PMC:7258756 / 35104-36491 JSONTXT

{"project":"LitCovid-PubTator","denotations":[{"id":"534","span":{"begin":516,"end":521},"obj":"Gene"},{"id":"535","span":{"begin":381,"end":386},"obj":"Gene"},{"id":"536","span":{"begin":44,"end":49},"obj":"Gene"},{"id":"537","span":{"begin":10,"end":18},"obj":"Species"},{"id":"538","span":{"begin":684,"end":692},"obj":"Species"},{"id":"539","span":{"begin":1000,"end":1008},"obj":"Species"},{"id":"540","span":{"begin":1293,"end":1303},"obj":"Species"},{"id":"541","span":{"begin":1308,"end":1316},"obj":"Species"}],"attributes":[{"id":"A534","pred":"tao:has_database_id","subj":"534","obj":"Gene:3458"},{"id":"A535","pred":"tao:has_database_id","subj":"535","obj":"Gene:43740568"},{"id":"A536","pred":"tao:has_database_id","subj":"536","obj":"Gene:43740568"},{"id":"A537","pred":"tao:has_database_id","subj":"537","obj":"Tax:694009"},{"id":"A538","pred":"tao:has_database_id","subj":"538","obj":"Tax:694009"},{"id":"A539","pred":"tao:has_database_id","subj":"539","obj":"Tax:694009"},{"id":"A540","pred":"tao:has_database_id","subj":"540","obj":"Tax:2697049"},{"id":"A541","pred":"tao:has_database_id","subj":"541","obj":"Tax:694009"}],"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":"Among the SARS-CoV structural proteins, the spike protein has been found to elicit neutralizing antibodies24. In this study, it was observed that of the five B-cell linear epitopes, which were predicted, four epitopes were present in the S1 domain and one in the S2 domain. Prediction of conformational B-cell epitopes revealed that one of these (residue positions 341-505) in the spike protein incorporates two of the predicted linear epitopes (327-342 and 404-419) having good antigenicity along with a favourable IFN-γ response that enables differentiation and proliferation of the B-cells25. Notably, an equivalent epitope (347-499) is predicted for the model generated using the SARS-CoV-1 S protein as a template. In both cases, this epitope lies within the RBD6. Although the epitope has two putative N-linked glycosylation sites within it at positions 330 and 332, the probability of these sites being actually glycosylated is very low. A major immuno-dominant epitope has been reported from SARS-CoV between residues 441 and 70026. Hence, the predicted B-cell conformational epitope identified in the present study may play an important role in initiating a B-cell response. Among the five linear epitopes predicted in this study, epitopes 327-342 and 1204-1219 are conserved between SARS-CoV-2 and SARS-CoV-1. Epitopes 243-258, 404-419 and 413-428 are found to have variations."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T236","span":{"begin":30,"end":38},"obj":"Body_part"},{"id":"T237","span":{"begin":50,"end":57},"obj":"Body_part"},{"id":"T238","span":{"begin":160,"end":164},"obj":"Body_part"},{"id":"T239","span":{"begin":305,"end":309},"obj":"Body_part"},{"id":"T240","span":{"begin":387,"end":394},"obj":"Body_part"},{"id":"T241","span":{"begin":697,"end":704},"obj":"Body_part"},{"id":"T242","span":{"begin":1064,"end":1068},"obj":"Body_part"},{"id":"T243","span":{"begin":1169,"end":1173},"obj":"Body_part"}],"attributes":[{"id":"A236","pred":"fma_id","subj":"T236","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A237","pred":"fma_id","subj":"T237","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A238","pred":"fma_id","subj":"T238","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A239","pred":"fma_id","subj":"T239","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A240","pred":"fma_id","subj":"T240","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A241","pred":"fma_id","subj":"T241","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A242","pred":"fma_id","subj":"T242","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A243","pred":"fma_id","subj":"T243","obj":"http://purl.org/sig/ont/fma/fma68646"}],"text":"Among the SARS-CoV structural proteins, the spike protein has been found to elicit neutralizing antibodies24. In this study, it was observed that of the five B-cell linear epitopes, which were predicted, four epitopes were present in the S1 domain and one in the S2 domain. Prediction of conformational B-cell epitopes revealed that one of these (residue positions 341-505) in the spike protein incorporates two of the predicted linear epitopes (327-342 and 404-419) having good antigenicity along with a favourable IFN-γ response that enables differentiation and proliferation of the B-cells25. Notably, an equivalent epitope (347-499) is predicted for the model generated using the SARS-CoV-1 S protein as a template. In both cases, this epitope lies within the RBD6. Although the epitope has two putative N-linked glycosylation sites within it at positions 330 and 332, the probability of these sites being actually glycosylated is very low. A major immuno-dominant epitope has been reported from SARS-CoV between residues 441 and 70026. Hence, the predicted B-cell conformational epitope identified in the present study may play an important role in initiating a B-cell response. Among the five linear epitopes predicted in this study, epitopes 327-342 and 1204-1219 are conserved between SARS-CoV-2 and SARS-CoV-1. Epitopes 243-258, 404-419 and 413-428 are found to have variations."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T192","span":{"begin":10,"end":18},"obj":"Disease"},{"id":"T193","span":{"begin":10,"end":14},"obj":"Disease"},{"id":"T194","span":{"begin":684,"end":692},"obj":"Disease"},{"id":"T195","span":{"begin":684,"end":688},"obj":"Disease"},{"id":"T196","span":{"begin":1000,"end":1008},"obj":"Disease"},{"id":"T197","span":{"begin":1000,"end":1004},"obj":"Disease"},{"id":"T198","span":{"begin":1293,"end":1301},"obj":"Disease"},{"id":"T199","span":{"begin":1293,"end":1297},"obj":"Disease"},{"id":"T200","span":{"begin":1308,"end":1316},"obj":"Disease"},{"id":"T201","span":{"begin":1308,"end":1312},"obj":"Disease"}],"attributes":[{"id":"A192","pred":"mondo_id","subj":"T192","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A193","pred":"mondo_id","subj":"T193","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A194","pred":"mondo_id","subj":"T194","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A195","pred":"mondo_id","subj":"T195","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A196","pred":"mondo_id","subj":"T196","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A197","pred":"mondo_id","subj":"T197","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A198","pred":"mondo_id","subj":"T198","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A199","pred":"mondo_id","subj":"T199","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A200","pred":"mondo_id","subj":"T200","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A201","pred":"mondo_id","subj":"T201","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"Among the SARS-CoV structural proteins, the spike protein has been found to elicit neutralizing antibodies24. In this study, it was observed that of the five B-cell linear epitopes, which were predicted, four epitopes were present in the S1 domain and one in the S2 domain. Prediction of conformational B-cell epitopes revealed that one of these (residue positions 341-505) in the spike protein incorporates two of the predicted linear epitopes (327-342 and 404-419) having good antigenicity along with a favourable IFN-γ response that enables differentiation and proliferation of the B-cells25. Notably, an equivalent epitope (347-499) is predicted for the model generated using the SARS-CoV-1 S protein as a template. In both cases, this epitope lies within the RBD6. Although the epitope has two putative N-linked glycosylation sites within it at positions 330 and 332, the probability of these sites being actually glycosylated is very low. A major immuno-dominant epitope has been reported from SARS-CoV between residues 441 and 70026. Hence, the predicted B-cell conformational epitope identified in the present study may play an important role in initiating a B-cell response. Among the five linear epitopes predicted in this study, epitopes 327-342 and 1204-1219 are conserved between SARS-CoV-2 and SARS-CoV-1. Epitopes 243-258, 404-419 and 413-428 are found to have variations."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T280","span":{"begin":58,"end":61},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T281","span":{"begin":158,"end":164},"obj":"http://purl.obolibrary.org/obo/CL_0000236"},{"id":"T282","span":{"begin":238,"end":240},"obj":"http://purl.obolibrary.org/obo/CLO_0050050"},{"id":"T283","span":{"begin":263,"end":265},"obj":"http://purl.obolibrary.org/obo/CLO_0008922"},{"id":"T284","span":{"begin":263,"end":265},"obj":"http://purl.obolibrary.org/obo/CLO_0050052"},{"id":"T285","span":{"begin":303,"end":309},"obj":"http://purl.obolibrary.org/obo/CL_0000236"},{"id":"T286","span":{"begin":503,"end":504},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T287","span":{"begin":585,"end":586},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T288","span":{"begin":708,"end":709},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T289","span":{"begin":791,"end":794},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T290","span":{"begin":945,"end":946},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T291","span":{"begin":977,"end":980},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T292","span":{"begin":1062,"end":1068},"obj":"http://purl.obolibrary.org/obo/CL_0000236"},{"id":"T293","span":{"begin":1165,"end":1166},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T294","span":{"begin":1167,"end":1173},"obj":"http://purl.obolibrary.org/obo/CL_0000236"},{"id":"T295","span":{"begin":1329,"end":1332},"obj":"http://purl.obolibrary.org/obo/CLO_0001178"},{"id":"T296","span":{"begin":1329,"end":1332},"obj":"http://purl.obolibrary.org/obo/CLO_0052433"}],"text":"Among the SARS-CoV structural proteins, the spike protein has been found to elicit neutralizing antibodies24. In this study, it was observed that of the five B-cell linear epitopes, which were predicted, four epitopes were present in the S1 domain and one in the S2 domain. Prediction of conformational B-cell epitopes revealed that one of these (residue positions 341-505) in the spike protein incorporates two of the predicted linear epitopes (327-342 and 404-419) having good antigenicity along with a favourable IFN-γ response that enables differentiation and proliferation of the B-cells25. Notably, an equivalent epitope (347-499) is predicted for the model generated using the SARS-CoV-1 S protein as a template. In both cases, this epitope lies within the RBD6. Although the epitope has two putative N-linked glycosylation sites within it at positions 330 and 332, the probability of these sites being actually glycosylated is very low. A major immuno-dominant epitope has been reported from SARS-CoV between residues 441 and 70026. Hence, the predicted B-cell conformational epitope identified in the present study may play an important role in initiating a B-cell response. Among the five linear epitopes predicted in this study, epitopes 327-342 and 1204-1219 are conserved between SARS-CoV-2 and SARS-CoV-1. Epitopes 243-258, 404-419 and 413-428 are found to have variations."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T150","span":{"begin":30,"end":38},"obj":"Chemical"},{"id":"T151","span":{"begin":50,"end":57},"obj":"Chemical"},{"id":"T152","span":{"begin":263,"end":265},"obj":"Chemical"},{"id":"T153","span":{"begin":387,"end":394},"obj":"Chemical"},{"id":"T154","span":{"begin":619,"end":626},"obj":"Chemical"},{"id":"T155","span":{"begin":697,"end":704},"obj":"Chemical"},{"id":"T156","span":{"begin":740,"end":747},"obj":"Chemical"},{"id":"T157","span":{"begin":783,"end":790},"obj":"Chemical"},{"id":"T158","span":{"begin":969,"end":976},"obj":"Chemical"},{"id":"T159","span":{"begin":1084,"end":1091},"obj":"Chemical"}],"attributes":[{"id":"A150","pred":"chebi_id","subj":"T150","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A151","pred":"chebi_id","subj":"T151","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A152","pred":"chebi_id","subj":"T152","obj":"http://purl.obolibrary.org/obo/CHEBI_29387"},{"id":"A153","pred":"chebi_id","subj":"T153","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A154","pred":"chebi_id","subj":"T154","obj":"http://purl.obolibrary.org/obo/CHEBI_53000"},{"id":"A155","pred":"chebi_id","subj":"T155","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A156","pred":"chebi_id","subj":"T156","obj":"http://purl.obolibrary.org/obo/CHEBI_53000"},{"id":"A157","pred":"chebi_id","subj":"T157","obj":"http://purl.obolibrary.org/obo/CHEBI_53000"},{"id":"A158","pred":"chebi_id","subj":"T158","obj":"http://purl.obolibrary.org/obo/CHEBI_53000"},{"id":"A159","pred":"chebi_id","subj":"T159","obj":"http://purl.obolibrary.org/obo/CHEBI_53000"}],"text":"Among the SARS-CoV structural proteins, the spike protein has been found to elicit neutralizing antibodies24. In this study, it was observed that of the five B-cell linear epitopes, which were predicted, four epitopes were present in the S1 domain and one in the S2 domain. Prediction of conformational B-cell epitopes revealed that one of these (residue positions 341-505) in the spike protein incorporates two of the predicted linear epitopes (327-342 and 404-419) having good antigenicity along with a favourable IFN-γ response that enables differentiation and proliferation of the B-cells25. Notably, an equivalent epitope (347-499) is predicted for the model generated using the SARS-CoV-1 S protein as a template. In both cases, this epitope lies within the RBD6. Although the epitope has two putative N-linked glycosylation sites within it at positions 330 and 332, the probability of these sites being actually glycosylated is very low. A major immuno-dominant epitope has been reported from SARS-CoV between residues 441 and 70026. Hence, the predicted B-cell conformational epitope identified in the present study may play an important role in initiating a B-cell response. Among the five linear epitopes predicted in this study, epitopes 327-342 and 1204-1219 are conserved between SARS-CoV-2 and SARS-CoV-1. Epitopes 243-258, 404-419 and 413-428 are found to have variations."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T26","span":{"begin":808,"end":830},"obj":"http://purl.obolibrary.org/obo/GO_0006487"},{"id":"T27","span":{"begin":817,"end":830},"obj":"http://purl.obolibrary.org/obo/GO_0070085"}],"text":"Among the SARS-CoV structural proteins, the spike protein has been found to elicit neutralizing antibodies24. In this study, it was observed that of the five B-cell linear epitopes, which were predicted, four epitopes were present in the S1 domain and one in the S2 domain. Prediction of conformational B-cell epitopes revealed that one of these (residue positions 341-505) in the spike protein incorporates two of the predicted linear epitopes (327-342 and 404-419) having good antigenicity along with a favourable IFN-γ response that enables differentiation and proliferation of the B-cells25. Notably, an equivalent epitope (347-499) is predicted for the model generated using the SARS-CoV-1 S protein as a template. In both cases, this epitope lies within the RBD6. Although the epitope has two putative N-linked glycosylation sites within it at positions 330 and 332, the probability of these sites being actually glycosylated is very low. A major immuno-dominant epitope has been reported from SARS-CoV between residues 441 and 70026. Hence, the predicted B-cell conformational epitope identified in the present study may play an important role in initiating a B-cell response. Among the five linear epitopes predicted in this study, epitopes 327-342 and 1204-1219 are conserved between SARS-CoV-2 and SARS-CoV-1. Epitopes 243-258, 404-419 and 413-428 are found to have variations."}

{"project":"LitCovid-sentences","denotations":[{"id":"T232","span":{"begin":0,"end":109},"obj":"Sentence"},{"id":"T233","span":{"begin":110,"end":273},"obj":"Sentence"},{"id":"T234","span":{"begin":274,"end":595},"obj":"Sentence"},{"id":"T235","span":{"begin":596,"end":719},"obj":"Sentence"},{"id":"T236","span":{"begin":720,"end":769},"obj":"Sentence"},{"id":"T237","span":{"begin":770,"end":944},"obj":"Sentence"},{"id":"T238","span":{"begin":945,"end":1040},"obj":"Sentence"},{"id":"T239","span":{"begin":1041,"end":1183},"obj":"Sentence"},{"id":"T240","span":{"begin":1184,"end":1319},"obj":"Sentence"},{"id":"T241","span":{"begin":1320,"end":1387},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Among the SARS-CoV structural proteins, the spike protein has been found to elicit neutralizing antibodies24. In this study, it was observed that of the five B-cell linear epitopes, which were predicted, four epitopes were present in the S1 domain and one in the S2 domain. Prediction of conformational B-cell epitopes revealed that one of these (residue positions 341-505) in the spike protein incorporates two of the predicted linear epitopes (327-342 and 404-419) having good antigenicity along with a favourable IFN-γ response that enables differentiation and proliferation of the B-cells25. Notably, an equivalent epitope (347-499) is predicted for the model generated using the SARS-CoV-1 S protein as a template. In both cases, this epitope lies within the RBD6. Although the epitope has two putative N-linked glycosylation sites within it at positions 330 and 332, the probability of these sites being actually glycosylated is very low. A major immuno-dominant epitope has been reported from SARS-CoV between residues 441 and 70026. Hence, the predicted B-cell conformational epitope identified in the present study may play an important role in initiating a B-cell response. Among the five linear epitopes predicted in this study, epitopes 327-342 and 1204-1219 are conserved between SARS-CoV-2 and SARS-CoV-1. Epitopes 243-258, 404-419 and 413-428 are found to have variations."}

{"project":"2_test","denotations":[{"id":"32242873-15210961-47036572","span":{"begin":106,"end":108},"obj":"15210961"},{"id":"32242873-9916700-47036573","span":{"begin":592,"end":594},"obj":"9916700"},{"id":"32242873-32007145-47036574","span":{"begin":767,"end":768},"obj":"32007145"},{"id":"32242873-26038429-47036575","span":{"begin":1034,"end":1039},"obj":"26038429"},{"id":"T80103","span":{"begin":106,"end":108},"obj":"15210961"},{"id":"T68904","span":{"begin":592,"end":594},"obj":"9916700"},{"id":"T89340","span":{"begin":767,"end":768},"obj":"32007145"},{"id":"T29055","span":{"begin":1034,"end":1039},"obj":"26038429"}],"text":"Among the SARS-CoV structural proteins, the spike protein has been found to elicit neutralizing antibodies24. In this study, it was observed that of the five B-cell linear epitopes, which were predicted, four epitopes were present in the S1 domain and one in the S2 domain. Prediction of conformational B-cell epitopes revealed that one of these (residue positions 341-505) in the spike protein incorporates two of the predicted linear epitopes (327-342 and 404-419) having good antigenicity along with a favourable IFN-γ response that enables differentiation and proliferation of the B-cells25. Notably, an equivalent epitope (347-499) is predicted for the model generated using the SARS-CoV-1 S protein as a template. In both cases, this epitope lies within the RBD6. Although the epitope has two putative N-linked glycosylation sites within it at positions 330 and 332, the probability of these sites being actually glycosylated is very low. A major immuno-dominant epitope has been reported from SARS-CoV between residues 441 and 70026. Hence, the predicted B-cell conformational epitope identified in the present study may play an important role in initiating a B-cell response. Among the five linear epitopes predicted in this study, epitopes 327-342 and 1204-1219 are conserved between SARS-CoV-2 and SARS-CoV-1. Epitopes 243-258, 404-419 and 413-428 are found to have variations."}