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LitCovid-PubTator

{"project":"LitCovid-PubTator","denotations":[{"id":"81","span":{"begin":61,"end":67},"obj":"Gene"},{"id":"82","span":{"begin":723,"end":726},"obj":"Gene"},{"id":"83","span":{"begin":732,"end":735},"obj":"Gene"},{"id":"84","span":{"begin":884,"end":889},"obj":"Gene"},{"id":"85","span":{"begin":941,"end":952},"obj":"Gene"},{"id":"86","span":{"begin":72,"end":78},"obj":"Gene"},{"id":"87","span":{"begin":91,"end":101},"obj":"Species"}],"attributes":[{"id":"A81","pred":"tao:has_database_id","subj":"81","obj":"Gene:43740569"},{"id":"A82","pred":"tao:has_database_id","subj":"82","obj":"Gene:920"},{"id":"A83","pred":"tao:has_database_id","subj":"83","obj":"Gene:925"},{"id":"A84","pred":"tao:has_database_id","subj":"84","obj":"Gene:43740568"},{"id":"A86","pred":"tao:has_database_id","subj":"86","obj":"Gene:43740573"},{"id":"A87","pred":"tao:has_database_id","subj":"87","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 our investigatory study, out of five, two proteins namely ORF-3a and ORF-7a specific to SARS-COV-2 were found to be putative T-cell epitope determinants that create useful information to distinguish, and these proteins are also important for viral replication and growth [41]. Both of these proteins may influence in viral pathogenesis and disease spread, although the literature lacks unanimity [43]. B-cell epitopes prediction is still considered to be untrustworthy for both linear and conformational epitopes as compared to T-cell epitopes. Furthermore, the B-cell epitopes do not elicit a strong antibody response. For this reason, only T-cell epitopes are considered in the present study. It is capable to produce CD4+ and CD8+ T-cells with long-lasting response [45]. . In one of the recent studies, epitopes were designed, but they have focused on the single protein (i.e. SPIKE protein) to generate multiple epitopes like 13 for MHC I and 3 for MHC II [46]. We have analyzed multiple proteins to screen only effective epitopes based on various in-silico filters, to provide the most appropriate and authentic epitopes, which can be further tested in a wet lab."}

LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T24","span":{"begin":45,"end":53},"obj":"Body_part"},{"id":"T25","span":{"begin":130,"end":134},"obj":"Body_part"},{"id":"T26","span":{"begin":213,"end":221},"obj":"Body_part"},{"id":"T27","span":{"begin":294,"end":302},"obj":"Body_part"},{"id":"T28","span":{"begin":407,"end":411},"obj":"Body_part"},{"id":"T29","span":{"begin":533,"end":537},"obj":"Body_part"},{"id":"T30","span":{"begin":567,"end":571},"obj":"Body_part"},{"id":"T31","span":{"begin":604,"end":612},"obj":"Body_part"},{"id":"T32","span":{"begin":647,"end":651},"obj":"Body_part"},{"id":"T33","span":{"begin":739,"end":744},"obj":"Body_part"},{"id":"T34","span":{"begin":870,"end":877},"obj":"Body_part"},{"id":"T35","span":{"begin":890,"end":897},"obj":"Body_part"},{"id":"T36","span":{"begin":941,"end":944},"obj":"Body_part"},{"id":"T37","span":{"begin":957,"end":960},"obj":"Body_part"},{"id":"T38","span":{"begin":996,"end":1004},"obj":"Body_part"}],"attributes":[{"id":"A24","pred":"fma_id","subj":"T24","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A25","pred":"fma_id","subj":"T25","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A26","pred":"fma_id","subj":"T26","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A27","pred":"fma_id","subj":"T27","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A28","pred":"fma_id","subj":"T28","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A29","pred":"fma_id","subj":"T29","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A30","pred":"fma_id","subj":"T30","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A31","pred":"fma_id","subj":"T31","obj":"http://purl.org/sig/ont/fma/fma62871"},{"id":"A32","pred":"fma_id","subj":"T32","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A33","pred":"fma_id","subj":"T33","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A34","pred":"fma_id","subj":"T34","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A35","pred":"fma_id","subj":"T35","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A36","pred":"fma_id","subj":"T36","obj":"http://purl.org/sig/ont/fma/fma84079"},{"id":"A37","pred":"fma_id","subj":"T37","obj":"http://purl.org/sig/ont/fma/fma84079"},{"id":"A38","pred":"fma_id","subj":"T38","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"In our investigatory study, out of five, two proteins namely ORF-3a and ORF-7a specific to SARS-COV-2 were found to be putative T-cell epitope determinants that create useful information to distinguish, and these proteins are also important for viral replication and growth [41]. Both of these proteins may influence in viral pathogenesis and disease spread, although the literature lacks unanimity [43]. B-cell epitopes prediction is still considered to be untrustworthy for both linear and conformational epitopes as compared to T-cell epitopes. Furthermore, the B-cell epitopes do not elicit a strong antibody response. For this reason, only T-cell epitopes are considered in the present study. It is capable to produce CD4+ and CD8+ T-cells with long-lasting response [45]. . In one of the recent studies, epitopes were designed, but they have focused on the single protein (i.e. SPIKE protein) to generate multiple epitopes like 13 for MHC I and 3 for MHC II [46]. We have analyzed multiple proteins to screen only effective epitopes based on various in-silico filters, to provide the most appropriate and authentic epitopes, which can be further tested in a wet lab."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T17","span":{"begin":91,"end":95},"obj":"Disease"}],"attributes":[{"id":"A17","pred":"mondo_id","subj":"T17","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"In our investigatory study, out of five, two proteins namely ORF-3a and ORF-7a specific to SARS-COV-2 were found to be putative T-cell epitope determinants that create useful information to distinguish, and these proteins are also important for viral replication and growth [41]. Both of these proteins may influence in viral pathogenesis and disease spread, although the literature lacks unanimity [43]. B-cell epitopes prediction is still considered to be untrustworthy for both linear and conformational epitopes as compared to T-cell epitopes. Furthermore, the B-cell epitopes do not elicit a strong antibody response. For this reason, only T-cell epitopes are considered in the present study. It is capable to produce CD4+ and CD8+ T-cells with long-lasting response [45]. . In one of the recent studies, epitopes were designed, but they have focused on the single protein (i.e. SPIKE protein) to generate multiple epitopes like 13 for MHC I and 3 for MHC II [46]. We have analyzed multiple proteins to screen only effective epitopes based on various in-silico filters, to provide the most appropriate and authentic epitopes, which can be further tested in a wet lab."}

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T42","span":{"begin":128,"end":134},"obj":"http://purl.obolibrary.org/obo/CL_0000084"},{"id":"T43","span":{"begin":275,"end":277},"obj":"http://purl.obolibrary.org/obo/CLO_0053794"},{"id":"T44","span":{"begin":405,"end":411},"obj":"http://purl.obolibrary.org/obo/CL_0000236"},{"id":"T45","span":{"begin":531,"end":537},"obj":"http://purl.obolibrary.org/obo/CL_0000084"},{"id":"T46","span":{"begin":565,"end":571},"obj":"http://purl.obolibrary.org/obo/CL_0000236"},{"id":"T47","span":{"begin":595,"end":596},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T48","span":{"begin":645,"end":651},"obj":"http://purl.obolibrary.org/obo/CL_0000084"},{"id":"T49","span":{"begin":723,"end":726},"obj":"http://purl.obolibrary.org/obo/PR_000001004"},{"id":"T50","span":{"begin":732,"end":735},"obj":"http://purl.obolibrary.org/obo/CLO_0053438"},{"id":"T51","span":{"begin":737,"end":744},"obj":"http://purl.obolibrary.org/obo/CL_0000084"},{"id":"T52","span":{"begin":773,"end":775},"obj":"http://purl.obolibrary.org/obo/CLO_0053799"},{"id":"T53","span":{"begin":848,"end":855},"obj":"http://purl.obolibrary.org/obo/CLO_0009985"},{"id":"T54","span":{"begin":1152,"end":1158},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T55","span":{"begin":1162,"end":1163},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"In our investigatory study, out of five, two proteins namely ORF-3a and ORF-7a specific to SARS-COV-2 were found to be putative T-cell epitope determinants that create useful information to distinguish, and these proteins are also important for viral replication and growth [41]. Both of these proteins may influence in viral pathogenesis and disease spread, although the literature lacks unanimity [43]. B-cell epitopes prediction is still considered to be untrustworthy for both linear and conformational epitopes as compared to T-cell epitopes. Furthermore, the B-cell epitopes do not elicit a strong antibody response. For this reason, only T-cell epitopes are considered in the present study. It is capable to produce CD4+ and CD8+ T-cells with long-lasting response [45]. . In one of the recent studies, epitopes were designed, but they have focused on the single protein (i.e. SPIKE protein) to generate multiple epitopes like 13 for MHC I and 3 for MHC II [46]. We have analyzed multiple proteins to screen only effective epitopes based on various in-silico filters, to provide the most appropriate and authentic epitopes, which can be further tested in a wet lab."}

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T23","span":{"begin":45,"end":53},"obj":"Chemical"},{"id":"T24","span":{"begin":135,"end":142},"obj":"Chemical"},{"id":"T25","span":{"begin":213,"end":221},"obj":"Chemical"},{"id":"T26","span":{"begin":294,"end":302},"obj":"Chemical"},{"id":"T27","span":{"begin":870,"end":877},"obj":"Chemical"},{"id":"T28","span":{"begin":890,"end":897},"obj":"Chemical"},{"id":"T29","span":{"begin":961,"end":963},"obj":"Chemical"},{"id":"T30","span":{"begin":996,"end":1004},"obj":"Chemical"}],"attributes":[{"id":"A23","pred":"chebi_id","subj":"T23","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A24","pred":"chebi_id","subj":"T24","obj":"http://purl.obolibrary.org/obo/CHEBI_53000"},{"id":"A25","pred":"chebi_id","subj":"T25","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A26","pred":"chebi_id","subj":"T26","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A27","pred":"chebi_id","subj":"T27","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A28","pred":"chebi_id","subj":"T28","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A29","pred":"chebi_id","subj":"T29","obj":"http://purl.obolibrary.org/obo/CHEBI_74067"},{"id":"A30","pred":"chebi_id","subj":"T30","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"}],"text":"In our investigatory study, out of five, two proteins namely ORF-3a and ORF-7a specific to SARS-COV-2 were found to be putative T-cell epitope determinants that create useful information to distinguish, and these proteins are also important for viral replication and growth [41]. Both of these proteins may influence in viral pathogenesis and disease spread, although the literature lacks unanimity [43]. B-cell epitopes prediction is still considered to be untrustworthy for both linear and conformational epitopes as compared to T-cell epitopes. Furthermore, the B-cell epitopes do not elicit a strong antibody response. For this reason, only T-cell epitopes are considered in the present study. It is capable to produce CD4+ and CD8+ T-cells with long-lasting response [45]. . In one of the recent studies, epitopes were designed, but they have focused on the single protein (i.e. SPIKE protein) to generate multiple epitopes like 13 for MHC I and 3 for MHC II [46]. We have analyzed multiple proteins to screen only effective epitopes based on various in-silico filters, to provide the most appropriate and authentic epitopes, which can be further tested in a wet lab."}

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T12","span":{"begin":245,"end":262},"obj":"http://purl.obolibrary.org/obo/GO_0019079"},{"id":"T13","span":{"begin":245,"end":262},"obj":"http://purl.obolibrary.org/obo/GO_0019058"},{"id":"T14","span":{"begin":267,"end":273},"obj":"http://purl.obolibrary.org/obo/GO_0040007"},{"id":"T15","span":{"begin":326,"end":338},"obj":"http://purl.obolibrary.org/obo/GO_0009405"}],"text":"In our investigatory study, out of five, two proteins namely ORF-3a and ORF-7a specific to SARS-COV-2 were found to be putative T-cell epitope determinants that create useful information to distinguish, and these proteins are also important for viral replication and growth [41]. Both of these proteins may influence in viral pathogenesis and disease spread, although the literature lacks unanimity [43]. B-cell epitopes prediction is still considered to be untrustworthy for both linear and conformational epitopes as compared to T-cell epitopes. Furthermore, the B-cell epitopes do not elicit a strong antibody response. For this reason, only T-cell epitopes are considered in the present study. It is capable to produce CD4+ and CD8+ T-cells with long-lasting response [45]. . In one of the recent studies, epitopes were designed, but they have focused on the single protein (i.e. SPIKE protein) to generate multiple epitopes like 13 for MHC I and 3 for MHC II [46]. We have analyzed multiple proteins to screen only effective epitopes based on various in-silico filters, to provide the most appropriate and authentic epitopes, which can be further tested in a wet lab."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T36","span":{"begin":0,"end":279},"obj":"Sentence"},{"id":"T37","span":{"begin":280,"end":404},"obj":"Sentence"},{"id":"T38","span":{"begin":405,"end":547},"obj":"Sentence"},{"id":"T39","span":{"begin":548,"end":622},"obj":"Sentence"},{"id":"T40","span":{"begin":623,"end":697},"obj":"Sentence"},{"id":"T41","span":{"begin":698,"end":779},"obj":"Sentence"},{"id":"T42","span":{"begin":780,"end":969},"obj":"Sentence"},{"id":"T43","span":{"begin":970,"end":1172},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"In our investigatory study, out of five, two proteins namely ORF-3a and ORF-7a specific to SARS-COV-2 were found to be putative T-cell epitope determinants that create useful information to distinguish, and these proteins are also important for viral replication and growth [41]. Both of these proteins may influence in viral pathogenesis and disease spread, although the literature lacks unanimity [43]. B-cell epitopes prediction is still considered to be untrustworthy for both linear and conformational epitopes as compared to T-cell epitopes. Furthermore, the B-cell epitopes do not elicit a strong antibody response. For this reason, only T-cell epitopes are considered in the present study. It is capable to produce CD4+ and CD8+ T-cells with long-lasting response [45]. . In one of the recent studies, epitopes were designed, but they have focused on the single protein (i.e. SPIKE protein) to generate multiple epitopes like 13 for MHC I and 3 for MHC II [46]. We have analyzed multiple proteins to screen only effective epitopes based on various in-silico filters, to provide the most appropriate and authentic epitopes, which can be further tested in a wet lab."}

LitCovid-PMC-OGER-BB

2_test

{"project":"2_test","denotations":[{"id":"32352026-30822457-47638065","span":{"begin":275,"end":277},"obj":"30822457"},{"id":"32352026-18367524-47638066","span":{"begin":400,"end":402},"obj":"18367524"},{"id":"T10377","span":{"begin":275,"end":277},"obj":"30822457"},{"id":"T68358","span":{"begin":400,"end":402},"obj":"18367524"}],"text":"In our investigatory study, out of five, two proteins namely ORF-3a and ORF-7a specific to SARS-COV-2 were found to be putative T-cell epitope determinants that create useful information to distinguish, and these proteins are also important for viral replication and growth [41]. Both of these proteins may influence in viral pathogenesis and disease spread, although the literature lacks unanimity [43]. B-cell epitopes prediction is still considered to be untrustworthy for both linear and conformational epitopes as compared to T-cell epitopes. Furthermore, the B-cell epitopes do not elicit a strong antibody response. For this reason, only T-cell epitopes are considered in the present study. It is capable to produce CD4+ and CD8+ T-cells with long-lasting response [45]. . In one of the recent studies, epitopes were designed, but they have focused on the single protein (i.e. SPIKE protein) to generate multiple epitopes like 13 for MHC I and 3 for MHC II [46]. We have analyzed multiple proteins to screen only effective epitopes based on various in-silico filters, to provide the most appropriate and authentic epitopes, which can be further tested in a wet lab."}

PMC:7189872 / 4913-6085 JSONTXT

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PMC:7189872 / 4913-6085 JSON TXT