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PMC:7307149 / 17479-21548 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T117 140-143 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T118 158-161 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T119 290-293 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T120 348-351 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T121 509-512 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T122 752-755 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T123 832-835 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T124 1005-1008 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T125 1449-1453 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T126 1472-1480 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T127 1492-1496 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T128 1539-1543 Body_part denotes mRNA http://purl.org/sig/ont/fma/fma67122
T129 1954-1957 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T130 2154-2157 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T131 2278-2281 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T132 2411-2414 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T133 2489-2493 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T134 2536-2540 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T135 2718-2722 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T136 2853-2856 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T137 3154-3157 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T138 3303-3311 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T139 3375-3381 Body_part denotes serine http://purl.org/sig/ont/fma/fma82764
T140 3419-3427 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T141 3455-3459 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T142 3694-3697 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T143 3739-3742 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T78 438-446 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T79 449-458 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T80 564-573 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T81 600-608 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T82 642-650 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T83 655-663 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T84 1074-1082 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T85 1086-1094 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T86 1353-1361 Disease denotes vaccinia http://purl.obolibrary.org/obo/MONDO_0002595
T87 1780-1788 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T88 2010-2018 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T89 2689-2698 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T90 2791-2800 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T91 3036-3044 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T92 3432-3440 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T93 3755-3763 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T182 124-125 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T183 162-169 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T184 513-514 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T185 666-673 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T186 701-702 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T187 1097-1105 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T188 1147-1154 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T189 1286-1291 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T190 1362-1367 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T191 1397-1404 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T192 1442-1445 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T193 1447-1453 http://purl.obolibrary.org/obo/CL_0000084 denotes T-cell
T194 1485-1488 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T195 1490-1496 http://purl.obolibrary.org/obo/CL_0000084 denotes T-cell
T196 1567-1574 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T197 1695-1696 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T198 1789-1797 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T199 1872-1873 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T200 2403-2410 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T201 2461-2462 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T202 2487-2493 http://purl.obolibrary.org/obo/CL_0000084 denotes T-cell
T203 2534-2540 http://purl.obolibrary.org/obo/CL_0000084 denotes T-cell
T204 2671-2672 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T205 2716-2722 http://purl.obolibrary.org/obo/CL_0000084 denotes T-cell
T206 2783-2784 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T207 2819-2820 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T208 2919-2920 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T209 2951-2953 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48
T210 3455-3459 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T211 3698-3705 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T212 3764-3771 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T213 3822-3823 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T214 4038-4039 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T215 4061-4068 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T101 162-169 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T102 302-309 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T103 666-673 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T104 1097-1105 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T105 1147-1154 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T106 1304-1311 Chemical denotes epitope http://purl.obolibrary.org/obo/CHEBI_53000
T107 1397-1404 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T108 1405-1413 Chemical denotes antigens http://purl.obolibrary.org/obo/CHEBI_59132
T109 1567-1574 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T110 1789-1797 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T111 1809-1811 Chemical denotes S4 http://purl.obolibrary.org/obo/CHEBI_29401
T112 2403-2410 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T113 3303-3311 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T114 3319-3330 Chemical denotes angiotensin http://purl.obolibrary.org/obo/CHEBI_48433
T115 3375-3381 Chemical denotes serine http://purl.obolibrary.org/obo/CHEBI_17822
T116 3419-3427 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
346 509-514 Gene denotes HLA-B Gene:3106
347 1442-1445 Gene denotes CD8 Gene:925
348 1485-1488 Gene denotes CD4 Gene:920
349 252-263 Species denotes coronavirus Tax:11118
350 600-608 Species denotes SARS-CoV Tax:694009
351 642-650 Species denotes SARS-CoV Tax:694009
352 655-665 Species denotes SARS-CoV-2 Tax:2697049
353 1074-1082 Species denotes SARS-CoV Tax:694009
354 1086-1096 Species denotes SARS-CoV-2 Tax:2697049
355 1286-1303 Species denotes human coronavirus Tax:694448
356 1353-1367 Species denotes vaccinia virus Tax:10245
357 290-309 Gene denotes MHC class I antigen Gene:100507703
358 438-458 Disease denotes SARS-CoV-2 infection MESH:C000657245
359 564-573 Disease denotes infection MESH:D007239
371 3319-3350 Gene denotes angiotensin converting enzyme 2 Gene:59272
372 3352-3356 Gene denotes ACE2 Gene:59272
373 3361-3392 Gene denotes transmembrane serine protease 2 Gene:7113
374 3394-3401 Gene denotes TMPRSS2 Gene:7113
375 1780-1788 Species denotes SARS-CoV Tax:694009
376 3036-3046 Species denotes SARS-CoV-2 Tax:2697049
377 3210-3214 Species denotes ncov Tax:2697049
378 3432-3442 Species denotes SARS-CoV-2 Tax:2697049
379 2010-2018 Disease denotes COVID-19 MESH:C000657245
380 2689-2698 Disease denotes infection MESH:D007239
381 2791-2800 Disease denotes infection MESH:D007239
383 3755-3763 Disease denotes COVID-19 MESH:C000657245

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T22 158-161 http://purl.obolibrary.org/obo/GO_0046776 denotes MHC
T23 290-293 http://purl.obolibrary.org/obo/GO_0046776 denotes MHC
T24 302-322 http://purl.obolibrary.org/obo/GO_0019882 denotes antigen presentation
T25 1177-1194 http://purl.obolibrary.org/obo/GO_0019079 denotes viral replication
T26 1177-1194 http://purl.obolibrary.org/obo/GO_0019058 denotes viral replication
T27 1326-1341 http://purl.obolibrary.org/obo/GO_0006955 denotes immune response
T28 2154-2157 http://purl.obolibrary.org/obo/GO_0046776 denotes MHC
T29 2411-2414 http://purl.obolibrary.org/obo/GO_0046776 denotes MHC
T30 2716-2729 http://purl.obolibrary.org/obo/GO_0002870 denotes T-cell anergy
T31 3138-3147 http://purl.obolibrary.org/obo/GO_0016032 denotes virulence
T32 3138-3147 http://purl.obolibrary.org/obo/GO_0009405 denotes virulence

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T3 300-309 GlycoEpitope denotes I antigen http://www.glycoepitope.jp/epitopes/EP0138

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T2 557-573 Phenotype denotes severe infection http://purl.obolibrary.org/obo/HP_0032169

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T95 0-10 Sentence denotes DISCUSSION
T96 11-198 Sentence denotes To the best of our knowledge, this was the first study to evaluate per-allele viral proteome presentation across a wide range of HLA alleles using MHC-peptide binding affinity predictors.
T97 199-323 Sentence denotes This report also introduces the relationship between coronavirus sequence conservation and MHC class I antigen presentation.
T98 324-614 Sentence denotes We show that individual HLA, haplotype, and full-genotype variability likely influence the capacity to respond to SARS-CoV-2 infection, and we note certain alleles in particular (e.g., HLA-B*46:01) that could be associated with more-severe infection, as previously shown with SARS-CoV (49).
T99 615-762 Sentence denotes Indeed, we further compare SARS-CoV and SARS-CoV-2 peptide presentation data and note a high degree of similarity between the two across HLA types.
T100 763-941 Sentence denotes Finally, this is the first report to present global distributions of HLA types and haplotypes with potential epidemiological ramifications in the setting of the current pandemic.
T101 942-1201 Sentence denotes We found that, in general, there is no correlation between the HLA allelic frequency in the population and allelic capacity to bind SARS-CoV or SARS-CoV-2 peptides, irrespective of the estimated timing of peptide production during the viral replication cycle.
T102 1202-1604 Sentence denotes While we are not aware of any studies explicitly reporting the relationship between human coronavirus epitope abundance and immune response, there are vaccinia virus data that suggest that early peptide antigens are more likely to generate CD8+ T-cell responses whereas antibody and CD4+ T-cell responses are more likely to target later mRNA expression with higher peptide abundance in the virion (53).
T103 1605-1655 Sentence denotes We note, however, several limitations to our work.
T104 1656-1909 Sentence denotes First and foremost, while we note that a few of our binding affinity predictions were borne out in experimentally validated SARS-CoV peptides (see Table S4 in the supplemental material), we acknowledge that ours was a study performed entirely in silico.
T105 1910-2217 Sentence denotes As we are unable to obtain individual-level HLA typing and clinical outcome data for any real-world COVID-19 populations at this time, the data presented are theoretical in nature and are subject to many of the same limitations implicit in the MHC binding affinity prediction tool(s) upon which it is based.
T106 2218-2381 Sentence denotes As such, we are unable to assess the relative importance of HLA type compared to known disease-modifying risk factors such as age and clinical comorbidities (4–9).
T107 2382-2556 Sentence denotes We further note that peptide-MHC binding affinity is limited in its utility as a predictor of subsequent T-cell responses (54–56), and we did not study T-cell responses here.
T108 2557-2801 Sentence denotes As such, we are ill-equipped to explore phenomena such as original antigenic sin (57–59), where prior exposure to a closely related infection(s) might trigger T-cell anergy (60–62) or immunopathogenesis (63) in the setting of a novel infection.
T109 2802-2955 Sentence denotes We explored only a limited set of 145 well-studied HLA alleles but note that this analysis could be performed across a wider diversity of genotypes (48).
T110 2956-3216 Sentence denotes Additionally, we did not assess genotypic heterogeneity or in vivo evolution of SARS-CoV-2, which could modify the repertoire of viral epitopes presented or could otherwise modulate virulence in an HLA-independent manner (64, 65) (https://nextstrain.org/ncov).
T111 3217-3512 Sentence denotes We also did not address the potential for individual-level genetic variation in other proteins (e.g., angiotensin converting enzyme 2 [ACE2] or transmembrane serine protease 2 [TMPRSS2], essential host proteins for SARS-CoV-2 priming and cell entry [66]) to modulate the host-pathogen interface.
T112 3513-3639 Sentence denotes Unless and until the findings we present here are clinically validated, they should not be employed for any clinical purposes.
T113 3640-3968 Sentence denotes However, we do at this juncture recommend integrating HLA testing into clinical trials and pairing HLA typing with COVID-19 testing where feasible to more rapidly develop and deploy a predictor(s) of viral severity in the population and, potentially, to tailor future vaccination strategies to genotypically at-risk populations.
T114 3969-4069 Sentence denotes This approach may have additional implications for the management of a broad array of other viruses.

2_test

Id Subject Object Predicate Lexical cue
32303592-12969506-65501637 610-612 12969506 denotes 49
32303592-20006135-65501638 1600-1602 20006135 denotes 53
32303592-30053426-65501639 2505-2507 30053426 denotes 54
32303592-30886616-65501639 2505-2507 30886616 denotes 54
32303592-19182777-65501640 2508-2510 19182777 denotes 56
32303592-28479213-65501641 2639-2641 28479213 denotes 57
32303592-27799871-65501641 2639-2641 27799871 denotes 57
32303592-15812491-65501642 2642-2644 15812491 denotes 59
32303592-12471109-65501643 2731-2733 12471109 denotes 60
32303592-23580623-65501643 2731-2733 23580623 denotes 60
32303592-9697771-65501644 2734-2736 9697771 denotes 62
32303592-21760609-65501645 2761-2763 21760609 denotes 63