PMC:7519301 / 46832-47592 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T147","span":{"begin":2,"end":6},"obj":"Body_part"},{"id":"T148","span":{"begin":139,"end":142},"obj":"Body_part"},{"id":"T149","span":{"begin":260,"end":267},"obj":"Body_part"},{"id":"T150","span":{"begin":352,"end":355},"obj":"Body_part"},{"id":"T151","span":{"begin":364,"end":367},"obj":"Body_part"},{"id":"T152","span":{"begin":377,"end":380},"obj":"Body_part"},{"id":"T153","span":{"begin":384,"end":387},"obj":"Body_part"},{"id":"T154","span":{"begin":395,"end":398},"obj":"Body_part"},{"id":"T155","span":{"begin":467,"end":470},"obj":"Body_part"},{"id":"T156","span":{"begin":527,"end":530},"obj":"Body_part"},{"id":"T157","span":{"begin":540,"end":543},"obj":"Body_part"},{"id":"T158","span":{"begin":567,"end":570},"obj":"Body_part"},{"id":"T159","span":{"begin":577,"end":580},"obj":"Body_part"},{"id":"T160","span":{"begin":596,"end":599},"obj":"Body_part"},{"id":"T161","span":{"begin":664,"end":667},"obj":"Body_part"},{"id":"T162","span":{"begin":738,"end":741},"obj":"Body_part"}],"attributes":[{"id":"A147","pred":"fma_id","subj":"T147","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A148","pred":"fma_id","subj":"T148","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A149","pred":"fma_id","subj":"T149","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A150","pred":"fma_id","subj":"T150","obj":"http://purl.org/sig/ont/fma/fma84079"},{"id":"A151","pred":"fma_id","subj":"T151","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A152","pred":"fma_id","subj":"T152","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A153","pred":"fma_id","subj":"T153","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A154","pred":"fma_id","subj":"T154","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A155","pred":"fma_id","subj":"T155","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A156","pred":"fma_id","subj":"T156","obj":"http://purl.org/sig/ont/fma/fma84079"},{"id":"A157","pred":"fma_id","subj":"T157","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A158","pred":"fma_id","subj":"T158","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A159","pred":"fma_id","subj":"T159","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A160","pred":"fma_id","subj":"T160","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A161","pred":"fma_id","subj":"T161","obj":"http://purl.org/sig/ont/fma/fma84079"},{"id":"A162","pred":"fma_id","subj":"T162","obj":"http://purl.org/sig/ont/fma/fma84795"}],"text":"T Cell Immunogenicity Index.\nFor each site in a predicted epitope, the immunogenicity index was defined as the sum of the frequency of the HLA alleles or haplotypes restricting the corresponding epitope (multiple epitopes can be predicted at a given site in a protein). Total frequencies from CIWD 3.0 were used as the frequencies of the corresponding MHC class I HLA alleles (HLA-A, HLA-B, and HLA-C), and the global frequencies from http://17ihiw.org/17th-ihiw-ngs-hla-data/ were used as the frequencies of the corresponding MHC class II HLA alleles or haplotypes (HLA-DQB1, HLA-DPA1-DPB1, and HLA-DQA1-DPB). This procedure was repeated using the frequencies of MHC alleles or haplotypes in different subpopulations listed in the above HLA frequency dataset."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T354","span":{"begin":0,"end":6},"obj":"http://purl.obolibrary.org/obo/CL_0000084"},{"id":"T355","span":{"begin":46,"end":47},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T356","span":{"begin":242,"end":243},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T357","span":{"begin":258,"end":259},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T358","span":{"begin":381,"end":382},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T359","span":{"begin":388,"end":389},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"}],"text":"T Cell Immunogenicity Index.\nFor each site in a predicted epitope, the immunogenicity index was defined as the sum of the frequency of the HLA alleles or haplotypes restricting the corresponding epitope (multiple epitopes can be predicted at a given site in a protein). Total frequencies from CIWD 3.0 were used as the frequencies of the corresponding MHC class I HLA alleles (HLA-A, HLA-B, and HLA-C), and the global frequencies from http://17ihiw.org/17th-ihiw-ngs-hla-data/ were used as the frequencies of the corresponding MHC class II HLA alleles or haplotypes (HLA-DQB1, HLA-DPA1-DPB1, and HLA-DQA1-DPB). This procedure was repeated using the frequencies of MHC alleles or haplotypes in different subpopulations listed in the above HLA frequency dataset."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T129","span":{"begin":58,"end":65},"obj":"Chemical"},{"id":"T130","span":{"begin":195,"end":202},"obj":"Chemical"},{"id":"T131","span":{"begin":260,"end":267},"obj":"Chemical"},{"id":"T132","span":{"begin":537,"end":539},"obj":"Chemical"}],"attributes":[{"id":"A129","pred":"chebi_id","subj":"T129","obj":"http://purl.obolibrary.org/obo/CHEBI_53000"},{"id":"A130","pred":"chebi_id","subj":"T130","obj":"http://purl.obolibrary.org/obo/CHEBI_53000"},{"id":"A131","pred":"chebi_id","subj":"T131","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A132","pred":"chebi_id","subj":"T132","obj":"http://purl.obolibrary.org/obo/CHEBI_74067"}],"text":"T Cell Immunogenicity Index.\nFor each site in a predicted epitope, the immunogenicity index was defined as the sum of the frequency of the HLA alleles or haplotypes restricting the corresponding epitope (multiple epitopes can be predicted at a given site in a protein). Total frequencies from CIWD 3.0 were used as the frequencies of the corresponding MHC class I HLA alleles (HLA-A, HLA-B, and HLA-C), and the global frequencies from http://17ihiw.org/17th-ihiw-ngs-hla-data/ were used as the frequencies of the corresponding MHC class II HLA alleles or haplotypes (HLA-DQB1, HLA-DPA1-DPB1, and HLA-DQA1-DPB). This procedure was repeated using the frequencies of MHC alleles or haplotypes in different subpopulations listed in the above HLA frequency dataset."}

{"project":"LitCovid-PubTator","denotations":[{"id":"596","span":{"begin":377,"end":382},"obj":"Gene"},{"id":"597","span":{"begin":384,"end":389},"obj":"Gene"},{"id":"598","span":{"begin":567,"end":575},"obj":"Gene"},{"id":"599","span":{"begin":577,"end":585},"obj":"Gene"},{"id":"600","span":{"begin":586,"end":590},"obj":"Gene"},{"id":"601","span":{"begin":596,"end":604},"obj":"Gene"},{"id":"602","span":{"begin":664,"end":667},"obj":"Gene"},{"id":"603","span":{"begin":527,"end":530},"obj":"Gene"},{"id":"604","span":{"begin":352,"end":355},"obj":"Gene"},{"id":"605","span":{"begin":738,"end":741},"obj":"Gene"},{"id":"606","span":{"begin":540,"end":543},"obj":"Gene"},{"id":"607","span":{"begin":467,"end":470},"obj":"Gene"},{"id":"608","span":{"begin":395,"end":398},"obj":"Gene"},{"id":"609","span":{"begin":364,"end":367},"obj":"Gene"}],"attributes":[{"id":"A596","pred":"tao:has_database_id","subj":"596","obj":"Gene:3105"},{"id":"A597","pred":"tao:has_database_id","subj":"597","obj":"Gene:3106"},{"id":"A598","pred":"tao:has_database_id","subj":"598","obj":"Gene:3119"},{"id":"A599","pred":"tao:has_database_id","subj":"599","obj":"Gene:3113"},{"id":"A600","pred":"tao:has_database_id","subj":"600","obj":"Gene:3115"},{"id":"A601","pred":"tao:has_database_id","subj":"601","obj":"Gene:3117"},{"id":"A602","pred":"tao:has_database_id","subj":"602","obj":"Gene:3107"},{"id":"A603","pred":"tao:has_database_id","subj":"603","obj":"Gene:3107"},{"id":"A604","pred":"tao:has_database_id","subj":"604","obj":"Gene:3107"},{"id":"A605","pred":"tao:has_database_id","subj":"605","obj":"Gene:3113"},{"id":"A606","pred":"tao:has_database_id","subj":"606","obj":"Gene:3113"},{"id":"A607","pred":"tao:has_database_id","subj":"607","obj":"Gene:3113"},{"id":"A608","pred":"tao:has_database_id","subj":"608","obj":"Gene:3113"},{"id":"A609","pred":"tao:has_database_id","subj":"609","obj":"Gene:3113"}],"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":"T Cell Immunogenicity Index.\nFor each site in a predicted epitope, the immunogenicity index was defined as the sum of the frequency of the HLA alleles or haplotypes restricting the corresponding epitope (multiple epitopes can be predicted at a given site in a protein). Total frequencies from CIWD 3.0 were used as the frequencies of the corresponding MHC class I HLA alleles (HLA-A, HLA-B, and HLA-C), and the global frequencies from http://17ihiw.org/17th-ihiw-ngs-hla-data/ were used as the frequencies of the corresponding MHC class II HLA alleles or haplotypes (HLA-DQB1, HLA-DPA1-DPB1, and HLA-DQA1-DPB). This procedure was repeated using the frequencies of MHC alleles or haplotypes in different subpopulations listed in the above HLA frequency dataset."}

{"project":"LitCovid-sentences","denotations":[{"id":"T294","span":{"begin":0,"end":28},"obj":"Sentence"},{"id":"T295","span":{"begin":29,"end":269},"obj":"Sentence"},{"id":"T296","span":{"begin":270,"end":610},"obj":"Sentence"},{"id":"T297","span":{"begin":611,"end":760},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"T Cell Immunogenicity Index.\nFor each site in a predicted epitope, the immunogenicity index was defined as the sum of the frequency of the HLA alleles or haplotypes restricting the corresponding epitope (multiple epitopes can be predicted at a given site in a protein). Total frequencies from CIWD 3.0 were used as the frequencies of the corresponding MHC class I HLA alleles (HLA-A, HLA-B, and HLA-C), and the global frequencies from http://17ihiw.org/17th-ihiw-ngs-hla-data/ were used as the frequencies of the corresponding MHC class II HLA alleles or haplotypes (HLA-DQB1, HLA-DPA1-DPB1, and HLA-DQA1-DPB). This procedure was repeated using the frequencies of MHC alleles or haplotypes in different subpopulations listed in the above HLA frequency dataset."}