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PMC:7565482 / 19167-20591 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T91 70-74 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T92 151-156 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T93 345-355 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T94 508-511 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T95 574-577 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T96 1148-1153 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T97 1248-1252 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T98 1363-1370 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T166 54-57 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T167 63-66 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T168 68-74 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T169 91-93 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T170 116-123 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T171 151-156 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T172 203-207 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T173 208-216 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T174 387-394 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T175 556-564 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T176 578-579 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T177 580-582 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T178 585-586 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T179 730-738 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T180 993-994 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T181 1011-1019 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T182 1071-1079 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T183 1148-1153 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T184 1170-1172 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T185 1231-1236 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T186 1246-1252 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
239 54-57 Gene denotes CD4 Gene:920
240 63-66 Gene denotes CD8 Gene:925
241 574-579 Gene denotes HLA-B Gene:3106
242 1093-1111 Chemical denotes dimethyl sulfoxide MESH:D004121
243 1113-1117 Chemical denotes DMSO MESH:D004121

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T18 116-133 http://purl.obolibrary.org/obo/GO_0043043 denotes peptide synthesis
T19 124-133 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T20 387-404 http://purl.obolibrary.org/obo/GO_0043043 denotes peptide synthesis
T21 395-404 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T137 0-186 Sentence denotes Fifteen-mer designs allow sensitive screens for both, CD4+ and CD8+ T cell responses while 18 mer allow for cheaper peptide synthesis and require less cells for comprehensive screenings.
T138 187-303 Sentence denotes However, longer test peptides tend to yield fewer responses and imply bigger efforts for subsequent epitope mapping.
T139 304-440 Sentence denotes For the 15 mer design, an alternative 10 amino acid overlap was proposed to reduce peptide synthesis, while maintaining the sensitivity.
T140 441-602 Sentence denotes This approach may be valuable, but may miss epitopes restricted by HLA class I molecules known to presented longer peptides (such as HLA-B*27, -B*57 and others).
T141 603-717 Sentence denotes Regardless of the final OLP design, the use of large OLP data sets for immune screening raises several challenges.
T142 718-939 Sentence denotes How to pool peptides in suitable numbers may depend on the downstream analyses, whether or not subsequent epitope identification are planned, on the experimental setup and whether long incubation periods will be required.
T143 940-1174 Sentence denotes The latter may be especially important as pooling of a large number of peptides will possibly require lyophilization of the pooled peptides to eliminate dimethyl sulfoxide (DMSO) as this can be toxic for the cells during culture [11].
T144 1175-1424 Sentence denotes Also, as we gain more insights into the distribution of virus-specific T cell responses across the full proteome, more or less reactive regions can be pooled based on expected reactivity, protein expression level, and/or degree of conservation [46].