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PMC:7565482 / 12654-14456 JSONTXT

Annnotations TAB JSON ListView MergeView

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T61 242-246 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T62 401-412 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T63 707-718 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T64 1373-1381 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T65 1400-1405 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T66 1601-1607 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T67 1723-1734 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T68 1779-1785 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T41 131-139 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T98 17-25 http://purl.obolibrary.org/obo/PR_000018263 denotes Peptides
T99 64-65 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T100 96-104 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T101 166-173 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T102 202-209 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T103 240-246 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T104 328-336 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T105 398-400 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T106 572-573 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T107 591-599 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T108 639-640 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T109 704-706 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T110 749-759 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing is
T111 949-957 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T112 1028-1036 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T113 1038-1040 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T114 1174-1176 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T115 1255-1256 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T116 1335-1336 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T117 1344-1349 http://purl.obolibrary.org/obo/CLO_0009985 denotes focus
T118 1400-1405 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T119 1421-1425 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T120 1509-1511 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T121 1529-1531 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T122 1564-1565 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T123 1595-1600 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T124 1679-1680 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T125 1773-1778 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
159 131-141 Species denotes SARS-CoV-2 Tax:2697049
160 1595-1600 Species denotes human Tax:9606
161 1773-1778 Species denotes human Tax:9606

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T13 166-183 http://purl.obolibrary.org/obo/GO_0043043 denotes peptide synthesis
T14 174-183 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T82 0-4 Sentence denotes 3.2.
T83 5-43 Sentence denotes Overlapping Peptides (OLP) Sets Design
T84 44-319 Sentence denotes In order to achieve a balance between the number of peptides needed to cover the whole SARS-CoV-2 proteome, the costs for peptide synthesis and the design of peptide sets that allow for detecting T cell responses with high sensitivity, three OLP sets were designed (Table 2).
T85 320-537 Sentence denotes Shorter peptides (15 mers) with longer sequence overlap between adjacent OLP (11 amino acids) offer high resolution detection of responses, thus lowering the risk of missing longer epitopes located in the OLP overlap.
T86 538-657 Sentence denotes The consequence, however, will be a higher number of peptides to synthesize and screen, in this case a set of 2821 OLP.
T87 658-845 Sentence denotes When the overlap between OLP was reduced from 11 amino acids to 10, the sensitivity of OLP testing is maintained, but some longer epitopes located in the overlap of two OLP may be missed.
T88 846-1009 Sentence denotes With this caveat in mind, an OLP set of 15-mers overlapping by 10 residues helped reduce the number of peptides needed by 560 OLP (total number OLP required 2262).
T89 1010-1150 Sentence denotes Similarly, longer peptides (18 mers) significantly reduce the number of OLP to be synthesized, but tend to reduce in vitro sensitivity [55].
T90 1151-1231 Sentence denotes This approach, with an 11 mer overlap, reduced the number of needed OLP to 1561.
T91 1232-1441 Sentence denotes The final decision for a specific design may also be driven by the assay system used for screening, an a-priori focus on fewer or more viral proteins and the available cells and funding to test immunogenicity.
T92 1442-1512 Sentence denotes The three full OLP sets with their entropies are included in Table S1.
T93 1513-1678 Sentence denotes Of note, the 15–11 OLP sequences were subjected to a search for homologies in the human genome to predict molecular mimicry events related to the autoimmune process.
T94 1679-1802 Sentence denotes A blastp search (>8aa consecutive identical amino acids per OLP) of the whole set against the human genome yielded no hits.