PMC:7574920 / 43694-44907 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T159","span":{"begin":202,"end":205},"obj":"Body_part"},{"id":"T160","span":{"begin":209,"end":212},"obj":"Body_part"},{"id":"T161","span":{"begin":472,"end":475},"obj":"Body_part"},{"id":"T162","span":{"begin":479,"end":482},"obj":"Body_part"},{"id":"T163","span":{"begin":547,"end":550},"obj":"Body_part"},{"id":"T164","span":{"begin":594,"end":597},"obj":"Body_part"},{"id":"T165","span":{"begin":613,"end":616},"obj":"Body_part"},{"id":"T166","span":{"begin":763,"end":766},"obj":"Body_part"}],"attributes":[{"id":"A159","pred":"fma_id","subj":"T159","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A160","pred":"fma_id","subj":"T160","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A161","pred":"fma_id","subj":"T161","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A162","pred":"fma_id","subj":"T162","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A163","pred":"fma_id","subj":"T163","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A164","pred":"fma_id","subj":"T164","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A165","pred":"fma_id","subj":"T165","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A166","pred":"fma_id","subj":"T166","obj":"http://purl.org/sig/ont/fma/fma67095"}],"text":"Our study was designed to investigate the sensitivity and specificity of a colorimetric RT-LAMP assay and to evaluate its suitability as an alternative to RT-qPCR testing for detecting SARS-CoV-2 viral RNA in RNA isolated from pharyngeal swab specimens. This study was conducted in Heidelberg, Germany in March and April of 2020. The study was designed to first evaluate different existing primer sets for RT-LAMP reactions and to use them for (i) detection of SARS-CoV-2 RNA in RNA isolated from pharyngeal swabs and (ii) detection of SARS-CoV-2 RNA directly from swab specimens without prior RNA isolation. All RNA samples used were pseudo-anonymized surplus material from the Heidelberg University Hospital diagnostic laboratory, and RT-qPCR results for these RNA samples were retrieved from the laboratory’s database only after the samples had been analyzed by the RT-LAMP assay. The study design was to conduct RT-LAMP testing until sufficient samples (at least several hundreds) had been analyzed to obtain a conclusive result. We also designed a deep sequencing-based method to validate the outcome of the RT-LAMP reactions using a Tn5 transposase–based fully scalable barcoding strategy (LAMP-sequencing)."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T96","span":{"begin":185,"end":193},"obj":"Disease"},{"id":"T97","span":{"begin":461,"end":469},"obj":"Disease"},{"id":"T98","span":{"begin":536,"end":544},"obj":"Disease"}],"attributes":[{"id":"A96","pred":"mondo_id","subj":"T96","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A97","pred":"mondo_id","subj":"T97","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A98","pred":"mondo_id","subj":"T98","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"Our study was designed to investigate the sensitivity and specificity of a colorimetric RT-LAMP assay and to evaluate its suitability as an alternative to RT-qPCR testing for detecting SARS-CoV-2 viral RNA in RNA isolated from pharyngeal swab specimens. This study was conducted in Heidelberg, Germany in March and April of 2020. The study was designed to first evaluate different existing primer sets for RT-LAMP reactions and to use them for (i) detection of SARS-CoV-2 RNA in RNA isolated from pharyngeal swabs and (ii) detection of SARS-CoV-2 RNA directly from swab specimens without prior RNA isolation. All RNA samples used were pseudo-anonymized surplus material from the Heidelberg University Hospital diagnostic laboratory, and RT-qPCR results for these RNA samples were retrieved from the laboratory’s database only after the samples had been analyzed by the RT-LAMP assay. The study design was to conduct RT-LAMP testing until sufficient samples (at least several hundreds) had been analyzed to obtain a conclusive result. We also designed a deep sequencing-based method to validate the outcome of the RT-LAMP reactions using a Tn5 transposase–based fully scalable barcoding strategy (LAMP-sequencing)."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T370","span":{"begin":73,"end":74},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T371","span":{"begin":163,"end":170},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T372","span":{"begin":924,"end":931},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T373","span":{"begin":1013,"end":1014},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T374","span":{"begin":1051,"end":1052},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T375","span":{"begin":1137,"end":1138},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"Our study was designed to investigate the sensitivity and specificity of a colorimetric RT-LAMP assay and to evaluate its suitability as an alternative to RT-qPCR testing for detecting SARS-CoV-2 viral RNA in RNA isolated from pharyngeal swab specimens. This study was conducted in Heidelberg, Germany in March and April of 2020. The study was designed to first evaluate different existing primer sets for RT-LAMP reactions and to use them for (i) detection of SARS-CoV-2 RNA in RNA isolated from pharyngeal swabs and (ii) detection of SARS-CoV-2 RNA directly from swab specimens without prior RNA isolation. All RNA samples used were pseudo-anonymized surplus material from the Heidelberg University Hospital diagnostic laboratory, and RT-qPCR results for these RNA samples were retrieved from the laboratory’s database only after the samples had been analyzed by the RT-LAMP assay. The study design was to conduct RT-LAMP testing until sufficient samples (at least several hundreds) had been analyzed to obtain a conclusive result. We also designed a deep sequencing-based method to validate the outcome of the RT-LAMP reactions using a Tn5 transposase–based fully scalable barcoding strategy (LAMP-sequencing)."}

{"project":"LitCovid-PubTator","denotations":[{"id":"285","span":{"begin":185,"end":195},"obj":"Species"},{"id":"286","span":{"begin":461,"end":471},"obj":"Species"},{"id":"287","span":{"begin":536,"end":546},"obj":"Species"}],"attributes":[{"id":"A285","pred":"tao:has_database_id","subj":"285","obj":"Tax:2697049"},{"id":"A286","pred":"tao:has_database_id","subj":"286","obj":"Tax:2697049"},{"id":"A287","pred":"tao:has_database_id","subj":"287","obj":"Tax:2697049"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"Our study was designed to investigate the sensitivity and specificity of a colorimetric RT-LAMP assay and to evaluate its suitability as an alternative to RT-qPCR testing for detecting SARS-CoV-2 viral RNA in RNA isolated from pharyngeal swab specimens. This study was conducted in Heidelberg, Germany in March and April of 2020. The study was designed to first evaluate different existing primer sets for RT-LAMP reactions and to use them for (i) detection of SARS-CoV-2 RNA in RNA isolated from pharyngeal swabs and (ii) detection of SARS-CoV-2 RNA directly from swab specimens without prior RNA isolation. All RNA samples used were pseudo-anonymized surplus material from the Heidelberg University Hospital diagnostic laboratory, and RT-qPCR results for these RNA samples were retrieved from the laboratory’s database only after the samples had been analyzed by the RT-LAMP assay. The study design was to conduct RT-LAMP testing until sufficient samples (at least several hundreds) had been analyzed to obtain a conclusive result. We also designed a deep sequencing-based method to validate the outcome of the RT-LAMP reactions using a Tn5 transposase–based fully scalable barcoding strategy (LAMP-sequencing)."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T262","span":{"begin":88,"end":90},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T263","span":{"begin":155,"end":157},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T264","span":{"begin":406,"end":408},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T265","span":{"begin":737,"end":739},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T266","span":{"begin":869,"end":871},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T267","span":{"begin":916,"end":918},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T268","span":{"begin":1113,"end":1115},"obj":"http://purl.obolibrary.org/obo/GO_0001171"}],"text":"Our study was designed to investigate the sensitivity and specificity of a colorimetric RT-LAMP assay and to evaluate its suitability as an alternative to RT-qPCR testing for detecting SARS-CoV-2 viral RNA in RNA isolated from pharyngeal swab specimens. This study was conducted in Heidelberg, Germany in March and April of 2020. The study was designed to first evaluate different existing primer sets for RT-LAMP reactions and to use them for (i) detection of SARS-CoV-2 RNA in RNA isolated from pharyngeal swabs and (ii) detection of SARS-CoV-2 RNA directly from swab specimens without prior RNA isolation. All RNA samples used were pseudo-anonymized surplus material from the Heidelberg University Hospital diagnostic laboratory, and RT-qPCR results for these RNA samples were retrieved from the laboratory’s database only after the samples had been analyzed by the RT-LAMP assay. The study design was to conduct RT-LAMP testing until sufficient samples (at least several hundreds) had been analyzed to obtain a conclusive result. We also designed a deep sequencing-based method to validate the outcome of the RT-LAMP reactions using a Tn5 transposase–based fully scalable barcoding strategy (LAMP-sequencing)."}

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T4","span":{"begin":1139,"end":1142},"obj":"GlycoEpitope"}],"attributes":[{"id":"A4","pred":"glyco_epitope_db_id","subj":"T4","obj":"http://www.glycoepitope.jp/epitopes/AN0083"}],"text":"Our study was designed to investigate the sensitivity and specificity of a colorimetric RT-LAMP assay and to evaluate its suitability as an alternative to RT-qPCR testing for detecting SARS-CoV-2 viral RNA in RNA isolated from pharyngeal swab specimens. This study was conducted in Heidelberg, Germany in March and April of 2020. The study was designed to first evaluate different existing primer sets for RT-LAMP reactions and to use them for (i) detection of SARS-CoV-2 RNA in RNA isolated from pharyngeal swabs and (ii) detection of SARS-CoV-2 RNA directly from swab specimens without prior RNA isolation. All RNA samples used were pseudo-anonymized surplus material from the Heidelberg University Hospital diagnostic laboratory, and RT-qPCR results for these RNA samples were retrieved from the laboratory’s database only after the samples had been analyzed by the RT-LAMP assay. The study design was to conduct RT-LAMP testing until sufficient samples (at least several hundreds) had been analyzed to obtain a conclusive result. We also designed a deep sequencing-based method to validate the outcome of the RT-LAMP reactions using a Tn5 transposase–based fully scalable barcoding strategy (LAMP-sequencing)."}

{"project":"LitCovid-sentences","denotations":[{"id":"T320","span":{"begin":0,"end":253},"obj":"Sentence"},{"id":"T321","span":{"begin":254,"end":329},"obj":"Sentence"},{"id":"T322","span":{"begin":330,"end":608},"obj":"Sentence"},{"id":"T323","span":{"begin":609,"end":883},"obj":"Sentence"},{"id":"T324","span":{"begin":884,"end":1033},"obj":"Sentence"},{"id":"T325","span":{"begin":1034,"end":1213},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Our study was designed to investigate the sensitivity and specificity of a colorimetric RT-LAMP assay and to evaluate its suitability as an alternative to RT-qPCR testing for detecting SARS-CoV-2 viral RNA in RNA isolated from pharyngeal swab specimens. This study was conducted in Heidelberg, Germany in March and April of 2020. The study was designed to first evaluate different existing primer sets for RT-LAMP reactions and to use them for (i) detection of SARS-CoV-2 RNA in RNA isolated from pharyngeal swabs and (ii) detection of SARS-CoV-2 RNA directly from swab specimens without prior RNA isolation. All RNA samples used were pseudo-anonymized surplus material from the Heidelberg University Hospital diagnostic laboratory, and RT-qPCR results for these RNA samples were retrieved from the laboratory’s database only after the samples had been analyzed by the RT-LAMP assay. The study design was to conduct RT-LAMP testing until sufficient samples (at least several hundreds) had been analyzed to obtain a conclusive result. We also designed a deep sequencing-based method to validate the outcome of the RT-LAMP reactions using a Tn5 transposase–based fully scalable barcoding strategy (LAMP-sequencing)."}