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PMC:7574920 / 9457-11869 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T48 83-86 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T49 117-120 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T50 193-196 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T51 201-204 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T52 688-691 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T53 811-814 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T54 869-872 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T55 900-906 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T56 936-940 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T57 1068-1072 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T58 1106-1119 Body_part denotes RNA molecules http://purl.org/sig/ont/fma/fma84126
T59 1106-1109 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T60 1152-1155 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T61 1608-1611 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T62 1727-1730 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T63 1782-1795 Body_part denotes RNA molecules http://purl.org/sig/ont/fma/fma84126
T64 1782-1785 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T65 1816-1820 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T66 2315-2328 Body_part denotes RNA molecules http://purl.org/sig/ont/fma/fma84126
T67 2315-2318 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T44 72-80 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T45 106-114 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T46 677-685 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T47 889-897 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T48 1803-1811 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T49 2304-2312 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T91 309-310 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T92 709-711 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T93 832-838 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T94 914-915 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T95 936-940 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T96 952-953 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T97 1003-1005 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T98 1008-1010 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T99 1068-1072 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T100 1123-1124 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T101 1125-1129 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T102 1291-1293 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T103 1420-1421 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T104 1733-1734 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T105 1816-1820 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T106 2127-2128 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T107 2184-2187 http://purl.obolibrary.org/obo/CLO_0001562 denotes a 2
T108 2184-2187 http://purl.obolibrary.org/obo/CLO_0001563 denotes a 2
T109 2230-2231 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T110 2365-2366 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T31 193-196 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T32 377-384 Chemical denotes mixture http://purl.obolibrary.org/obo/CHEBI_60004
T33 394-409 Chemical denotes oligonucleotide http://purl.obolibrary.org/obo/CHEBI_7754
T34 416-424 Chemical denotes aptamers http://purl.obolibrary.org/obo/CHEBI_140488
T35 475-485 Chemical denotes inhibitors http://purl.obolibrary.org/obo/CHEBI_35222
T36 1038-1053 Chemical denotes oligonucleotide http://purl.obolibrary.org/obo/CHEBI_7754
T37 1110-1119 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T38 1156-1164 Chemical denotes solution http://purl.obolibrary.org/obo/CHEBI_75958
T39 1594-1603 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T40 1786-1795 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T41 2189-2196 Chemical denotes agarose http://purl.obolibrary.org/obo/CHEBI_2511
T42 2319-2328 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
123 72-82 Species denotes SARS-CoV-2 Tax:2697049
135 968-995 Gene denotes open reading frame (ORF) 1a Gene:43740578
136 237-240 Gene denotes mix Gene:83881
137 188-191 Gene denotes Mix Gene:83881
138 1066-1067 Gene denotes N Gene:43740575
139 934-935 Gene denotes N Gene:43740575
140 912-913 Gene denotes N Gene:43740575
141 106-116 Species denotes SARS-CoV-2 Tax:2697049
142 677-687 Species denotes SARS-CoV-2 Tax:2697049
143 889-899 Species denotes SARS-CoV-2 Tax:2697049
144 394-409 Chemical denotes oligonucleotide MESH:D009841
145 1038-1053 Chemical denotes oligonucleotide MESH:D009841
151 1814-1815 Gene denotes N Gene:43740575
152 1803-1813 Species denotes SARS-CoV-2 Tax:2697049
153 2304-2314 Species denotes SARS-CoV-2 Tax:2697049
154 1957-1960 Chemical denotes ice MESH:D007053
155 2189-2196 Chemical denotes agarose MESH:D012685

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T51 26-28 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T52 126-128 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T53 170-172 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T54 285-298 http://purl.obolibrary.org/obo/GO_0003968 denotes transcriptase
T55 285-298 http://purl.obolibrary.org/obo/GO_0003899 denotes transcriptase
T56 650-652 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T57 1446-1448 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T58 1551-1553 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T59 1692-1694 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T60 1839-1841 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T61 2134-2136 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T62 2243-2245 http://purl.obolibrary.org/obo/GO_0001171 denotes RT

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T60 0-95 Sentence denotes Establishing colorimetric RT-LAMP assay sensitivity using an artificial SARS-CoV-2 RNA template
T61 96-231 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 232-350 Sentence denotes This mix contains two enzymes, an engineered reverse transcriptase (RTx) and a strand-displacing polymerase (Bst 2.0).
T63 351-602 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 603-815 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 816-1012 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 1013-1213 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 1214-1266 Sentence denotes The reaction was conducted for up to 1 hour at 65°C.
T68 1267-1358 Sentence denotes For time points > 30 to 35 min, the negative control frequently became yellowish (Fig. 1A).
T69 1359-1459 Sentence denotes This was caused by spurious amplification products, which is a well-known problem with RT-LAMP (14).
T70 1460-1664 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).
T71 1665-1731 Sentence denotes Fig. 1 Sensitivity of the RT-LAMP assay determined using IVT RNA.
T72 1732-1878 Sentence denotes (A) Defined numbers of in vitro transcribed (IVT) RNA molecules of the SARS-CoV-2 N gene were added to the RT-LAMP reaction and incubated at 65°C.
T73 1879-1982 Sentence denotes At indicated times, samples were removed from the heating block and cooled on ice to stop the reaction.
T74 1983-2201 Sentence denotes Photographs were taken using the color scanner function of an office copy machine and show the red to yellow color change in positive samples. (B) The RT-LAMP reaction product (2.5 μl) was analyzed on a 2% agarose gel.
T75 2202-2412 Sentence denotes The typical band pattern of a successful RT-LAMP reaction was visible in the samples with 100 or more SARS-CoV-2 RNA molecules, i.e., in those samples that showed a color change from red to yellow after 30 min.