immunogenicity score, and iii) 44 + 19 nCoV peptides predicted to be immunogenic by the iPred algorithm and 1G4 TCR positional weight matrices respectively."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T5","span":{"begin":605,"end":609},"obj":"Body_part"}],"attributes":[{"id":"A5","pred":"fma_id","subj":"T5","obj":"http://purl.org/sig/ont/fma/fma68646"}],"text":"In this regard, we report our recent effort to computationally identify immunogenic and/or cross-reactive peptides from 2019-nCoV. We provide a detailed screen of candidate peptides based on comparison with immunogenic peptides deposited in the Immune Epitope Database and Analysis Resource (IEDB) database including those derived from Severe acute respiratory syndrome-related coronavirus (SARS CoV) along with de novo prediction from 2019-nCoV 9-mer peptides. Here, we found i) 28 SARS-derived peptides having exact matches in 2019-nCoV proteome previously characterized to be immunogenic by in vitro T cell assays, ii) 22 nCoV peptides having a high sequence similarity with immunogenic peptides but with a greater predicted immunogenicity score, and iii) 44 + 19 nCoV peptides predicted to be immunogenic by the iPred algorithm and 1G4 TCR positional weight matrices respectively."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T3","span":{"begin":336,"end":369},"obj":"Disease"},{"id":"T4","span":{"begin":391,"end":395},"obj":"Disease"},{"id":"T5","span":{"begin":483,"end":487},"obj":"Disease"}],"attributes":[{"id":"A3","pred":"mondo_id","subj":"T3","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A4","pred":"mondo_id","subj":"T4","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A5","pred":"mondo_id","subj":"T5","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"In this regard, we report our recent effort to computationally identify immunogenic and/or cross-reactive peptides from 2019-nCoV. We provide a detailed screen of candidate peptides based on comparison with immunogenic peptides deposited in the Immune Epitope Database and Analysis Resource (IEDB) database including those derived from Severe acute respiratory syndrome-related coronavirus (SARS CoV) along with de novo prediction from 2019-nCoV 9-mer peptides. Here, we found i) 28 SARS-derived peptides having exact matches in 2019-nCoV proteome previously characterized to be immunogenic by in vitro T cell assays, ii) 22 nCoV peptides having a high sequence similarity with immunogenic peptides but with a greater predicted immunogenicity score, and iii) 44 + 19 nCoV peptides predicted to be immunogenic by the iPred algorithm and 1G4 TCR positional weight matrices respectively."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T36","span":{"begin":106,"end":114},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T37","span":{"begin":142,"end":143},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T38","span":{"begin":173,"end":181},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T39","span":{"begin":219,"end":227},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T40","span":{"begin":452,"end":460},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T41","span":{"begin":496,"end":504},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T42","span":{"begin":603,"end":609},"obj":"http://purl.obolibrary.org/obo/CL_0000084"},{"id":"T43","span":{"begin":622,"end":624},"obj":"http://purl.obolibrary.org/obo/CLO_0050507"},{"id":"T44","span":{"begin":630,"end":638},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T45","span":{"begin":646,"end":647},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T46","span":{"begin":690,"end":698},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T47","span":{"begin":708,"end":709},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T48","span":{"begin":772,"end":780},"obj":"http://purl.obolibrary.org/obo/PR_000018263"}],"text":"In this regard, we report our recent effort to computationally identify immunogenic and/or cross-reactive peptides from 2019-nCoV. We provide a detailed screen of candidate peptides based on comparison with immunogenic peptides deposited in the Immune Epitope Database and Analysis Resource (IEDB) database including those derived from Severe acute respiratory syndrome-related coronavirus (SARS CoV) along with de novo prediction from 2019-nCoV 9-mer peptides. Here, we found i) 28 SARS-derived peptides having exact matches in 2019-nCoV proteome previously characterized to be immunogenic by in vitro T cell assays, ii) 22 nCoV peptides having a high sequence similarity with immunogenic peptides but with a greater predicted immunogenicity score, and iii) 44 + 19 nCoV peptides predicted to be immunogenic by the iPred algorithm and 1G4 TCR positional weight matrices respectively."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T9","span":{"begin":106,"end":114},"obj":"Chemical"},{"id":"T10","span":{"begin":173,"end":181},"obj":"Chemical"},{"id":"T11","span":{"begin":219,"end":227},"obj":"Chemical"},{"id":"T12","span":{"begin":452,"end":460},"obj":"Chemical"},{"id":"T13","span":{"begin":496,"end":504},"obj":"Chemical"},{"id":"T14","span":{"begin":630,"end":638},"obj":"Chemical"},{"id":"T15","span":{"begin":690,"end":698},"obj":"Chemical"},{"id":"T16","span":{"begin":772,"end":780},"obj":"Chemical"}],"attributes":[{"id":"A9","pred":"chebi_id","subj":"T9","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A10","pred":"chebi_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A11","pred":"chebi_id","subj":"T11","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A12","pred":"chebi_id","subj":"T12","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A13","pred":"chebi_id","subj":"T13","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A14","pred":"chebi_id","subj":"T14","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A15","pred":"chebi_id","subj":"T15","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A16","pred":"chebi_id","subj":"T16","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"}],"text":"In this regard, we report our recent effort to computationally identify immunogenic and/or cross-reactive peptides from 2019-nCoV. We provide a detailed screen of candidate peptides based on comparison with immunogenic peptides deposited in the Immune Epitope Database and Analysis Resource (IEDB) database including those derived from Severe acute respiratory syndrome-related coronavirus (SARS CoV) along with de novo prediction from 2019-nCoV 9-mer peptides. Here, we found i) 28 SARS-derived peptides having exact matches in 2019-nCoV proteome previously characterized to be immunogenic by in vitro T cell assays, ii) 22 nCoV peptides having a high sequence similarity with immunogenic peptides but with a greater predicted immunogenicity score, and iii) 44 + 19 nCoV peptides predicted to be immunogenic by the iPred algorithm and 1G4 TCR positional weight matrices respectively."}

{"project":"LitCovid-sentences","denotations":[{"id":"T23","span":{"begin":0,"end":130},"obj":"Sentence"},{"id":"T24","span":{"begin":131,"end":461},"obj":"Sentence"},{"id":"T25","span":{"begin":462,"end":884},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"In this regard, we report our recent effort to computationally identify immunogenic and/or cross-reactive peptides from 2019-nCoV. We provide a detailed screen of candidate peptides based on comparison with immunogenic peptides deposited in the Immune Epitope Database and Analysis Resource (IEDB) database including those derived from Severe acute respiratory syndrome-related coronavirus (SARS CoV) along with de novo prediction from 2019-nCoV 9-mer peptides. Here, we found i) 28 SARS-derived peptides having exact matches in 2019-nCoV proteome previously characterized to be immunogenic by in vitro T cell assays, ii) 22 nCoV peptides having a high sequence similarity with immunogenic peptides but with a greater predicted immunogenicity score, and iii) 44 + 19 nCoV peptides predicted to be immunogenic by the iPred algorithm and 1G4 TCR positional weight matrices respectively."}