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PMC:7574920 / 9553-11121 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T49 21-24 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T50 97-100 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T51 105-108 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T52 592-595 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T53 715-718 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T54 773-776 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T55 804-810 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T56 840-844 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T57 972-976 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T58 1010-1023 Body_part denotes RNA molecules http://purl.org/sig/ont/fma/fma84126
T59 1010-1013 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T60 1056-1059 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T61 1512-1515 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T45 10-18 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T46 581-589 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T47 793-801 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T91 213-214 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T92 613-615 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T93 736-742 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T94 818-819 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T95 840-844 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T96 856-857 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T97 907-909 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T98 912-914 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T99 972-976 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T100 1027-1028 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T101 1029-1033 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T102 1195-1197 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T103 1324-1325 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T31 97-100 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T32 281-288 Chemical denotes mixture http://purl.obolibrary.org/obo/CHEBI_60004
T33 298-313 Chemical denotes oligonucleotide http://purl.obolibrary.org/obo/CHEBI_7754
T34 320-328 Chemical denotes aptamers http://purl.obolibrary.org/obo/CHEBI_140488
T35 379-389 Chemical denotes inhibitors http://purl.obolibrary.org/obo/CHEBI_35222
T36 942-957 Chemical denotes oligonucleotide http://purl.obolibrary.org/obo/CHEBI_7754
T37 1014-1023 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T38 1060-1068 Chemical denotes solution http://purl.obolibrary.org/obo/CHEBI_75958
T39 1498-1507 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
135 872-899 Gene denotes open reading frame (ORF) 1a Gene:43740578
136 141-144 Gene denotes mix Gene:83881
137 92-95 Gene denotes Mix Gene:83881
138 970-971 Gene denotes N Gene:43740575
139 838-839 Gene denotes N Gene:43740575
140 816-817 Gene denotes N Gene:43740575
141 10-20 Species denotes SARS-CoV-2 Tax:2697049
142 581-591 Species denotes SARS-CoV-2 Tax:2697049
143 793-803 Species denotes SARS-CoV-2 Tax:2697049
144 298-313 Chemical denotes oligonucleotide MESH:D009841
145 942-957 Chemical denotes oligonucleotide MESH:D009841

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T52 30-32 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T53 74-76 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T54 189-202 http://purl.obolibrary.org/obo/GO_0003968 denotes transcriptase
T55 189-202 http://purl.obolibrary.org/obo/GO_0003899 denotes transcriptase
T56 554-556 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T57 1350-1352 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T58 1455-1457 http://purl.obolibrary.org/obo/GO_0001171 denotes RT

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T61 0-135 Sentence denotes To detect SARS-CoV-2 RNA with RT-LAMP, we used the WarmStart Colorimetric RT-LAMP 2X Master Mix (DNA and RNA) from New England Biolabs.
T62 136-254 Sentence denotes This mix contains two enzymes, an engineered reverse transcriptase (RTx) and a strand-displacing polymerase (Bst 2.0).
T63 255-506 Sentence denotes In addition, the reaction mixture contains oligonucleotide-based aptamers that function as reversible temperature-dependent inhibitors, ensuring that the reaction only runs at an elevated temperature (WarmStart) to avoid nonspecific priming reactions.
T64 507-719 Sentence denotes Several primer sets were recently proposed for RT-LAMP–based detection of SARS-CoV-2 RNA by Zhang et al. (11) and by Yu et al. (10), and these primer sets were subsequently validated with in vitro–translated RNA.
T65 720-916 Sentence denotes We prepared and tested two primer sets for different RNA sections of the SARS-CoV-2 genome, the N-A set targeting the N gene and the 1a-A set targeting open reading frame (ORF) 1a (table S1) (11).
T66 917-1117 Sentence denotes Figure 1A shows that the oligonucleotide set for the N gene was capable of detecting 100 IVT RNA molecules in a test reaction with 1 μl of RNA solution, as evidenced by the red-to-yellow color change.
T67 1118-1170 Sentence denotes The reaction was conducted for up to 1 hour at 65°C.
T68 1171-1262 Sentence denotes For time points > 30 to 35 min, the negative control frequently became yellowish (Fig. 1A).
T69 1263-1363 Sentence denotes This was caused by spurious amplification products, which is a well-known problem with RT-LAMP (14).
T70 1364-1568 Sentence denotes Analysis by gel electrophoresis revealed clearly distinct banding patterns for the correct RT-LAMP reaction products (lanes with ≥100 molecules IVT RNA input) and the spurious reaction products (Fig. 1B).