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PMC:7565482 / 7438-11920 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T31 346-356 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T32 405-416 Body_part denotes nucleotides http://purl.org/sig/ont/fma/fma82740
T33 480-490 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T34 676-686 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T35 819-829 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T36 864-873 Body_part denotes aminoacid http://purl.org/sig/ont/fma/fma82739
T37 1254-1257 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T38 1477-1488 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T39 1587-1590 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T40 1918-1929 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T41 2112-2121 Body_part denotes glutamine http://purl.org/sig/ont/fma/fma82752
T42 2187-2196 Body_part denotes glutamine http://purl.org/sig/ont/fma/fma82752
T43 2295-2306 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T44 2587-2594 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T45 3035-3043 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T46 3149-3157 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T47 3174-3180 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T48 3405-3412 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T49 3502-3512 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T50 4179-4182 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T51 4291-4295 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T52 4340-4347 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T53 4442-4445 Body_part denotes map http://purl.org/sig/ont/fma/fma67847

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 1944-1953 Body_part denotes extension http://purl.obolibrary.org/obo/UBERON_2000106

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T34 103-111 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T35 1855-1863 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T36 2713-2721 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T37 3222-3230 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T38 3246-3257 Disease denotes common cold http://purl.obolibrary.org/obo/MONDO_0005709
T39 3950-3958 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T61 75-76 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T62 315-316 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T63 339-341 http://purl.obolibrary.org/obo/CLO_0053799 denotes 45
T64 344-345 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T65 861-863 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T66 1041-1048 http://purl.obolibrary.org/obo/PR_000018263 denotes Peptide
T67 1122-1130 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T68 1279-1281 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48
T69 1322-1329 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T70 1892-1893 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T71 1915-1917 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T72 2092-2094 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T73 2185-2186 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T74 2244-2251 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T75 2536-2544 http://purl.obolibrary.org/obo/PR_000018263 denotes Peptides
T76 2631-2632 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T77 2927-2928 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T78 2992-2995 http://purl.obolibrary.org/obo/NCBITaxon_9596 denotes pan
T79 3052-3059 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T80 3191-3196 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T81 3290-3295 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T82 3362-3368 http://purl.obolibrary.org/obo/UBERON_0001630 denotes MUSCLE
T83 3362-3368 http://purl.obolibrary.org/obo/UBERON_0005090 denotes MUSCLE
T84 3362-3368 http://www.ebi.ac.uk/efo/EFO_0000801 denotes MUSCLE
T85 3362-3368 http://www.ebi.ac.uk/efo/EFO_0001949 denotes MUSCLE
T86 3390-3392 http://purl.obolibrary.org/obo/CLO_0001407 denotes 52
T87 3610-3617 http://purl.obolibrary.org/obo/CLO_0003453 denotes gap per
T88 3673-3681 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T89 3864-3867 http://purl.obolibrary.org/obo/NCBITaxon_9596 denotes pan
T90 3904-3909 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T91 4127-4134 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T92 4161-4173 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Homo sapiens
T93 4289-4295 http://purl.obolibrary.org/obo/CL_0000236 denotes B-cell
T94 4325-4326 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
97 103-113 Species denotes SARS-CoV-2 Tax:2697049
101 1855-1865 Species denotes SARS-CoV-2 Tax:2697049
102 2112-2121 Chemical denotes glutamine MESH:D005973
103 2187-2196 Chemical denotes glutamine MESH:D005973
118 2662-2673 Species denotes coronavirus Tax:11118
119 2713-2723 Species denotes SARS-CoV-2 Tax:2697049
120 2748-2759 Species denotes coronavirus Tax:11118
121 2996-3007 Species denotes coronavirus Tax:11118
122 3077-3092 Species denotes Betacoronavirus Tax:694002
123 3100-3116 Species denotes beta-coronavirus Tax:694002
124 3191-3196 Species denotes human Tax:9606
125 3197-3210 Species denotes coronaviruses Tax:11118
126 3222-3230 Species denotes SARS-CoV Tax:694009
127 3232-3240 Species denotes MERS-CoV Tax:1335626
128 3290-3307 Species denotes human-coronavirus Tax:694448
129 3278-3282 Species denotes 229E Tax:11137
130 3253-3257 Disease denotes cold MESH:D000067390
131 3284-3288 CellLine denotes HKU1 CVCL:B526
133 3756-3761 Species denotes CoV-2 Tax:2697049
141 3849-3862 Species denotes coronaviruses Tax:11118
142 3868-3879 Species denotes coronavirus Tax:11118
143 3881-3898 Species denotes betacoronaviruses Tax:694002
144 3904-3909 Species denotes human Tax:9606
145 3910-3923 Species denotes coronaviruses Tax:11118
146 3950-3960 Species denotes SARS-CoV-2 Tax:2697049
147 4161-4173 Species denotes Homo sapiens Tax:9606

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T11 2244-2261 http://purl.obolibrary.org/obo/GO_0043043 denotes peptide synthesis
T12 2252-2261 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T39 0-2 Sentence denotes 2.
T40 3-10 Sentence denotes Methods
T41 12-16 Sentence denotes 2.1.
T42 17-74 Sentence denotes Consensus Sequence ORF Generation and Entropy Calculation
T43 75-236 Sentence denotes A total of 1731 full-length SARS-CoV-2 sequences were downloaded from NCBI (30 April 2020, txid2697049, minimum length = 29,000 bp) and aligned using MAFFT [44].
T44 237-343 Sentence denotes The alignment was visually inspected and curated using Genbank NC_045512.2 as a coordinate reference [45].
T45 344-475 Sentence denotes A nucleotide consensus sequence was generated by keeping all nucleotides present in at least 25% of the sequences in the alignment.
T46 476-669 Sentence denotes The amino acid consensus sequence was then created by using NC_045512.2 annotated Open Reading Frames (ORFs) plus additional ORFs described in Finkel et al. [46] using the Biostrings R package.
T47 670-777 Sentence denotes Mixed nucleotide positions were either resolved if they were synonymous or flagged for downstream analysis.
T48 778-1022 Sentence denotes Positional entropy was calculated at the amino acid level both as the standard and 22-aminoacid-normalized Shannon entropy for every ORF using Bio3d R package on the alignment [47], and afterward, the mean OLP normalized entropy was calculated.
T49 1024-1028 Sentence denotes 2.2.
T50 1029-1081 Sentence denotes Overlapping Peptide Set Design and Variability Plots
T51 1082-1283 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 1284-1391 Sentence denotes This OLP generator allows predefining peptide length and level of the desired overlap between adjacent OLP.
T53 1392-1623 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 1624-1820 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 1821-2028 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 2029-2104 Sentence denotes In addition, the overlap between adjacent OLP was set at 10 or 11 residues.
T57 2105-2262 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 2263-2425 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 2426-2506 Sentence denotes Sequence logos were generated for these cases with the ggseqlogo R package [50].
T60 2508-2512 Sentence denotes 2.3.
T61 2513-2562 Sentence denotes Detection of Conserved Peptides Among Coronavirus
T62 2563-2770 Sentence denotes In an attempt to detect protein fragments that are conserved across a wide range of members of the coronavirus family, full-length consensus ORF from SARS-CoV-2 were aligned with other coronavirus sequences.
T63 2771-3319 Sentence denotes Three alignments were performed based on different sequence selection criteria: (i) 50 reference sequences (RefSeq) with the lowest E-values resulting from a pBLAST search [51] using the ORF-specific consensus sequences (pan-coronavirus alignment) (ii) homologous proteins from 17 viruses representing the Betacoronavirus taxon (beta-coronavirus alignment) or, (iii) homologous proteins from the 7 full-genome sequenced human coronaviruses (including SARS-CoV, MERS-CoV, and common cold species OC43, NL63, 229E, HKU1, human-coronavirus alignment).
T64 3320-3394 Sentence denotes Selected sequences were aligned using the MUSCLE algorithm in MEGA X [52].
T65 3395-3626 Sentence denotes Conserved protein fragments were identified using BioEdit with the following criteria: minimum length of 8 amino acid, maximum average entropy of 0.25, maximum entropy per position of 1 and limiting the search to 1 gap per segment.
T66 3627-3698 Sentence denotes Sequence logos were generated for the aligned peptides on Weblogo [53].
T67 3700-3704 Sentence denotes 2.4.
T68 3705-3779 Sentence denotes Identification of Previously Described Epitopes in CoV-2 Conserved Regions
T69 3780-4081 Sentence denotes To identify previously reported epitopes in the conserved regions of coronaviruses (pan-coronavirus, betacoronaviruses, and human coronaviruses), and match them with the SARS-CoV-2 consensus sequence, searches for experimentally described epitopes were carried out in the Immune Epitope Database [54].
T70 4082-4149 Sentence denotes The search criteria were as follows: “linear peptide; blast option:
T71 4150-4160 Sentence denotes 90%; Host:
T72 4161-4243 Sentence denotes Homo sapiens; Any MHC restriction; Positive assays only; All assays; Any disease”.
T73 4244-4361 Sentence denotes The search yielded 141 epitopes, of which 14 B-cell epitopes and 2 epitopes from a hypothetical protein were removed.
T74 4362-4482 Sentence denotes The remaining identified epitopes were subsequently used to generate an epitope map of the respective conserved regions.