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PMC:7565482 / 8520-9944 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T37 172-175 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T38 395-406 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T39 505-508 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T40 836-847 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T41 1030-1039 Body_part denotes glutamine http://purl.org/sig/ont/fma/fma82752
T42 1105-1114 Body_part denotes glutamine http://purl.org/sig/ont/fma/fma82752
T43 1213-1224 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 862-871 Body_part denotes extension http://purl.obolibrary.org/obo/UBERON_2000106

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T35 773-781 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T67 40-48 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T68 197-199 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48
T69 240-247 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T70 810-811 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T71 833-835 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T72 1010-1012 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T73 1103-1104 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T74 1162-1169 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
101 773-783 Species denotes SARS-CoV-2 Tax:2697049
102 1030-1039 Chemical denotes glutamine MESH:D005973
103 1105-1114 Chemical denotes glutamine MESH:D005973

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T11 1162-1179 http://purl.obolibrary.org/obo/GO_0043043 denotes peptide synthesis
T12 1170-1179 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T51 0-201 Sentence denotes For the automated design of overlapping peptides with variable length, we used the previously described Peptgen algorithm available at the Los Alamos National Laboratories HIV Immunology database [48].
T52 202-309 Sentence denotes This OLP generator allows predefining peptide length and level of the desired overlap between adjacent OLP.
T53 310-541 Sentence denotes Peptgen is also set up to exclude from the C-terminal end of OLP certain “forbidden” amino acids (G, P, E, D, Q, N, T, S and C) that are rarely seen to serve as the C-terminal anchor position of HLA class I presented epitopes [49].
T54 542-738 Sentence denotes Using this optional modification can lead to length variation in the OLP set, which can be controlled by limiting the maximal length of an OLP in regions with numerous serial “forbidden” residues.
T55 739-946 Sentence denotes The settings used for the present SARS-CoV-2 consensus OLP design were a) OLP length of 15 or 18 amino acids, with maximal extension or truncation of up to ±3 residues to avoid forbidden C-terminal residues.
T56 947-1022 Sentence denotes In addition, the overlap between adjacent OLP was set at 10 or 11 residues.
T57 1023-1180 Sentence denotes The no-glutamine at N-terminal setting was applied to prevent OLP starting with a glutamine residue as this can lead to complications with peptide synthesis.
T58 1181-1343 Sentence denotes For positions where two or more amino acids were present above 25% of the sequences in the alignment, two or more sequence variants for those OLPs were generated.
T59 1344-1424 Sentence denotes Sequence logos were generated for these cases with the ggseqlogo R package [50].