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PMC:7571312 / 1155-2827 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T54374 34-51 Body_part denotes respiratory tract http://purl.org/sig/ont/fma/fma265130
T26446 205-211 Body_part denotes Genome http://purl.org/sig/ont/fma/fma84116
T37694 774-780 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T78312 910-918 Body_part denotes cysteine http://purl.org/sig/ont/fma/fma82751
T72980 1024-1032 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T62636 1199-1207 Body_part denotes cysteine http://purl.org/sig/ont/fma/fma82751

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 34-51 Body_part denotes respiratory tract http://purl.obolibrary.org/obo/UBERON_0000065

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T10 34-61 Disease denotes respiratory tract infection http://purl.obolibrary.org/obo/MONDO_0024355
T11 52-61 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T12 139-143 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T13 265-269 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T14 305-338 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T15 340-344 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T16 368-372 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T17 441-445 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T18 568-572 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T19 616-620 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T20 691-701 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T21 763-767 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T22 1074-1078 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T23 1268-1272 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T24 1305-1309 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T25 1320-1324 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T26 1563-1567 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T27 1619-1623 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T83605 229-234 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T83875 244-245 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T73484 579-582 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T36915 636-637 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T8644 900-904 http://purl.obolibrary.org/obo/CLO_0053943 denotes a 3C
T48219 1099-1100 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T88436 1417-1423 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T85651 1431-1432 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T20594 1522-1530 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T11 910-918 Chemical denotes cysteine http://purl.obolibrary.org/obo/CHEBI_15356
T12 1024-1032 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T13 1199-1207 Chemical denotes cysteine http://purl.obolibrary.org/obo/CHEBI_15356
T14 1637-1647 Chemical denotes inhibitors http://purl.obolibrary.org/obo/CHEBI_35222
T15 1653-1662 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T75111 495-504 http://purl.obolibrary.org/obo/GO_0007585 denotes breathing
T3 1050-1067 http://purl.obolibrary.org/obo/GO_0019079 denotes viral replication
T4 1050-1067 http://purl.obolibrary.org/obo/GO_0019058 denotes viral replication

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T9 0-98 Sentence denotes In late 2019, cases of an unknown respiratory tract infection were first reported in Wuhan, China.
T10 99-553 Sentence denotes By February 2020, the novel coronavirus SARS CoV-2 was identified as the causative agent for COVID-19.1,2 Genome analysis of this virus revealed a high similarity to SARS CoV-1, the coronavirus that caused severe acute respiratory syndrome (SARS) in 2002–2003.2−4 Like SARS CoV-1, which resulted in 799 deaths among the 8464 probable cases,5 SARS CoV-2 can induce fever, coughing, and difficulty breathing that rapidly becomes more serious in some cases.
T11 554-937 Sentence denotes The spread of SARS CoV-2 has been more extensive than that of SARS CoV-1, causing a global pandemic with the current number of worldwide infections surpassing eight million and deaths surpassing 400,000.6 The SARS CoV-1 genome encodes for two large polyproteins pp1a (∼450 kDa) and pp1ab (∼750 kDa) that contain overlapping sequences and include a 3C-like cysteine protease (3CLpro).
T12 938-1286 Sentence denotes The function of this internally encoded 3CLpro is integral to the processing of these proteins and critical for viral replication.7 The SARS CoV-1 3CLpro shares a high degree of structural homology and similar substrate specificity with the coronavirus 3C-like cysteine proteases of hCoV 229E and TGEV8 but is most similar to the SARS CoV-2 3CLpro.
T13 1287-1672 Sentence denotes Specifically, the SARS CoV-1 and SARS CoV-2 share 96% identity between their respective 3CLpro sequences and 100% identity in the active site.8 A recent report by Dai et al. demonstrates that crystallographic information and structure–activity relationships obtained with the SARS CoV-1 3CLpro could facilitate the design of potent SARS CoV-2 3CLpro inhibitors with antiviral potency.9

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 34-61 Phenotype denotes respiratory tract infection http://purl.obolibrary.org/obo/HP_0011947
T2 463-468 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T3 470-478 Phenotype denotes coughing http://purl.obolibrary.org/obo/HP_0012735
T4 484-504 Phenotype denotes difficulty breathing http://purl.obolibrary.org/obo/HP_0002098

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
59 816-820 Gene denotes pp1a Gene:5499
60 121-138 Species denotes novel coronavirus Tax:2697049
61 139-149 Species denotes SARS CoV-2 Tax:2697049
62 265-273 Species denotes SARS CoV Tax:694009
63 281-292 Species denotes coronavirus Tax:11118
64 368-376 Species denotes SARS CoV Tax:694009
65 441-451 Species denotes SARS CoV-2 Tax:2697049
66 568-578 Species denotes SARS CoV-2 Tax:2697049
67 616-624 Species denotes SARS CoV Tax:694009
68 763-771 Species denotes SARS CoV Tax:694009
69 1074-1082 Species denotes SARS CoV Tax:694009
70 1179-1190 Species denotes coronavirus Tax:11118
71 1221-1230 Species denotes hCoV 229E Tax:11137
72 1235-1239 Species denotes TGEV Tax:11149
73 1268-1278 Species denotes SARS CoV-2 Tax:2697049
74 1305-1313 Species denotes SARS CoV Tax:694009
75 1320-1330 Species denotes SARS CoV-2 Tax:2697049
76 1563-1571 Species denotes SARS CoV Tax:694009
77 1619-1629 Species denotes SARS CoV-2 Tax:2697049
78 34-61 Disease denotes respiratory tract infection MESH:D012141
79 192-200 Disease denotes COVID-19 MESH:C000657245
80 312-338 Disease denotes acute respiratory syndrome MESH:D012120
81 402-408 Disease denotes deaths MESH:D003643
82 463-468 Disease denotes fever MESH:D005334
83 470-478 Disease denotes coughing MESH:D003371
84 691-701 Disease denotes infections MESH:D007239
85 731-737 Disease denotes deaths MESH:D003643

2_test

Id Subject Object Predicate Lexical cue
33054210-32015508-61913438 201-202 32015508 denotes 1
33054210-32015507-61913439 203-204 32015507 denotes 2
33054210-32015507-61913440 359-360 32015507 denotes 2
33054210-12730500-61913441 361-362 12730500 denotes 4
33054210-12917450-61913442 1068-1069 12917450 denotes 7
33054210-32321856-61913443 1671-1672 32321856 denotes 9