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PMC:7574920 / 21712-23152 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T104 735-739 Body_part denotes axis http://purl.org/sig/ont/fma/fma12520
T105 757-761 Body_part denotes axis http://purl.org/sig/ont/fma/fma12520
T106 865-868 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T107 1305-1309 Body_part denotes axis http://purl.org/sig/ont/fma/fma12520
T108 1383-1387 Body_part denotes axis http://purl.org/sig/ont/fma/fma12520

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T66 854-862 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T205 80-81 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T206 122-123 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T207 217-219 http://purl.obolibrary.org/obo/CLO_0007653 denotes ME
T208 233-234 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T209 576-577 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T210 799-800 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T211 1108-1109 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T212 1437-1438 http://purl.obolibrary.org/obo/CLO_0001021 denotes B

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
209 854-864 Species denotes SARS-CoV-2 Tax:2697049

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T128 34-36 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T129 274-276 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T130 699-701 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T131 746-748 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T132 1077-1079 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T133 1280-1282 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T134 1362-1364 http://purl.obolibrary.org/obo/GO_0001171 denotes RT

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T3 250-253 GlycoEpitope denotes Tn5 http://www.glycoepitope.jp/epitopes/AN0083

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T148 0-78 Sentence denotes Fig. 4 Multiplexed sequencing of RT-LAMP reaction products (LAMP-sequencing).
T149 79-121 Sentence denotes (A) Workflow for LAMP-sequencing is shown.
T150 122-300 Sentence denotes A plate of 96 barcoded (BC) adapters with unique molecular identifiers (UMIs) and mosaic ends (ME) was used as a seed plate for Tn5 tagmentation of all RT-LAMP reaction products.
T151 301-417 Sentence denotes After tagmentation, each plate was pooled individually, followed by removal of excess adapters using size selection.
T152 418-763 Sentence denotes Each pool of tagmentation products was then amplified using primers with plate-specific barcodes, and the PCR products were analyzed by Illumina sequencing. (B) Comparison of the outcome of the three assays: LAMP-sequencing (purple, negative; green, positive; gray, too few UMIs), RT-LAMP (after 30-min incubation, y axis), and RT-qPCR (x axis).
T153 764-795 Sentence denotes Each dot represents one sample.
T154 796-955 Sentence denotes If a substantial number of the sequencing reads contained SARS-CoV-2 RNA, the sample was called positive (green), if not, then it was called negative (purple).
T155 956-1258 Sentence denotes For some samples (gray), no LAMP-sequencing call could be made due to too few UMIs. (See also Table 2). (C) Although the RT-LAMP assay was scored after a 30-min incubation at 65°C (left), LAMP-sequencing was performed only after the samples had been incubated for another 10 min (15 min for one plate).
T156 1259-1440 Sentence denotes This panel shows the RT-LAMP assay outcome (y axis) scored after the full incubation time, whereas the RT-qPCR CT values (x axis) and LAMP-sequencing results are the same as in (B).