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PMC:7045880 / 3166-7857 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
115 153-161 Species denotes patients Tax:9606
116 172-182 Species denotes SARS-CoV-2 Tax:2697049
117 524-532 Disease denotes COVID-19 MESH:C000657245
119 703-711 Species denotes SARS-CoV Tax:694009
131 1865-1873 Species denotes patients Tax:9606
132 2423-2433 Species denotes SARS-CoV-2 Tax:2697049
133 1986-1994 Chemical denotes Nystadin
134 1996-2006 Chemical denotes penicillin MESH:D010406
135 2007-2019 Chemical denotes streptomycin MESH:D013307
136 2169-2172 Chemical denotes CO2 MESH:D002245
137 2179-2213 Chemical denotes Dulbecco’s modified Eagle’s medium
138 2215-2219 Chemical denotes DMEM
139 2265-2275 Chemical denotes penicillin MESH:D010406
140 2276-2288 Chemical denotes streptomycin MESH:D013307
141 1856-1864 Disease denotes COVID-19 MESH:C000657245
143 2952-2962 Species denotes SARS-CoV-2 Tax:2697049
146 3261-3266 Species denotes human Tax:9606
147 3278-3289 Species denotes coronavirus Tax:11118
159 3698-3714 Chemical denotes paraformaldehyde MESH:C003043
160 3724-3738 Chemical denotes glutaraldehyde MESH:D005976
161 3748-3757 Chemical denotes phosphate MESH:D010710
162 4003-4019 Chemical denotes osmium tetroxide MESH:D009993
163 4058-4063 Chemical denotes water MESH:D014867
164 4169-4176 Chemical denotes ethanol MESH:D000431
165 4271-4286 Chemical denotes propylene oxide MESH:C009068
166 4491-4497 Chemical denotes nickel MESH:D009532
167 4531-4545 Chemical denotes uranyl acetate MESH:C005460
168 3812-3820 Disease denotes infected MESH:D007239
169 4231-4242 Disease denotes dehydration MESH:D003681

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T13 49-52 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T14 106-112 Body_part denotes sputum http://purl.org/sig/ont/fma/fma312401
T15 228-231 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T16 288-291 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T17 684-687 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T18 753-756 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T19 767-770 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T20 782-786 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T21 999-1003 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T22 1222-1225 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T23 2114-2119 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T24 2137-2142 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T25 2255-2260 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T26 2365-2369 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T27 2630-2636 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T28 2692-2695 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T29 2724-2728 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T30 2963-2966 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T31 3137-3143 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T32 3169-3173 Body_part denotes Gene http://purl.org/sig/ont/fma/fma74402
T33 3658-3663 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T34 3806-3811 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T4 106-112 Body_part denotes sputum http://purl.obolibrary.org/obo/UBERON_0007311
T5 2255-2260 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T23 172-180 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T24 524-532 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T25 703-711 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T26 1856-1864 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T27 2423-2431 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T28 2952-2960 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T29 3205-3208 Disease denotes CLC http://purl.obolibrary.org/obo/MONDO_0004315
T30 3347-3356 Disease denotes Influenza http://purl.obolibrary.org/obo/MONDO_0005812

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T33 273-274 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T34 403-404 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T35 633-634 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T36 782-786 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T37 999-1003 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T38 1172-1173 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T39 1714-1724 http://purl.obolibrary.org/obo/OBI_0000968 denotes instrument
T40 1757-1762 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Virus
T41 1777-1782 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T42 2020-2023 http://purl.obolibrary.org/obo/CLO_0053733 denotes 1:1
T43 2034-2038 http://purl.obolibrary.org/obo/CLO_0001757 denotes at 1
T44 2075-2078 http://purl.obolibrary.org/obo/CLO_0001387 denotes 4°C
T45 2109-2113 http://purl.obolibrary.org/obo/CLO_0009524 denotes Vero
T46 2109-2113 http://purl.obolibrary.org/obo/CLO_0050515 denotes Vero
T47 2114-2119 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T48 2132-2136 http://purl.obolibrary.org/obo/CLO_0009524 denotes Vero
T49 2132-2136 http://purl.obolibrary.org/obo/CLO_0050515 denotes Vero
T50 2137-2142 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T51 2163-2167 http://purl.obolibrary.org/obo/CLO_0002131 denotes C, 5
T52 2290-2295 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Virus
T53 2365-2369 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T54 2451-2452 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T55 2715-2728 http://purl.obolibrary.org/obo/CL_0000010 denotes cultured cell
T56 2749-2754 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T57 2771-2772 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T58 2863-2868 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T59 3123-3124 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T60 3169-3173 http://purl.obolibrary.org/obo/OGG_0000000002 denotes Gene
T61 3205-3208 http://purl.obolibrary.org/obo/CLO_0002494 denotes CLC
T62 3261-3266 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T63 3271-3277 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animal
T64 3658-3663 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T65 3806-3811 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T66 3826-3831 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T67 4065-4067 http://purl.obolibrary.org/obo/CLO_0037161 denotes en
T68 4372-4374 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48
T69 4480-4481 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T70 4579-4580 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T9 728-733 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T10 932-937 Chemical denotes 5-FAM http://purl.obolibrary.org/obo/CHEBI_51617
T11 972-977 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T12 1150-1155 Chemical denotes 5-FAM http://purl.obolibrary.org/obo/CHEBI_51617
T13 1251-1257 Chemical denotes buffer http://purl.obolibrary.org/obo/CHEBI_35225
T14 1371-1378 Chemical denotes mixture http://purl.obolibrary.org/obo/CHEBI_60004
T15 1445-1450 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T16 1973-1984 Chemical denotes antibiotics http://purl.obolibrary.org/obo/CHEBI_33281
T17 1996-2006 Chemical denotes penicillin http://purl.obolibrary.org/obo/CHEBI_17334|http://purl.obolibrary.org/obo/CHEBI_51356
T19 2007-2019 Chemical denotes streptomycin http://purl.obolibrary.org/obo/CHEBI_17076|http://purl.obolibrary.org/obo/CHEBI_58007
T21 2169-2172 Chemical denotes CO2 http://purl.obolibrary.org/obo/CHEBI_16526
T22 2265-2275 Chemical denotes penicillin http://purl.obolibrary.org/obo/CHEBI_17334|http://purl.obolibrary.org/obo/CHEBI_51356
T24 2276-2288 Chemical denotes streptomycin http://purl.obolibrary.org/obo/CHEBI_17076|http://purl.obolibrary.org/obo/CHEBI_58007
T26 2385-2393 Chemical denotes electron http://purl.obolibrary.org/obo/CHEBI_10545
T27 2963-2966 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T28 3039-3041 Chemical denotes PE http://purl.obolibrary.org/obo/CHEBI_16038|http://purl.obolibrary.org/obo/CHEBI_17553|http://purl.obolibrary.org/obo/CHEBI_74762
T31 3585-3593 Chemical denotes electron http://purl.obolibrary.org/obo/CHEBI_10545
T32 3622-3630 Chemical denotes electron http://purl.obolibrary.org/obo/CHEBI_10545
T33 3724-3738 Chemical denotes glutaraldehyde http://purl.obolibrary.org/obo/CHEBI_64276
T34 3748-3757 Chemical denotes phosphate http://purl.obolibrary.org/obo/CHEBI_18367|http://purl.obolibrary.org/obo/CHEBI_26020|http://purl.obolibrary.org/obo/CHEBI_35780|http://purl.obolibrary.org/obo/CHEBI_43474
T38 3758-3764 Chemical denotes buffer http://purl.obolibrary.org/obo/CHEBI_35225
T39 3945-3951 Chemical denotes buffer http://purl.obolibrary.org/obo/CHEBI_35225
T40 3962-3970 Chemical denotes fixative http://purl.obolibrary.org/obo/CHEBI_50913
T41 3971-3979 Chemical denotes solution http://purl.obolibrary.org/obo/CHEBI_75958
T42 4003-4019 Chemical denotes osmium tetroxide http://purl.obolibrary.org/obo/CHEBI_88215
T43 4003-4009 Chemical denotes osmium http://purl.obolibrary.org/obo/CHEBI_30687
T44 4058-4063 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T45 4065-4067 Chemical denotes en http://purl.obolibrary.org/obo/CHEBI_30347
T46 4114-4121 Chemical denotes acetate http://purl.obolibrary.org/obo/CHEBI_30089|http://purl.obolibrary.org/obo/CHEBI_47622
T48 4169-4176 Chemical denotes ethanol http://purl.obolibrary.org/obo/CHEBI_16236
T49 4271-4286 Chemical denotes propylene oxide http://purl.obolibrary.org/obo/CHEBI_38685
T50 4271-4280 Chemical denotes propylene http://purl.obolibrary.org/obo/CHEBI_16052
T51 4281-4286 Chemical denotes oxide http://purl.obolibrary.org/obo/CHEBI_25741|http://purl.obolibrary.org/obo/CHEBI_29356
T53 4491-4497 Chemical denotes nickel http://purl.obolibrary.org/obo/CHEBI_28112
T54 4538-4545 Chemical denotes acetate http://purl.obolibrary.org/obo/CHEBI_30089|http://purl.obolibrary.org/obo/CHEBI_47622
T56 4594-4602 Chemical denotes electron http://purl.obolibrary.org/obo/CHEBI_10545

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T2 204-217 http://purl.obolibrary.org/obo/GO_0003968 denotes transcriptase
T3 204-217 http://purl.obolibrary.org/obo/GO_0003899 denotes transcriptase
T4 1461-1482 http://purl.obolibrary.org/obo/GO_0001171 denotes Reverse transcription
T5 1469-1482 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription
T6 1561-1574 http://purl.obolibrary.org/obo/GO_0003968 denotes transcriptase
T7 1561-1574 http://purl.obolibrary.org/obo/GO_0003899 denotes transcriptase
T8 2651-2664 http://purl.obolibrary.org/obo/GO_0003968 denotes transcriptase
T9 2651-2664 http://purl.obolibrary.org/obo/GO_0003899 denotes transcriptase
T10 3789-3798 http://purl.obolibrary.org/obo/GO_0097264 denotes autolysis
T11 3789-3798 http://purl.obolibrary.org/obo/GO_0001896 denotes autolysis

2_test

Id Subject Object Predicate Lexical cue
32149036-26235643-81764452 4684-4686 26235643 denotes 13
32149036-19844604-81764452 4684-4686 19844604 denotes 13

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T31 0-21 Sentence denotes Materials and Methods
T32 23-25 Sentence denotes 1.
T33 26-63 Sentence denotes Clinical specimens and RNA extraction
T34 64-227 Sentence denotes Nasopharyngeal and oropharyngeal swab and sputum samples were collected from symptomatic patients to detect SARS-CoV-2 by real-time reverse transcriptase (RT)-PCR.
T35 228-369 Sentence denotes RNA was extracted from clinical samples with a QIAamp viral RNA mini kit (QIAGEN, Hilden, Germany) following the manufacturer’s instructions.
T36 370-533 Sentence denotes All specimens were handled under a biosafety cabinet according to laboratory biosafety guidelines of Korea Centers for Disease Control and Prevention for COVID-19.
T37 535-537 Sentence denotes 2.
T38 538-554 Sentence denotes Real-time RT-PCR
T39 555-712 Sentence denotes The optimal concentration of primers and probes, which were synthesized using a published sequence [12], was determined with the RNA transcripts of SARS-CoV.
T40 713-802 Sentence denotes The primer and probe sequences used for RNA-dependent RNA polymerase gene detection were:
T41 803-1019 Sentence denotes 5′-GTGARATGGTCATGTGTGGCGG-3′ (Forward), 5′-CARATGTTAAASACACTATTAGCATA-3′ (Reverse) and 5′-CAGGTGGAACCTCATCAGGAGATGC-3′ (Probe in 5-FAM/3′-BHQ format) and the primer and probe sequences used for E gene detection were:
T42 1020-1171 Sentence denotes 5′-ACAGGTACGTTAATAGTTAATAGCGT-3′ (Forward), 5′-ATATTGCAGCAGTACGCACACA-3′ (Reverse) and 5′-ACACTAGCCATCCTTACTGCGCTTCG-3′ (Probe in 5-FAM/3′-BHQ format).
T43 1172-1460 Sentence denotes A 25-μL reaction was setup that contained 5 μL of RNA, 12.5 μL of 2 × reaction buffer provided with the Agpath IDTM 1 step RT-PCR system (Thermo Fisher Scientific, Waltham, USA), 1 μL of 25 × enzyme mixture, 1 μL of forward and reverse primers at 10 pM, and 0.5 μL of each probe at 10 pM.
T44 1461-1598 Sentence denotes Reverse transcription was performed at 50°C for 30 minutes, followed by inactivation of the reverse transcriptase at 95°C for 10 minutes.
T45 1599-1752 Sentence denotes PCR amplification was performed with 40 cycles at 95°C for 15 seconds and 60°C for 1 minute using an ABI 7500 Fast instrument (Thermo Fisher Scientific).
T46 1754-1756 Sentence denotes 3.
T47 1757-1772 Sentence denotes Virus isolation
T48 1773-1874 Sentence denotes The virus was isolated from nasopharyngeal and oropharyngeal samples from putative COVID-19 patients.
T49 1875-2120 Sentence denotes Oropharyngeal samples were diluted with viral transfer medium containing nasopharyngeal swabs and antibiotics (Nystadin, penicillin-streptomycin 1:1 dilution) at 1:4 ratio and incubated for 1 hour at 4°C, before being inoculated onto Vero cells.
T50 2121-2289 Sentence denotes Inoculated Vero cells were cultured at 37°C, 5% CO2 in 1× Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 2% fetal bovine serum and penicillin-streptomycin.
T51 2290-2405 Sentence denotes Virus replication and isolation were confirmed through cytopathic effects, gene detection, and electron microscopy.
T52 2406-2577 Sentence denotes Viral culture of SARS-CoV-2 was conducted in a biosafety Level-3 facility according to laboratory biosafety guidelines of Korea Centers for Disease Control and Prevention.
T53 2579-2581 Sentence denotes 4.
T54 2582-2636 Sentence denotes Next generation sequencing of viral full-length genome
T55 2637-2770 Sentence denotes Using reverse transcriptase, cDNA was synthesized from RNA extracted from the cultured cell medium in which the virus was replicated.
T56 2771-2976 Sentence denotes A next generation sequencing (NGS) library was constructed after amplifying the full-length genes of the isolates using the synthesized cDNA and primers designed based on published SARS-CoV-2 DNA sequence.
T57 2977-3042 Sentence denotes The prepared library was purified and analyzed with Miseq 150 PE.
T58 3043-3144 Sentence denotes De novo assembly was performed on the sequenced product using Megahit to secure a full-length genome.
T59 3146-3148 Sentence denotes 5.
T60 3149-3168 Sentence denotes Sequencing analysis
T61 3169-3230 Sentence denotes Gene sequencing was performed using CLC Main Workbench 7.9.1.
T62 3231-3388 Sentence denotes Alignment was conducted using human and animal coronavirus sequences registered in Global Initiative on Sharing All Influenza Data (GISAID) and NCBI GenBank.
T63 3389-3567 Sentence denotes The phylogenetic tree was analyzed using MEGA6 with the neighbor-joining method, maximum composite likelihood-parameter distance matrix, and bootstrap values of 1,000 replicates.
T64 3569-3571 Sentence denotes 6.
T65 3572-3604 Sentence denotes Transmission electron microscopy
T66 3605-3832 Sentence denotes For transmission electron microscopy, the inoculated cells were prefixed by incubating in 2% paraformaldehyde and 2.5% glutaraldehyde in 0.1 M phosphate buffer (pH 7.4) to prevent the autolysis of the cells infected with virus.
T67 3833-4020 Sentence denotes To minimize the chemical reaction between pre- and post-fixation, the slides were washed 3 times using the same buffer as in the fixative solution and post-fixed with 1% osmium tetroxide.
T68 4021-4122 Sentence denotes After washing 3 times with deionized water, en bloc staining was performed using 0.5% uranyl acetate.
T69 4123-4287 Sentence denotes Thereafter, 30%, 50%, 70%, 80%, 90%, and 100% ethanol were used sequentially in ascending concentration for dehydration, which was substituted with propylene oxide.
T70 4288-4381 Sentence denotes The slides were then embedded in Epon812 plastic resin, and polymerized at 70°C for 48 hours.
T71 4382-4546 Sentence denotes The prepared plastic block was cut to 70-nm thick sections using an ultramicrotome and mounted on a 100-mesh nickel grid, and electrostained with 5% uranyl acetate.
T72 4547-4691 Sentence denotes The sections were observed with a transmission electron microscope (Libra120, Carl Zeiss, Germany) at an acceleration voltage of 120 kV [13–15].

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T8 4231-4242 Phenotype denotes dehydration http://purl.obolibrary.org/obo/HP_0001944