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PMC:7574920 / 17164-20486 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T93 60-63 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T94 170-173 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T95 209-212 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T96 578-581 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T97 692-695 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T98 737-740 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T99 1471-1475 Body_part denotes axis http://purl.org/sig/ont/fma/fma12520
T100 2417-2420 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T101 2712-2715 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T60 49-57 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T61 567-575 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T62 2333-2335 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178
T63 2406-2414 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T64 2701-2709 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T65 3059-3061 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T173 194-195 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T174 254-256 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T175 396-397 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T176 407-410 http://purl.obolibrary.org/obo/CLO_0050884 denotes ten
T177 419-423 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T178 608-609 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T179 630-631 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T180 704-710 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T181 773-774 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T182 813-814 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T183 1129-1130 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T184 1219-1220 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T185 1476-1482 http://purl.obolibrary.org/obo/CLO_0007225 denotes labels
T186 1615-1616 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T187 1892-1894 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T188 1892-1894 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T189 1935-1942 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T190 2030-2032 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T191 2030-2032 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T192 2184-2186 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T193 2198-2200 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T194 2317-2318 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T195 2346-2347 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T196 2462-2463 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T197 2617-2619 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T198 2744-2745 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T199 3117-3125 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test was
T200 3318-3320 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T201 3318-3320 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T53 1892-1894 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T54 2030-2032 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T55 2896-2903 Chemical denotes reagent http://purl.obolibrary.org/obo/CHEBI_33893
T56 3318-3320 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
191 49-59 Species denotes SARS-CoV-2 Tax:2697049
193 437-451 Gene denotes 3A and Table 1
195 567-577 Species denotes SARS-CoV-2 Tax:2697049
197 1836-1842 Disease denotes Wilson MESH:D006527
203 3000-3014 Gene denotes 3A and Table 1
204 2406-2416 Species denotes SARS-CoV-2 Tax:2697049
205 2701-2711 Species denotes SARS-CoV-2 Tax:2697049
206 3133-3139 Disease denotes Wilson MESH:D006527
207 3250-3256 Disease denotes Wilson MESH:D006527

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T94 31-33 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T95 126-128 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T96 280-282 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T97 369-377 http://purl.obolibrary.org/obo/GO_0007610 denotes behavior
T98 474-476 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T99 592-594 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T100 646-648 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T101 672-674 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T102 899-901 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T103 1096-1098 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T104 1112-1114 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T105 1182-1184 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T106 1281-1283 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T107 1346-1348 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T108 1382-1384 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T109 1640-1642 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T110 1915-1917 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T111 1927-1929 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T112 2104-2106 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T113 2132-2134 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T114 2432-2434 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T115 2495-2497 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T116 2670-2672 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T117 2927-2929 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T118 2980-2982 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T119 3109-3111 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T120 3231-3233 http://purl.obolibrary.org/obo/GO_0001171 denotes RT

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T108 0-73 Sentence denotes Validation of the colorimetric RT-LAMP assay for SARS-CoV-2 RNA detection
T109 74-182 Sentence denotes To determine the specificity and sensitivity of the RT-LAMP assay, we continued to analyze more RNA samples.
T110 183-258 Sentence denotes We assayed a total of 768 RNA samples obtained on different days (fig. S1).
T111 259-545 Sentence denotes Visualization of the RT-LAMP assay results 30 min after the start of the incubation at 65°C showed comparable behavior of the samples in a total of ten 96-well test plates (Fig. 3A and Table 1), indicating that the RT-LAMP assay was reproducible from day to day and from plate to plate.
T112 546-606 Sentence denotes Fig. 3 Detection of SARS-CoV-2 RNA using the RT-LAMP assay.
T113 607-732 Sentence denotes (A) Scatter plot shows a comparison of RT-LAMP assay results and RT-qPCR results for RNA samples tested on 10 96-well plates.
T114 733-847 Sentence denotes The RNA extraction method (QC, QiaCube, a column-based method; QS, QiaSymphony, a bead-based method) is indicated.
T115 848-963 Sentence denotes The time point for measurement by the colorimetric RT-LAMP assay was 30 min after the start of the 65°C incubation.
T116 964-1019 Sentence denotes The 96-well plate shown in Fig. 2 is not included here.
T117 1020-1245 Sentence denotes Table 1 shows numbers of samples stratified according to the results of the RT-LAMP and the RT-qPCR assays. (B) Sensitivity (right) and specificity (left) of the RT-LAMP assay [derived from data in (A) and Table 1] are shown.
T118 1246-1360 Sentence denotes The specificity is the fraction of RT-qPCR–negative samples correctly identified as negative by the RT-LAMP assay.
T119 1361-1654 Sentence denotes For sensitivity, the RT-qPCR–positive samples were stratified by CT values into three bins (as indicated by x axis labels), and for each bin, the sensitivity is given as the fraction of qPCR-positive samples in the respective CT bin that have also given a positive result in the RT-LAMP assay.
T120 1655-1896 Sentence denotes The thick black lines indicate the values of these fractions (i.e., the specificity and sensitivity estimates); the black boxes indicate the corresponding 95% confidence intervals (Wilson’s binomial confidence interval). (See also table S2).
T121 1897-2011 Sentence denotes Table 1 Shown is RT-qPCR and RT-LAMP testing of 768 clinical samples stratified into CT value bins (see Fig. 3A).
T122 2012-2103 Sentence denotes Fig. 3B and table S2 show specificity and sensitivity values calculated from these numbers.
T123 2104-2111 Sentence denotes RT-LAMP
T124 2112-2131 Sentence denotes CT Pos Neg Sum
T125 2132-2163 Sentence denotes RT-qPCR Pos 0–25 51 0 51
T126 2164-2180 Sentence denotes 25–30 28 2 30
T127 2181-2197 Sentence denotes 30–35 4 16 20
T128 2198-2214 Sentence denotes 35–40 0 16 16
T129 2215-2237 Sentence denotes Neg Neg 2 649 651
T130 2238-2431 Sentence denotes Sum 85 683 768 The consistency of the results during the analysis confirmed a threshold of ΔOD > +0.3 as a robust measure to identify samples that were positive for SARS-CoV-2 RNA (Fig. 3A).
T131 2432-2631 Sentence denotes RT-qPCR–positive samples with a CT < 30 scored positive in the RT-LAMP assay (79 of 81), whereas almost all samples with CT values between 30 and 40 scored negative (only 4 positive of 36) (Fig. 3B).
T132 2632-2754 Sentence denotes This confirmed the sensitivity of the RT-LAMP assay for detection of SARS-CoV-2 RNA in samples corresponding to a CT < 30.
T133 2755-2913 Sentence denotes We observed small differences between different plates on the exact sensitivity threshold, probably caused by slight variability in plate or reagent handling.
T134 2914-3077 Sentence denotes We found two RT-qPCR–negative samples that scored positive in the RT-LAMP assay (Fig. 3A and Table 1) and one sample that scored just below the ΔOD cutoff of +0.3.
T135 3078-3166 Sentence denotes The overall specificity of the RT-LAMP test was 99.7% (Wilson’s 95% confidence interval:
T136 3167-3283 Sentence denotes 98.9 to 99.9%), and the sensitivity for samples with CT < 30 on RT-qPCR was 97.5% (Wilson’s 95% confidence interval:
T137 3284-3322 Sentence denotes 91.4 to 99.3%) (Fig. 3B and table S2).