PMC:7258756 / 17871-18945 JSONTXT

{"project":"LitCovid-PubTator","denotations":[{"id":"271","span":{"begin":658,"end":663},"obj":"Gene"},{"id":"272","span":{"begin":875,"end":880},"obj":"Gene"},{"id":"273","span":{"begin":96,"end":106},"obj":"Species"}],"attributes":[{"id":"A271","pred":"tao:has_database_id","subj":"271","obj":"Gene:3458"},{"id":"A272","pred":"tao:has_database_id","subj":"272","obj":"Gene:3458"},{"id":"A273","pred":"tao:has_database_id","subj":"273","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":"Epitope predictions: Thirty one linear B-cell epitopes were predicted by Bepipred in the Indian SARS-CoV-2, of which three were found to have a length of \u003c6 amino acids and hence not considered. Linear epitopes were also predicted using the ABCpred prediction tool, which predicted 47 epitopes based on the threshold of 0.8. Regions common to both the prediction methods (n=17) were identified manually. The 17 epitopes were screened for their antigenicity using the VaxiJen v2.0 tool (http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html), and nine of these epitopes were shortlisted. These epitopes were further screened for their ability to elicit an IFN-γ response, which was predicted using the IFNepitope tool. Finally, five epitopes, four in the S1 domain and one in the S2 domain, were predicted, which could possibly generate an immune response and suppress the IFN-γ response (Table II). N-linked glycosylation site prediction revealed that two putative glycosylation sites (with a low value for jury agreement) were present within the epitope stretch 328-344."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T94","span":{"begin":41,"end":45},"obj":"Body_part"},{"id":"T95","span":{"begin":157,"end":168},"obj":"Body_part"}],"attributes":[{"id":"A94","pred":"fma_id","subj":"T94","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A95","pred":"fma_id","subj":"T95","obj":"http://purl.org/sig/ont/fma/fma82739"}],"text":"Epitope predictions: Thirty one linear B-cell epitopes were predicted by Bepipred in the Indian SARS-CoV-2, of which three were found to have a length of \u003c6 amino acids and hence not considered. Linear epitopes were also predicted using the ABCpred prediction tool, which predicted 47 epitopes based on the threshold of 0.8. Regions common to both the prediction methods (n=17) were identified manually. The 17 epitopes were screened for their antigenicity using the VaxiJen v2.0 tool (http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html), and nine of these epitopes were shortlisted. These epitopes were further screened for their ability to elicit an IFN-γ response, which was predicted using the IFNepitope tool. Finally, five epitopes, four in the S1 domain and one in the S2 domain, were predicted, which could possibly generate an immune response and suppress the IFN-γ response (Table II). N-linked glycosylation site prediction revealed that two putative glycosylation sites (with a low value for jury agreement) were present within the epitope stretch 328-344."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T149","span":{"begin":96,"end":104},"obj":"Disease"},{"id":"T150","span":{"begin":96,"end":100},"obj":"Disease"}],"attributes":[{"id":"A149","pred":"mondo_id","subj":"T149","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A150","pred":"mondo_id","subj":"T150","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"Epitope predictions: Thirty one linear B-cell epitopes were predicted by Bepipred in the Indian SARS-CoV-2, of which three were found to have a length of \u003c6 amino acids and hence not considered. Linear epitopes were also predicted using the ABCpred prediction tool, which predicted 47 epitopes based on the threshold of 0.8. Regions common to both the prediction methods (n=17) were identified manually. The 17 epitopes were screened for their antigenicity using the VaxiJen v2.0 tool (http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html), and nine of these epitopes were shortlisted. These epitopes were further screened for their ability to elicit an IFN-γ response, which was predicted using the IFNepitope tool. Finally, five epitopes, four in the S1 domain and one in the S2 domain, were predicted, which could possibly generate an immune response and suppress the IFN-γ response (Table II). N-linked glycosylation site prediction revealed that two putative glycosylation sites (with a low value for jury agreement) were present within the epitope stretch 328-344."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T123","span":{"begin":39,"end":45},"obj":"http://purl.obolibrary.org/obo/CL_0000236"},{"id":"T124","span":{"begin":142,"end":143},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T125","span":{"begin":757,"end":759},"obj":"http://purl.obolibrary.org/obo/CLO_0050050"},{"id":"T126","span":{"begin":782,"end":784},"obj":"http://purl.obolibrary.org/obo/CLO_0008922"},{"id":"T127","span":{"begin":782,"end":784},"obj":"http://purl.obolibrary.org/obo/CLO_0050052"},{"id":"T128","span":{"begin":994,"end":995},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"Epitope predictions: Thirty one linear B-cell epitopes were predicted by Bepipred in the Indian SARS-CoV-2, of which three were found to have a length of \u003c6 amino acids and hence not considered. Linear epitopes were also predicted using the ABCpred prediction tool, which predicted 47 epitopes based on the threshold of 0.8. Regions common to both the prediction methods (n=17) were identified manually. The 17 epitopes were screened for their antigenicity using the VaxiJen v2.0 tool (http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html), and nine of these epitopes were shortlisted. These epitopes were further screened for their ability to elicit an IFN-γ response, which was predicted using the IFNepitope tool. Finally, five epitopes, four in the S1 domain and one in the S2 domain, were predicted, which could possibly generate an immune response and suppress the IFN-γ response (Table II). N-linked glycosylation site prediction revealed that two putative glycosylation sites (with a low value for jury agreement) were present within the epitope stretch 328-344."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T90","span":{"begin":157,"end":168},"obj":"Chemical"},{"id":"T91","span":{"begin":157,"end":162},"obj":"Chemical"},{"id":"T92","span":{"begin":163,"end":168},"obj":"Chemical"},{"id":"T93","span":{"begin":782,"end":784},"obj":"Chemical"},{"id":"T94","span":{"begin":897,"end":899},"obj":"Chemical"},{"id":"T95","span":{"begin":1050,"end":1057},"obj":"Chemical"}],"attributes":[{"id":"A90","pred":"chebi_id","subj":"T90","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"},{"id":"A91","pred":"chebi_id","subj":"T91","obj":"http://purl.obolibrary.org/obo/CHEBI_46882"},{"id":"A92","pred":"chebi_id","subj":"T92","obj":"http://purl.obolibrary.org/obo/CHEBI_37527"},{"id":"A93","pred":"chebi_id","subj":"T93","obj":"http://purl.obolibrary.org/obo/CHEBI_29387"},{"id":"A94","pred":"chebi_id","subj":"T94","obj":"http://purl.obolibrary.org/obo/CHEBI_74067"},{"id":"A95","pred":"chebi_id","subj":"T95","obj":"http://purl.obolibrary.org/obo/CHEBI_53000"}],"text":"Epitope predictions: Thirty one linear B-cell epitopes were predicted by Bepipred in the Indian SARS-CoV-2, of which three were found to have a length of \u003c6 amino acids and hence not considered. Linear epitopes were also predicted using the ABCpred prediction tool, which predicted 47 epitopes based on the threshold of 0.8. Regions common to both the prediction methods (n=17) were identified manually. The 17 epitopes were screened for their antigenicity using the VaxiJen v2.0 tool (http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html), and nine of these epitopes were shortlisted. These epitopes were further screened for their ability to elicit an IFN-γ response, which was predicted using the IFNepitope tool. Finally, five epitopes, four in the S1 domain and one in the S2 domain, were predicted, which could possibly generate an immune response and suppress the IFN-γ response (Table II). N-linked glycosylation site prediction revealed that two putative glycosylation sites (with a low value for jury agreement) were present within the epitope stretch 328-344."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T19","span":{"begin":842,"end":857},"obj":"http://purl.obolibrary.org/obo/GO_0006955"},{"id":"T20","span":{"begin":902,"end":924},"obj":"http://purl.obolibrary.org/obo/GO_0006487"},{"id":"T21","span":{"begin":911,"end":924},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T22","span":{"begin":968,"end":981},"obj":"http://purl.obolibrary.org/obo/GO_0070085"}],"text":"Epitope predictions: Thirty one linear B-cell epitopes were predicted by Bepipred in the Indian SARS-CoV-2, of which three were found to have a length of \u003c6 amino acids and hence not considered. Linear epitopes were also predicted using the ABCpred prediction tool, which predicted 47 epitopes based on the threshold of 0.8. Regions common to both the prediction methods (n=17) were identified manually. The 17 epitopes were screened for their antigenicity using the VaxiJen v2.0 tool (http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html), and nine of these epitopes were shortlisted. These epitopes were further screened for their ability to elicit an IFN-γ response, which was predicted using the IFNepitope tool. Finally, five epitopes, four in the S1 domain and one in the S2 domain, were predicted, which could possibly generate an immune response and suppress the IFN-γ response (Table II). N-linked glycosylation site prediction revealed that two putative glycosylation sites (with a low value for jury agreement) were present within the epitope stretch 328-344."}

{"project":"LitCovid-sentences","denotations":[{"id":"T135","span":{"begin":0,"end":20},"obj":"Sentence"},{"id":"T136","span":{"begin":21,"end":194},"obj":"Sentence"},{"id":"T137","span":{"begin":195,"end":324},"obj":"Sentence"},{"id":"T138","span":{"begin":325,"end":403},"obj":"Sentence"},{"id":"T139","span":{"begin":404,"end":589},"obj":"Sentence"},{"id":"T140","span":{"begin":590,"end":720},"obj":"Sentence"},{"id":"T141","span":{"begin":721,"end":901},"obj":"Sentence"},{"id":"T142","span":{"begin":902,"end":1074},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Epitope predictions: Thirty one linear B-cell epitopes were predicted by Bepipred in the Indian SARS-CoV-2, of which three were found to have a length of \u003c6 amino acids and hence not considered. Linear epitopes were also predicted using the ABCpred prediction tool, which predicted 47 epitopes based on the threshold of 0.8. Regions common to both the prediction methods (n=17) were identified manually. The 17 epitopes were screened for their antigenicity using the VaxiJen v2.0 tool (http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html), and nine of these epitopes were shortlisted. These epitopes were further screened for their ability to elicit an IFN-γ response, which was predicted using the IFNepitope tool. Finally, five epitopes, four in the S1 domain and one in the S2 domain, were predicted, which could possibly generate an immune response and suppress the IFN-γ response (Table II). N-linked glycosylation site prediction revealed that two putative glycosylation sites (with a low value for jury agreement) were present within the epitope stretch 328-344."}