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PMC:7307149 / 21550-27712 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T144 99-106 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T145 121-128 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T146 143-150 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T147 173-180 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T148 445-452 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T149 652-659 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T150 851-858 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257
T151 1647-1657 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T152 2358-2369 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T153 2612-2622 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T154 2988-2991 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T155 3052-3059 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T156 3287-3290 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T157 3352-3355 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T158 3428-3431 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T159 3674-3685 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T160 3816-3819 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T161 4804-4807 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T162 4899-4902 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T163 4937-4940 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T164 5150-5155 Body_part denotes digit http://purl.org/sig/ont/fma/fma85518
T165 5270-5273 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T166 5316-5319 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T167 5351-5354 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T2 5150-5155 Body_part denotes digit http://purl.obolibrary.org/obo/UBERON_0002544

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T94 368-376 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T95 378-386 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T96 2178-2186 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T97 2399-2407 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T98 2640-2648 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T99 3086-3094 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T100 3101-3109 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T101 4172-4180 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T102 4475-4483 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T103 4497-4505 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T216 108-116 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T217 217-219 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T218 341-346 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T219 521-523 http://purl.obolibrary.org/obo/CLO_0008933 denotes S5
T220 686-690 http://purl.obolibrary.org/obo/CLO_0007653 denotes M, E
T221 704-706 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T222 1148-1155 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T223 1198-1206 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T224 1236-1244 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T225 1321-1328 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T226 1396-1398 http://purl.obolibrary.org/obo/CLO_0054055 denotes 71
T227 1585-1587 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T228 1602-1603 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T229 1749-1750 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T230 2019-2024 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T231 2165-2167 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T232 2277-2282 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T233 2295-2303 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T234 2331-2332 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T235 2433-2438 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T236 2496-2498 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T237 2496-2498 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T238 2529-2537 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T239 2685-2690 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T240 2760-2768 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T241 2770-2775 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T242 2836-2837 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T243 2980-2987 http://purl.obolibrary.org/obo/PR_000018263 denotes Peptide
T244 3299-3306 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T245 3534-3536 http://purl.obolibrary.org/obo/CLO_0008933 denotes S5
T246 3657-3665 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T247 3703-3705 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T248 3747-3755 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T249 4028-4030 http://purl.obolibrary.org/obo/CLO_0008935 denotes S9
T250 4124-4132 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T251 4411-4418 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T252 4583-4590 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T253 4700-4701 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T254 4750-4758 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T255 4868-4877 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide’s
T256 4941-4942 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T257 4945-4946 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T258 5045-5047 http://purl.obolibrary.org/obo/CLO_0001407 denotes 52
T259 5150-5155 http://www.ebi.ac.uk/efo/EFO_0000881 denotes digit
T260 5454-5455 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T117 99-106 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T118 121-128 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T119 143-150 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T120 173-180 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T121 248-253 Chemical denotes alpha http://purl.obolibrary.org/obo/CHEBI_30216
T122 445-452 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T123 521-523 Chemical denotes S5 http://purl.obolibrary.org/obo/CHEBI_29386
T124 652-659 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T125 851-858 Chemical denotes Protein http://purl.obolibrary.org/obo/CHEBI_16541
T126 1077-1080 Chemical denotes HMM http://purl.obolibrary.org/obo/CHEBI_24564
T127 1148-1155 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T128 1198-1206 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T129 1236-1244 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T130 1321-1328 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T131 1647-1657 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T132 1647-1652 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T133 1653-1657 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T134 2114-2119 Chemical denotes alpha http://purl.obolibrary.org/obo/CHEBI_30216
T135 2295-2303 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T136 2358-2369 Chemical denotes amino acids http://purl.obolibrary.org/obo/CHEBI_33709
T137 2358-2363 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T138 2364-2369 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T139 2496-2498 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T140 2529-2537 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T141 2612-2622 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T142 2612-2617 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T143 2618-2622 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T144 2747-2749 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T145 2760-2768 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T146 2777-2781 Chemical denotes beta http://purl.obolibrary.org/obo/CHEBI_10545
T147 2980-2987 Chemical denotes Peptide http://purl.obolibrary.org/obo/CHEBI_16670
T148 3052-3059 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T149 3299-3306 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T150 3534-3536 Chemical denotes S5 http://purl.obolibrary.org/obo/CHEBI_29386
T151 3657-3665 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T152 3674-3685 Chemical denotes amino acids http://purl.obolibrary.org/obo/CHEBI_33709
T153 3674-3679 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T154 3680-3685 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T155 3747-3755 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T156 4020-4022 Chemical denotes S8 http://purl.obolibrary.org/obo/CHEBI_29385
T157 4124-4132 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T158 4236-4238 Chemical denotes S4 http://purl.obolibrary.org/obo/CHEBI_29401
T159 4411-4418 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T160 4583-4590 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T161 4750-4758 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T162 4816-4823 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T163 6043-6046 Chemical denotes MIT http://purl.obolibrary.org/obo/CHEBI_27847|http://purl.obolibrary.org/obo/CHEBI_53620
T165 6067-6069 Chemical denotes S4 http://purl.obolibrary.org/obo/CHEBI_29401

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
107 2640-2650 Species denotes SARS-CoV-2 Tax:2697049
395 80-86 Gene denotes ORF1ab Gene:43740578
396 675-681 Gene denotes ORF1ab Gene:43740578
397 1182-1187 Gene denotes ORF1a Gene:43740578
398 1192-1197 Gene denotes ORF1b Gene:43740578
399 258-275 Species denotes betacoronaviruses Tax:694002
400 341-346 Species denotes human Tax:9606
401 347-360 Species denotes coronaviruses Tax:11118
402 368-376 Species denotes SARS-CoV Tax:694009
403 378-388 Species denotes SARS-CoV-2 Tax:2697049
404 390-398 Species denotes MERS-CoV Tax:1335626
405 707-718 Species denotes coronavirus Tax:11118
418 2019-2024 Species denotes human Tax:9606
419 2035-2046 Species denotes coronavirus Tax:11118
420 2070-2085 Species denotes betacoronavirus Tax:694002
421 2125-2140 Species denotes betacoronavirus Tax:694002
422 2178-2188 Species denotes SARS-CoV-2 Tax:2697049
423 2277-2294 Species denotes human coronavirus Tax:694448
424 2399-2409 Species denotes SARS-CoV-2 Tax:2697049
425 2433-2450 Species denotes human coronavirus Tax:694448
427 2685-2690 Species denotes human Tax:9606
428 2691-2704 Species denotes coronaviruses Tax:11118
429 2770-2775 Species denotes human Tax:9606
436 4804-4823 Gene denotes MHC class I antigen Gene:100507703
437 3086-3096 Species denotes SARS-CoV-2 Tax:2697049
438 3101-3109 Species denotes SARS-CoV Tax:694009
439 4172-4180 Species denotes SARS-CoV Tax:694009
440 4475-4483 Species denotes SARS-CoV Tax:694009
441 4497-4507 Species denotes SARS-CoV-2 Tax:2697049
444 4937-4954 Gene denotes HLA-A, -B, and -C Gene:3106
445 5135-5146 Species denotes major/minor Tax:1925466

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T33 2988-2991 http://purl.obolibrary.org/obo/GO_0046776 denotes MHC
T34 3287-3290 http://purl.obolibrary.org/obo/GO_0046776 denotes MHC
T35 3352-3355 http://purl.obolibrary.org/obo/GO_0046776 denotes MHC
T36 3816-3819 http://purl.obolibrary.org/obo/GO_0046776 denotes MHC
T37 4804-4807 http://purl.obolibrary.org/obo/GO_0046776 denotes MHC
T38 4816-4834 http://purl.obolibrary.org/obo/GO_0019882 denotes antigen processing

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T4 4814-4823 GlycoEpitope denotes I antigen http://www.glycoepitope.jp/epitopes/EP0138

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T115 0-21 Sentence denotes MATERIALS AND METHODS
T116 23-57 Sentence denotes Sequence retrieval and alignments.
T117 58-428 Sentence denotes Full polyprotein 1ab (ORF1ab), spike (S) protein, membrane (M) protein, envelope (E) protein, and nucleocapsid (N) protein sequences were obtained for each of 34 distinct but representative alpha and betacoronaviruses from broad genus and subgenus distributions, including all known human coronaviruses (i.e., SARS-CoV, SARS-CoV-2, MERS-CoV, HKU1, OC43, NL63, and 229E).
T118 429-635 Sentence denotes FASTA-formatted protein sequence data (the full accession number list is available in Table S5 in the supplemental material) were retrieved from the National Center of Biotechnology Information (NCBI) (67).
T119 636-1102 Sentence denotes For each of the protein classes (i.e., ORF1ab, S, M, E, and N), all 34 coronavirus sequences were aligned using the Clustal Omega v1.2.4 multisequence aligner tool employing the following parameters: sequence type [Protein], output alignment format [clustal_num], dealign [false], mBed-like clustering guide-tree [true], mBed-like clustering iteration [true], number of combined iterations 0, maximum guide tree iterations [-1], and maximum HMM iterations [-1] (68).
T120 1103-1309 Sentence denotes For the purposes of estimating time of viral peptide production, we classified ORF1a and ORF1b peptides as “early” whereas all other peptides produced by subgenomic mRNAs were classified as “late” (69, 70).
T121 1311-1340 Sentence denotes Conserved peptide assessment.
T122 1341-1388 Sentence denotes Aligned sequences were imported into Jalview v.
T123 1389-1924 Sentence denotes 2.1.1 (71) with automated generation of the following alignment annotations: (i) sequence consensus, calculated as the percentage of the modal residue per column; (ii) sequence conservation (0 to 11), measured as a numerical index reflecting conservation of amino acid physicochemical properties in the alignment; (iii) alignment quality (0 to 1), measured as a normalized sum of BLOSUM62 ratios for all residues at each position; and (iv) occupancy, calculated as the number of aligned residues (not including gaps) for each position.
T124 1925-2169 Sentence denotes In all cases, sequence conservation was assessed for each of the following three groups: only human-infecting coronavirus sequences (n = 7), all betacoronavirus sequences (n = 16), and all alpha- and betacoronavirus sequences combined (n = 34).
T125 2170-2266 Sentence denotes Aligned SARS-CoV-2 sequences and all annotations were manually exported for subsequent analysis.
T126 2267-2500 Sentence denotes Conserved human coronavirus peptides were defined as those with a length of ≥8 consecutive amino acids, each showing agreement with SARS-CoV-2 sequences and ≥4 other human coronavirus sequences with the consensus sequence (Table S2).
T127 2501-2751 Sentence denotes For each of these conserved peptides, we also assessed the component number of 8- to 12-mers sharing identical amino acid sequence between SARS-CoV-2 and each of the four other common human coronaviruses (i.e., OC43, HKU1, NL63, and 229E) (Table S3).
T128 2752-2978 Sentence denotes For all peptides, human, beta, and combined conservation scores were obtained using a custom R v.3.6.2 script representing mean sequence conservation (minus gap penalties where relevant) (see https://github.com/pdxgx/covid19).
T129 2980-3029 Sentence denotes Peptide-MHC class I binding affinity predictions.
T130 3030-3221 Sentence denotes FASTA-formatted input protein sequences from the entire SARS-CoV-2 and SARS-CoV proteomes were obtained from the NCBI RefSeq database (67) under accession numbers NC_045512.2 and NC_004718.3.
T131 3222-3351 Sentence denotes We kmerized each of these sequences into 8- to 12-mers to assess MHC class I-peptide binding affinity across the entire proteome.
T132 3352-3707 Sentence denotes MHC class I binding affinity predictions were performed using 145 different HLA alleles for which global allele frequency data were available as described previously (72) (see Table S5) with netMHCpan v4.0 (73) using the ‘-BA’ option to include binding affinity predictions and the ‘-l’ option to specify peptides 8 to 12 amino acids in length (Table S1).
T133 3708-3804 Sentence denotes Binding affinity was not predicted for peptides containing the character ‘|’ in their sequences.
T134 3805-4080 Sentence denotes Additional MHC class I binding affinity predictions were performed on all 66 MHCflurry-supported alleles (–list-supported-alleles; Table S6) using both MHCnuggets 2.3.2 (74) and MHCflurry 1.4.3 (75) (see Tables S7, S8, and S9 and Fig. S7 to S10 in the supplemental material).
T135 4081-4245 Sentence denotes We further cross-referenced these lists of peptides with existing experimentally validated SARS-CoV epitopes present in the Immune Epitope Database (Table S4) (76).
T136 4246-4466 Sentence denotes We then performed consensus binding affinity predictions for the 66 supported alleles shared by all three tools by taking the union set of alleles and filtering for peptide-allele pairs matching the union set of alleles.
T137 4467-4635 Sentence denotes For the SARS-CoV-specific and SARS-CoV-2-specific distributions of per-allele proteome presentation, we exclude all peptide-allele pairs with >500 nM predicted binding.
T138 4636-4890 Sentence denotes In all cases, we used the netchop v3.0 (77) “C-term” model with a cleavage threshold of 0.1 to further remove any peptides that were not predicted to undergo canonical MHC class I antigen processing via proteasomal cleavage (of the peptide’s C terminus).
T139 4892-4936 Sentence denotes Global HLA allele and haplotype frequencies.
T140 4937-5245 Sentence denotes HLA-A, -B, and -C allele and haplotype frequency data were obtained from the Allele Frequency Net Database (52) for 805 distinct populations pertaining to 101 different countries and 2,628 distinct major/minor (4-digit) alleles, corresponding to 20,478 distinct haplotypes (https://github.com/pdxgx/covid19).
T141 5246-5376 Sentence denotes We also identified full HLA genotype data for 3,382 individuals whose HLA types were confined to the 145 HLA alleles studied here.
T142 5377-5649 Sentence denotes Population allele and haplotype frequency data were aggregated by country as a mean of all constituent population allele or haplotype frequencies weighted by sample size of the population but not accounting for the representative ethnic demographic size of the population.
T143 5650-5912 Sentence denotes Global allele frequency maps were generated using the rworldmap v1.3-6 package (78), with total global allele and haplotype frequency estimates calculated as the mean of per-country allele and haplotype frequencies, weighted by each country’s population in 2005.
T144 5914-5932 Sentence denotes Data availability.
T145 5933-6056 Sentence denotes Source code is available at https://github.com/pdxgx/covid19 under the Massachusetts Institute of Technology (MIT) license.
T146 6057-6162 Sentence denotes Data File S4 can be found at https://github.com/pdxgx/covid19/blob/master/supporting_data/Appendix_4.zip.

2_test

Id Subject Object Predicate Lexical cue
32303592-26553804-65501646 631-633 26553804 denotes 67
32303592-21988835-65501647 1098-1100 21988835 denotes 68
32303592-15680415-65501648 1301-1303 15680415 denotes 69
32303592-19151095-65501649 1396-1398 19151095 denotes 71
32303592-26553804-65501650 3165-3167 26553804 denotes 67
32303592-29653567-65501651 3519-3521 29653567 denotes 72
32303592-28978689-65501652 3559-3561 28978689 denotes 73
32303592-31871119-65501653 3975-3977 31871119 denotes 74
32303592-29960884-65501654 4000-4002 29960884 denotes 75
32303592-30357391-65501655 4241-4243 30357391 denotes 76
32303592-15744535-65501656 4676-4678 15744535 denotes 77
32303592-25414323-65501657 5045-5047 25414323 denotes 52