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PMC:7073332 / 8564-10184 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
205 796-809 Species denotes coronaviruses Tax:11118
214 1419-1424 Gene denotes spike Gene:43740568
215 834-845 Species denotes coronavirus Tax:11118
216 847-850 Species denotes CoV Tax:11118
217 937-950 Species denotes coronaviruses Tax:11118
218 993-1015 Species denotes coronavirus, 2019-nCoV Tax:2697049
219 1016-1026 Species denotes SARS-CoV-2 Tax:2697049
220 1384-1392 Species denotes SARS-CoV Tax:694009
221 1188-1192 Species denotes HCoV Tax:694448
241 70-79 Species denotes 2019-nCoV Tax:2697049
242 80-90 Species denotes SARS-CoV-2 Tax:2697049
243 92-100 Species denotes SARS-CoV Tax:694009
244 102-110 Species denotes MERS-CoV Tax:1335626
245 112-121 Species denotes HCoV-OC43 Tax:31631
246 127-136 Species denotes HCoV-HKU1 Tax:290028
247 160-169 Species denotes HCoV-NL63 Tax:277944
248 174-183 Species denotes HCoV-229E Tax:11137
249 332-341 Species denotes 2019-nCoV Tax:2697049
250 342-352 Species denotes SARS-CoV-2 Tax:2697049
251 406-415 Species denotes 2019-nCoV Tax:2697049
252 416-426 Species denotes SARS-CoV-2 Tax:2697049
253 491-499 Species denotes patients Tax:9606
254 530-539 Species denotes 2019-nCoV Tax:2697049
255 540-550 Species denotes SARS-CoV-2 Tax:2697049
256 612-620 Species denotes SARS-CoV Tax:694009
257 719-728 Species denotes 2019-nCoV Tax:2697049
258 729-739 Species denotes SARS-CoV-2 Tax:2697049
259 744-752 Species denotes SARS-CoV Tax:694009

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T31 253-259 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T32 395-402 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T33 439-449 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T34 570-580 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T35 923-930 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T36 1193-1200 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T37 1520-1526 Body_part denotes Genome http://purl.org/sig/ont/fma/fma84116

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T3 1091-1096 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T30 80-88 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T31 92-100 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T32 342-350 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T33 416-424 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T34 540-548 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T35 612-620 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T36 729-737 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T37 744-752 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T38 1016-1024 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T39 1384-1392 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T59 38-40 http://purl.obolibrary.org/obo/CLO_0001236 denotes 2a
T60 42-43 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T61 521-523 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T62 759-761 http://purl.obolibrary.org/obo/CLO_0001236 denotes 2a
T63 811-812 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T64 1167-1168 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T65 1236-1243 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T66 1248-1255 http://purl.obolibrary.org/obo/CLO_0007225 denotes labeled
T67 1610-1612 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T68 1617-1619 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T69 1617-1619 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T90 439-449 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T91 570-580 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T92 1404-1406 Chemical denotes ID http://purl.obolibrary.org/obo/CHEBI_141439
T93 1430-1432 Chemical denotes ID http://purl.obolibrary.org/obo/CHEBI_141439
T94 1467-1469 Chemical denotes ID http://purl.obolibrary.org/obo/CHEBI_141439
T95 1617-1619 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T44 0-197 Sentence denotes To date, seven pathogenic HCoVs (Fig. 2a, b) have been found:1,29 (i) 2019-nCoV/SARS-CoV-2, SARS-CoV, MERS-CoV, HCoV-OC43, and HCoV-HKU1 are β genera, and (ii) HCoV-NL63 and HCoV-229E are α genera.
T45 198-370 Sentence denotes We performed the phylogenetic analyses using the whole-genome sequence data from 15 HCoVs to inspect the evolutionary relationship of 2019-nCoV/SARS-CoV-2 with other HCoVs.
T46 371-525 Sentence denotes We found that the whole genomes of 2019-nCoV/SARS-CoV-2 had ~99.99% nucleotide sequence identity across three diagnosed patients (Supplementary Table S1).
T47 526-763 Sentence denotes The 2019-nCoV/SARS-CoV-2 shares the highest nucleotide sequence identity (79.7%) with SARS-CoV among the six other known pathogenic HCoVs, revealing conserved evolutionary relationship between 2019-nCoV/SARS-CoV-2 and SARS-CoV (Fig. 2a).
T48 764-810 Sentence denotes Fig. 2 Phylogenetic analysis of coronaviruses.
T49 811-852 Sentence denotes a Phylogenetic tree of coronavirus (CoV).
T50 853-951 Sentence denotes Phylogenetic algorithm analyzed evolutionary conservation among whole genomes of 15 coronaviruses.
T51 952-1027 Sentence denotes Red color highlights the recent emergent coronavirus, 2019-nCoV/SARS-CoV-2.
T52 1028-1086 Sentence denotes Numbers on the branches indicate bootstrap support values.
T53 1087-1201 Sentence denotes The scale shows the evolutionary distance computed using the p-distance method. b Schematic plot for HCoV genomes.
T54 1202-1288 Sentence denotes The genus and host information of viruses was labeled on the left by different colors.
T55 1289-1407 Sentence denotes Empty dark gray boxes represent accessory open reading frames (ORFs). c–e The 3D structures of SARS-CoV nsp12 (PDB ID:
T56 1408-1433 Sentence denotes 6NUR) (c), spike (PDB ID:
T57 1434-1470 Sentence denotes 6ACK) (d), and nucleocapsid (PDB ID:
T58 1471-1519 Sentence denotes 2CJR) (e) shown were based on homology modeling.
T59 1520-1620 Sentence denotes Genome information and phylogenetic analysis results are provided in Supplementary Tables S1 and S2.

2_test

Id Subject Object Predicate Lexical cue
32194980-26868298-19614170 61-62 26868298 denotes 1
32194980-27743750-19614171 63-65 27743750 denotes 29