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PMC:7073332 / 8518-12240 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
203 25-34 Species denotes 2019-nCoV Tax:2697049
205 842-855 Species denotes coronaviruses Tax:11118
214 1465-1470 Gene denotes spike Gene:43740568
215 880-891 Species denotes coronavirus Tax:11118
216 893-896 Species denotes CoV Tax:11118
217 983-996 Species denotes coronaviruses Tax:11118
218 1039-1061 Species denotes coronavirus, 2019-nCoV Tax:2697049
219 1062-1072 Species denotes SARS-CoV-2 Tax:2697049
220 1430-1438 Species denotes SARS-CoV Tax:694009
221 1234-1238 Species denotes HCoV Tax:694448
241 116-125 Species denotes 2019-nCoV Tax:2697049
242 126-136 Species denotes SARS-CoV-2 Tax:2697049
243 138-146 Species denotes SARS-CoV Tax:694009
244 148-156 Species denotes MERS-CoV Tax:1335626
245 158-167 Species denotes HCoV-OC43 Tax:31631
246 173-182 Species denotes HCoV-HKU1 Tax:290028
247 206-215 Species denotes HCoV-NL63 Tax:277944
248 220-229 Species denotes HCoV-229E Tax:11137
249 378-387 Species denotes 2019-nCoV Tax:2697049
250 388-398 Species denotes SARS-CoV-2 Tax:2697049
251 452-461 Species denotes 2019-nCoV Tax:2697049
252 462-472 Species denotes SARS-CoV-2 Tax:2697049
253 537-545 Species denotes patients Tax:9606
254 576-585 Species denotes 2019-nCoV Tax:2697049
255 586-596 Species denotes SARS-CoV-2 Tax:2697049
256 658-666 Species denotes SARS-CoV Tax:694009
257 765-774 Species denotes 2019-nCoV Tax:2697049
258 775-785 Species denotes SARS-CoV-2 Tax:2697049
259 790-798 Species denotes SARS-CoV Tax:694009
287 1789-1795 Gene denotes ORF1ab Gene:43740578
288 1798-1803 Gene denotes spike Gene:43740568
289 1805-1806 Gene denotes S Gene:43740568
290 1819-1820 Gene denotes E Gene:43740570
291 1823-1831 Gene denotes membrane Gene:43740571
292 1833-1834 Gene denotes M Gene:43740571
293 1882-1888 Gene denotes ORF1ab Gene:43740578
294 2077-2081 Gene denotes nsp7 Gene:43740578
295 2086-2090 Gene denotes nsp8 Gene:43740578
296 2240-2244 Gene denotes nsp7 Gene:43740578
297 2249-2253 Gene denotes nsp8 Gene:43740578
298 2292-2297 Gene denotes spike Gene:43740568
299 2465-2470 Gene denotes spike Gene:43740568
300 2541-2545 Gene denotes ACE2 Gene:59272
301 2642-2646 Gene denotes ACE2 Gene:59272
302 2671-2675 Gene denotes ACE2 Gene:59272
303 2863-2868 Gene denotes spike Gene:43740568
304 2875-2879 Gene denotes ACE2 Gene:59272
305 2797-2802 Gene denotes spike Gene:43740568
306 2166-2174 Species denotes SARS-CoV Tax:694009
307 2550-2558 Species denotes SARS-CoV Tax:694009
308 2602-2611 Species denotes 2019-nCoV Tax:2697049
309 2612-2622 Species denotes SARS-CoV-2 Tax:2697049
310 2842-2851 Species denotes 2019-nCoV Tax:2697049
311 2852-2862 Species denotes SARS-CoV-2 Tax:2697049
312 2906-2914 Species denotes SARS-CoV Tax:694009
313 2369-2384 Disease denotes viral infection MESH:D001102
328 3488-3493 Gene denotes spike Gene:43740568
329 3630-3635 Gene denotes spike Gene:43740568
330 3157-3166 Species denotes 2019-nCoV Tax:2697049
331 3167-3177 Species denotes SARS-CoV-2 Tax:2697049
332 3217-3225 Species denotes SARS-CoV Tax:694009
333 3308-3317 Species denotes 2019-nCoV Tax:2697049
334 3318-3328 Species denotes SARS-CoV-2 Tax:2697049
335 3440-3448 Species denotes SARS-CoV Tax:694009
336 3580-3589 Species denotes 2019-nCoV Tax:2697049
337 3590-3600 Species denotes SARS-CoV-2 Tax:2697049
338 3605-3613 Species denotes SARS-CoV Tax:694009
339 3647-3656 Species denotes 2019-nCoV Tax:2697049
340 3657-3667 Species denotes SARS-CoV-2 Tax:2697049
341 3713-3721 Species denotes MERS-CoV Tax:1335626

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T31 299-305 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T32 441-448 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T33 485-495 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T34 616-626 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T35 969-976 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T36 1239-1246 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T37 1566-1572 Body_part denotes Genome http://purl.org/sig/ont/fma/fma84116
T38 1689-1696 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T39 1858-1866 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T40 1889-1893 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T41 1921-1929 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T42 1945-1948 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T43 2022-2025 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T44 2036-2039 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T45 2137-2144 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T46 2317-2329 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T47 2471-2478 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T48 3001-3007 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T49 3016-3023 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T50 3102-3109 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257
T51 3296-3304 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T52 3494-3501 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T53 3636-3643 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T3 1137-1142 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542
T4 2214-2223 Body_part denotes extension http://purl.obolibrary.org/obo/UBERON_2000106

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T29 35-43 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T30 126-134 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T31 138-146 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T32 388-396 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T33 462-470 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T34 586-594 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T35 658-666 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T36 775-783 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T37 790-798 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T38 1062-1070 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T39 1430-1438 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T40 2166-2174 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T41 2369-2384 Disease denotes viral infection http://purl.obolibrary.org/obo/MONDO_0005108
T42 2375-2384 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T43 2550-2558 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T44 2612-2620 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T45 2852-2860 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T46 2906-2910 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T47 3167-3175 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T48 3217-3225 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T49 3318-3326 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T50 3440-3448 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T51 3590-3598 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T52 3605-3613 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T53 3657-3665 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T59 84-86 http://purl.obolibrary.org/obo/CLO_0001236 denotes 2a
T60 88-89 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T61 567-569 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T62 805-807 http://purl.obolibrary.org/obo/CLO_0001236 denotes 2a
T63 857-858 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T64 1213-1214 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T65 1282-1289 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T66 1294-1301 http://purl.obolibrary.org/obo/CLO_0007225 denotes labeled
T67 1656-1658 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T68 1663-1665 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T69 1663-1665 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T70 1709-1714 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T71 1823-1831 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T72 1889-1893 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T73 2014-2015 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T74 2118-2126 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T75 2194-2195 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T76 2301-2302 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T77 2341-2342 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T78 2575-2576 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T79 3247-3249 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T80 3247-3249 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T81 3470-3472 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T82 3470-3472 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T83 3673-3676 http://purl.obolibrary.org/obo/CLO_0051582 denotes has

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T90 485-495 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T91 616-626 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T92 1450-1452 Chemical denotes ID http://purl.obolibrary.org/obo/CHEBI_141439
T93 1476-1478 Chemical denotes ID http://purl.obolibrary.org/obo/CHEBI_141439
T94 1513-1515 Chemical denotes ID http://purl.obolibrary.org/obo/CHEBI_141439
T95 1663-1665 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T96 1689-1696 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T97 1858-1866 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T98 1921-1929 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T99 2137-2144 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T100 2317-2329 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T101 2471-2478 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T102 2508-2519 Chemical denotes angiotensin http://purl.obolibrary.org/obo/CHEBI_48433
T103 2564-2566 Chemical denotes ID http://purl.obolibrary.org/obo/CHEBI_141439
T104 2717-2721 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T105 2777-2779 Chemical denotes EM http://purl.obolibrary.org/obo/CHEBI_73507
T106 3016-3023 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T107 3102-3109 Chemical denotes Protein http://purl.obolibrary.org/obo/CHEBI_16541
T108 3247-3249 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T109 3296-3304 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T110 3470-3472 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T111 3494-3501 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T112 3636-3643 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T3 1945-1958 http://purl.obolibrary.org/obo/GO_0032774 denotes RNA synthesis
T4 1949-1958 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T5 2369-2384 http://purl.obolibrary.org/obo/GO_0016032 denotes viral infection

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T43 0-45 Sentence denotes Phylogenetic analyses of 2019-nCoV/SARS-CoV-2
T44 46-243 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 244-416 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 417-571 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 572-809 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 810-856 Sentence denotes Fig. 2 Phylogenetic analysis of coronaviruses.
T49 857-898 Sentence denotes a Phylogenetic tree of coronavirus (CoV).
T50 899-997 Sentence denotes Phylogenetic algorithm analyzed evolutionary conservation among whole genomes of 15 coronaviruses.
T51 998-1073 Sentence denotes Red color highlights the recent emergent coronavirus, 2019-nCoV/SARS-CoV-2.
T52 1074-1132 Sentence denotes Numbers on the branches indicate bootstrap support values.
T53 1133-1247 Sentence denotes The scale shows the evolutionary distance computed using the p-distance method. b Schematic plot for HCoV genomes.
T54 1248-1334 Sentence denotes The genus and host information of viruses was labeled on the left by different colors.
T55 1335-1453 Sentence denotes Empty dark gray boxes represent accessory open reading frames (ORFs). c–e The 3D structures of SARS-CoV nsp12 (PDB ID:
T56 1454-1479 Sentence denotes 6NUR) (c), spike (PDB ID:
T57 1480-1516 Sentence denotes 6ACK) (d), and nucleocapsid (PDB ID:
T58 1517-1565 Sentence denotes 2CJR) (e) shown were based on homology modeling.
T59 1566-1666 Sentence denotes Genome information and phylogenetic analysis results are provided in Supplementary Tables S1 and S2.
T60 1667-1877 Sentence denotes HCoVs have five major protein regions for virus structure assembly and viral replications29, including replicase complex (ORF1ab), spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins (Fig. 2b).
T61 1878-2000 Sentence denotes The ORF1ab gene encodes the non-structural proteins (nsp) of viral RNA synthesis complex through proteolytic processing30.
T62 2001-2127 Sentence denotes The nsp12 is a viral RNA-dependent RNA polymerase, together with co-factors nsp7 and nsp8 possessing high polymerase activity.
T63 2128-2287 Sentence denotes From the protein 3D structure view of SARS-CoV nsp12, it contains a larger N-terminal extension (which binds to nsp7 and nsp8) and polymerase domain (Fig. 2c).
T64 2288-2424 Sentence denotes The spike is a transmembrane glycoprotein that plays a pivotal role in mediating viral infection through binding the host receptor31,32.
T65 2425-2567 Sentence denotes Figure 2d shows the 3D structure of the spike protein bound with the host receptor angiotensin converting enznyme2 (ACE2) in SARS-CoV (PDB ID:
T66 2568-2574 Sentence denotes 6ACK).
T67 2575-2758 Sentence denotes A recent study showed that 2019-nCoV/SARS-CoV-2 is able to utilize ACE2 as an entry receptor in ACE2-expressing cells33, suggesting potential drug targets for therapeutic development.
T68 2759-2917 Sentence denotes Furthermore, cryo-EM structure of the spike and biophysical assays reveal that the 2019-nCoV/SARS-CoV-2 spike binds ACE2 with higher affinity than SARS-CoV34.
T69 2918-3101 Sentence denotes In addition, the nucleocapsid is also an important subunit for packaging the viral genome through protein oligomerization35, and the single nucleocapsid structure is shown in Fig. 2e.
T70 3102-3251 Sentence denotes Protein sequence alignment analyses indicated that the 2019-nCoV/SARS-CoV-2 was most evolutionarily conserved with SARS-CoV (Supplementary Table S2).
T71 3252-3474 Sentence denotes Specifically, the envelope and nucleocapsid proteins of 2019-nCoV/SARS-CoV-2 are two evolutionarily conserved regions, with sequence identities of 96% and 89.6%, respectively, compared to SARS-CoV (Supplementary Table S2).
T72 3475-3614 Sentence denotes However, the spike protein exhibited the lowest sequence conservation (sequence identity of 77%) between 2019-nCoV/SARS-CoV-2 and SARS-CoV.
T73 3615-3722 Sentence denotes Meanwhile, the spike protein of 2019-nCoV/SARS-CoV-2 only has 31.9% sequence identity compared to MERS-CoV.

2_test

Id Subject Object Predicate Lexical cue
32194980-26868298-19614170 107-108 26868298 denotes 1
32194980-27743750-19614171 109-111 27743750 denotes 29
32194980-27743750-19614172 1756-1758 27743750 denotes 29
32194980-31138817-19614173 1997-1999 31138817 denotes 30
32194980-16166518-19614174 2418-2420 16166518 denotes 31
32194980-32007145-19614175 2421-2423 32007145 denotes 32
32194980-32015507-19614176 2692-2694 32015507 denotes 33
32194980-32075877-19614177 2914-2916 32075877 denotes 34
32194980-23717688-19614178 3039-3041 23717688 denotes 35