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PMC:7565482 / 12698-14456 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T61 198-202 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T62 357-368 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T63 663-674 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T64 1329-1337 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T65 1356-1361 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T66 1557-1563 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T67 1679-1690 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T68 1735-1741 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T41 87-95 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T99 20-21 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T100 52-60 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T101 122-129 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T102 158-165 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T103 196-202 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T104 284-292 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T105 354-356 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T106 528-529 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T107 547-555 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T108 595-596 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T109 660-662 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T110 705-715 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing is
T111 905-913 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T112 984-992 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T113 994-996 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T114 1130-1132 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T115 1211-1212 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T116 1291-1292 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T117 1300-1305 http://purl.obolibrary.org/obo/CLO_0009985 denotes focus
T118 1356-1361 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T119 1377-1381 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T120 1465-1467 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T121 1485-1487 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T122 1520-1521 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T123 1551-1556 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T124 1635-1636 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T125 1729-1734 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
159 87-97 Species denotes SARS-CoV-2 Tax:2697049
160 1551-1556 Species denotes human Tax:9606
161 1729-1734 Species denotes human Tax:9606

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T13 122-139 http://purl.obolibrary.org/obo/GO_0043043 denotes peptide synthesis
T14 130-139 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T84 0-275 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 276-493 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 494-613 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 614-801 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 802-965 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 966-1106 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 1107-1187 Sentence denotes This approach, with an 11 mer overlap, reduced the number of needed OLP to 1561.
T91 1188-1397 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 1398-1468 Sentence denotes The three full OLP sets with their entropies are included in Table S1.
T93 1469-1634 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 1635-1758 Sentence denotes A blastp search (>8aa consecutive identical amino acids per OLP) of the whole set against the human genome yielded no hits.