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PMC:7307149 / 19084-20991 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T129 349-352 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T130 549-552 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T131 673-676 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T132 806-809 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T133 884-888 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T134 931-935 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T135 1113-1117 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T136 1248-1251 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T137 1549-1552 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T138 1698-1706 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T139 1770-1776 Body_part denotes serine http://purl.org/sig/ont/fma/fma82764
T140 1814-1822 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T141 1850-1854 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T87 175-183 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T88 405-413 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T89 1084-1093 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T90 1186-1195 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T91 1431-1439 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T92 1827-1835 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T197 90-91 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T198 184-192 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T199 267-268 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T200 798-805 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T201 856-857 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T202 882-888 http://purl.obolibrary.org/obo/CL_0000084 denotes T-cell
T203 929-935 http://purl.obolibrary.org/obo/CL_0000084 denotes T-cell
T204 1066-1067 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T205 1111-1117 http://purl.obolibrary.org/obo/CL_0000084 denotes T-cell
T206 1178-1179 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T207 1214-1215 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T208 1314-1315 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T209 1346-1348 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48
T210 1850-1854 http://purl.obolibrary.org/obo/GO_0005623 denotes cell

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T110 184-192 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T111 204-206 Chemical denotes S4 http://purl.obolibrary.org/obo/CHEBI_29401
T112 798-805 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T113 1698-1706 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T114 1714-1725 Chemical denotes angiotensin http://purl.obolibrary.org/obo/CHEBI_48433
T115 1770-1776 Chemical denotes serine http://purl.obolibrary.org/obo/CHEBI_17822
T116 1814-1822 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
371 1714-1745 Gene denotes angiotensin converting enzyme 2 Gene:59272
372 1747-1751 Gene denotes ACE2 Gene:59272
373 1756-1787 Gene denotes transmembrane serine protease 2 Gene:7113
374 1789-1796 Gene denotes TMPRSS2 Gene:7113
375 175-183 Species denotes SARS-CoV Tax:694009
376 1431-1441 Species denotes SARS-CoV-2 Tax:2697049
377 1605-1609 Species denotes ncov Tax:2697049
378 1827-1837 Species denotes SARS-CoV-2 Tax:2697049
379 405-413 Disease denotes COVID-19 MESH:C000657245
380 1084-1093 Disease denotes infection MESH:D007239
381 1186-1195 Disease denotes infection MESH:D007239

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T28 549-552 http://purl.obolibrary.org/obo/GO_0046776 denotes MHC
T29 806-809 http://purl.obolibrary.org/obo/GO_0046776 denotes MHC
T30 1111-1124 http://purl.obolibrary.org/obo/GO_0002870 denotes T-cell anergy
T31 1533-1542 http://purl.obolibrary.org/obo/GO_0016032 denotes virulence
T32 1533-1542 http://purl.obolibrary.org/obo/GO_0009405 denotes virulence

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T103 0-50 Sentence denotes We note, however, several limitations to our work.
T104 51-304 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 305-612 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 613-776 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 777-951 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 952-1196 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 1197-1350 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 1351-1611 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 1612-1907 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.

2_test

Id Subject Object Predicate Lexical cue
32303592-30053426-65501639 900-902 30053426 denotes 54
32303592-30886616-65501639 900-902 30886616 denotes 54
32303592-19182777-65501640 903-905 19182777 denotes 56
32303592-28479213-65501641 1034-1036 28479213 denotes 57
32303592-27799871-65501641 1034-1036 27799871 denotes 57
32303592-15812491-65501642 1037-1039 15812491 denotes 59
32303592-12471109-65501643 1126-1128 12471109 denotes 60
32303592-23580623-65501643 1126-1128 23580623 denotes 60
32303592-9697771-65501644 1129-1131 9697771 denotes 62
32303592-21760609-65501645 1156-1158 21760609 denotes 63