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LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T13","span":{"begin":693,"end":697},"obj":"Body_part"},{"id":"T14","span":{"begin":722,"end":727},"obj":"Body_part"}],"attributes":[{"id":"A13","pred":"uberon_id","subj":"T13","obj":"http://purl.obolibrary.org/obo/UBERON_0000004"},{"id":"A14","pred":"uberon_id","subj":"T14","obj":"http://purl.obolibrary.org/obo/UBERON_0000165"}],"text":"Study design\nThe intent of this study was to develop a clinical method for detecting SARS-CoV-2 RNA in RNA samples isolated from pharyngeal swab specimens from individuals being tested for COVID-19. We used pseudo-anonymized surplus RNA sample material that had been collected for clinical diagnosis of SARS-CoV-2 infection by RT-qPCR carried out by the diagnostic laboratory of Heidelberg University Hospital. Such reuse of material is in accordance with German regulations, which allow development and improvement of diagnostic assays using patient samples collected specifically to perform the testing in question. Pharyngeal swab specimens provided to us were either collected through the nose (nasopharyngeal) or the mouth (oropharyngeal), or sometimes one swab was used to collect both.\nOur 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)."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T92","span":{"begin":85,"end":93},"obj":"Disease"},{"id":"T93","span":{"begin":189,"end":197},"obj":"Disease"},{"id":"T94","span":{"begin":303,"end":311},"obj":"Disease"},{"id":"T95","span":{"begin":314,"end":323},"obj":"Disease"},{"id":"T96","span":{"begin":978,"end":986},"obj":"Disease"},{"id":"T97","span":{"begin":1254,"end":1262},"obj":"Disease"},{"id":"T98","span":{"begin":1329,"end":1337},"obj":"Disease"}],"attributes":[{"id":"A92","pred":"mondo_id","subj":"T92","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A93","pred":"mondo_id","subj":"T93","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A94","pred":"mondo_id","subj":"T94","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A95","pred":"mondo_id","subj":"T95","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"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":"Study design\nThe intent of this study was to develop a clinical method for detecting SARS-CoV-2 RNA in RNA samples isolated from pharyngeal swab specimens from individuals being tested for COVID-19. We used pseudo-anonymized surplus RNA sample material that had been collected for clinical diagnosis of SARS-CoV-2 infection by RT-qPCR carried out by the diagnostic laboratory of Heidelberg University Hospital. Such reuse of material is in accordance with German regulations, which allow development and improvement of diagnostic assays using patient samples collected specifically to perform the testing in question. Pharyngeal swab specimens provided to us were either collected through the nose (nasopharyngeal) or the mouth (oropharyngeal), or sometimes one swab was used to collect both.\nOur 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)."}

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T365","span":{"begin":53,"end":54},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T366","span":{"begin":178,"end":184},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T367","span":{"begin":597,"end":604},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T368","span":{"begin":693,"end":697},"obj":"http://www.ebi.ac.uk/efo/EFO_0000828"},{"id":"T369","span":{"begin":722,"end":727},"obj":"http://www.ebi.ac.uk/efo/EFO_0000825"},{"id":"T370","span":{"begin":866,"end":867},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T371","span":{"begin":956,"end":963},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T372","span":{"begin":1717,"end":1724},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T373","span":{"begin":1806,"end":1807},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T374","span":{"begin":1844,"end":1845},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T375","span":{"begin":1930,"end":1931},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"Study design\nThe intent of this study was to develop a clinical method for detecting SARS-CoV-2 RNA in RNA samples isolated from pharyngeal swab specimens from individuals being tested for COVID-19. We used pseudo-anonymized surplus RNA sample material that had been collected for clinical diagnosis of SARS-CoV-2 infection by RT-qPCR carried out by the diagnostic laboratory of Heidelberg University Hospital. Such reuse of material is in accordance with German regulations, which allow development and improvement of diagnostic assays using patient samples collected specifically to perform the testing in question. Pharyngeal swab specimens provided to us were either collected through the nose (nasopharyngeal) or the mouth (oropharyngeal), or sometimes one swab was used to collect both.\nOur 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)."}

LitCovid-PubTator

{"project":"LitCovid-PubTator","denotations":[{"id":"278","span":{"begin":85,"end":95},"obj":"Species"},{"id":"279","span":{"begin":543,"end":550},"obj":"Species"},{"id":"280","span":{"begin":189,"end":197},"obj":"Disease"},{"id":"281","span":{"begin":303,"end":323},"obj":"Disease"},{"id":"285","span":{"begin":978,"end":988},"obj":"Species"},{"id":"286","span":{"begin":1254,"end":1264},"obj":"Species"},{"id":"287","span":{"begin":1329,"end":1339},"obj":"Species"}],"attributes":[{"id":"A278","pred":"tao:has_database_id","subj":"278","obj":"Tax:2697049"},{"id":"A279","pred":"tao:has_database_id","subj":"279","obj":"Tax:9606"},{"id":"A280","pred":"tao:has_database_id","subj":"280","obj":"MESH:C000657245"},{"id":"A281","pred":"tao:has_database_id","subj":"281","obj":"MESH:C000657245"},{"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":"Study design\nThe intent of this study was to develop a clinical method for detecting SARS-CoV-2 RNA in RNA samples isolated from pharyngeal swab specimens from individuals being tested for COVID-19. We used pseudo-anonymized surplus RNA sample material that had been collected for clinical diagnosis of SARS-CoV-2 infection by RT-qPCR carried out by the diagnostic laboratory of Heidelberg University Hospital. Such reuse of material is in accordance with German regulations, which allow development and improvement of diagnostic assays using patient samples collected specifically to perform the testing in question. Pharyngeal swab specimens provided to us were either collected through the nose (nasopharyngeal) or the mouth (oropharyngeal), or sometimes one swab was used to collect both.\nOur 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)."}

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T260","span":{"begin":327,"end":329},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T261","span":{"begin":463,"end":474},"obj":"http://purl.obolibrary.org/obo/GO_0065007"},{"id":"T262","span":{"begin":881,"end":883},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T263","span":{"begin":948,"end":950},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T264","span":{"begin":1199,"end":1201},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T265","span":{"begin":1530,"end":1532},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T266","span":{"begin":1662,"end":1664},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T267","span":{"begin":1709,"end":1711},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T268","span":{"begin":1906,"end":1908},"obj":"http://purl.obolibrary.org/obo/GO_0001171"}],"text":"Study design\nThe intent of this study was to develop a clinical method for detecting SARS-CoV-2 RNA in RNA samples isolated from pharyngeal swab specimens from individuals being tested for COVID-19. We used pseudo-anonymized surplus RNA sample material that had been collected for clinical diagnosis of SARS-CoV-2 infection by RT-qPCR carried out by the diagnostic laboratory of Heidelberg University Hospital. Such reuse of material is in accordance with German regulations, which allow development and improvement of diagnostic assays using patient samples collected specifically to perform the testing in question. Pharyngeal swab specimens provided to us were either collected through the nose (nasopharyngeal) or the mouth (oropharyngeal), or sometimes one swab was used to collect both.\nOur 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)."}

LitCovid-PD-GlycoEpitope

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T4","span":{"begin":1932,"end":1935},"obj":"GlycoEpitope"}],"attributes":[{"id":"A4","pred":"glyco_epitope_db_id","subj":"T4","obj":"http://www.glycoepitope.jp/epitopes/AN0083"}],"text":"Study design\nThe intent of this study was to develop a clinical method for detecting SARS-CoV-2 RNA in RNA samples isolated from pharyngeal swab specimens from individuals being tested for COVID-19. We used pseudo-anonymized surplus RNA sample material that had been collected for clinical diagnosis of SARS-CoV-2 infection by RT-qPCR carried out by the diagnostic laboratory of Heidelberg University Hospital. Such reuse of material is in accordance with German regulations, which allow development and improvement of diagnostic assays using patient samples collected specifically to perform the testing in question. Pharyngeal swab specimens provided to us were either collected through the nose (nasopharyngeal) or the mouth (oropharyngeal), or sometimes one swab was used to collect both.\nOur 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)."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T315","span":{"begin":0,"end":12},"obj":"Sentence"},{"id":"T316","span":{"begin":13,"end":198},"obj":"Sentence"},{"id":"T317","span":{"begin":199,"end":410},"obj":"Sentence"},{"id":"T318","span":{"begin":411,"end":617},"obj":"Sentence"},{"id":"T319","span":{"begin":618,"end":792},"obj":"Sentence"},{"id":"T320","span":{"begin":793,"end":1046},"obj":"Sentence"},{"id":"T321","span":{"begin":1047,"end":1122},"obj":"Sentence"},{"id":"T322","span":{"begin":1123,"end":1401},"obj":"Sentence"},{"id":"T323","span":{"begin":1402,"end":1676},"obj":"Sentence"},{"id":"T324","span":{"begin":1677,"end":1826},"obj":"Sentence"},{"id":"T325","span":{"begin":1827,"end":2006},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Study design\nThe intent of this study was to develop a clinical method for detecting SARS-CoV-2 RNA in RNA samples isolated from pharyngeal swab specimens from individuals being tested for COVID-19. We used pseudo-anonymized surplus RNA sample material that had been collected for clinical diagnosis of SARS-CoV-2 infection by RT-qPCR carried out by the diagnostic laboratory of Heidelberg University Hospital. Such reuse of material is in accordance with German regulations, which allow development and improvement of diagnostic assays using patient samples collected specifically to perform the testing in question. Pharyngeal swab specimens provided to us were either collected through the nose (nasopharyngeal) or the mouth (oropharyngeal), or sometimes one swab was used to collect both.\nOur 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)."}

PMC:7574920 / 42901-44907 JSONTXT

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PMC:7574920 / 42901-44907 JSON TXT