PMC:7574920 / 4552-5214 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T18","span":{"begin":219,"end":222},"obj":"Body_part"},{"id":"T19","span":{"begin":260,"end":266},"obj":"Body_part"},{"id":"T20","span":{"begin":362,"end":365},"obj":"Body_part"},{"id":"T21","span":{"begin":371,"end":374},"obj":"Body_part"},{"id":"T22","span":{"begin":407,"end":410},"obj":"Body_part"},{"id":"T23","span":{"begin":536,"end":542},"obj":"Body_part"}],"attributes":[{"id":"A18","pred":"fma_id","subj":"T18","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A19","pred":"fma_id","subj":"T19","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A20","pred":"fma_id","subj":"T20","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A21","pred":"fma_id","subj":"T21","obj":"http://purl.org/sig/ont/fma/fma74412"},{"id":"A22","pred":"fma_id","subj":"T22","obj":"http://purl.org/sig/ont/fma/fma74412"},{"id":"A23","pred":"fma_id","subj":"T23","obj":"http://purl.org/sig/ont/fma/fma84116"}],"text":"The SARS-CoV-2 diagnostic pipeline that has proven to be successful and that is currently used in many test centers consists of three steps: collecting nasopharyngeal or oropharyngeal swab specimens, isolation of total RNA, and specific detection of the viral genome by RT-qPCR. The latter comprises a reverse transcriptase (RT) step, which translates the viral RNA into DNA, followed by a semiquantitative DNA polymerase chain reaction using oligonucleotides specific for the viral cDNA (qPCR). As a result, a short piece of the viral genome is strongly amplified and then is detected by a sequence-specific oligonucleotide probe labeled with a fluorescent dye."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T34","span":{"begin":4,"end":12},"obj":"Disease"}],"attributes":[{"id":"A34","pred":"mondo_id","subj":"T34","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"The SARS-CoV-2 diagnostic pipeline that has proven to be successful and that is currently used in many test centers consists of three steps: collecting nasopharyngeal or oropharyngeal swab specimens, isolation of total RNA, and specific detection of the viral genome by RT-qPCR. The latter comprises a reverse transcriptase (RT) step, which translates the viral RNA into DNA, followed by a semiquantitative DNA polymerase chain reaction using oligonucleotides specific for the viral cDNA (qPCR). As a result, a short piece of the viral genome is strongly amplified and then is detected by a sequence-specific oligonucleotide probe labeled with a fluorescent dye."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T50","span":{"begin":40,"end":43},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T51","span":{"begin":103,"end":107},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T52","span":{"begin":300,"end":301},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T53","span":{"begin":388,"end":389},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T54","span":{"begin":499,"end":500},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T55","span":{"begin":509,"end":510},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T56","span":{"begin":589,"end":590},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T57","span":{"begin":631,"end":638},"obj":"http://purl.obolibrary.org/obo/CLO_0007225"},{"id":"T58","span":{"begin":644,"end":645},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"The SARS-CoV-2 diagnostic pipeline that has proven to be successful and that is currently used in many test centers consists of three steps: collecting nasopharyngeal or oropharyngeal swab specimens, isolation of total RNA, and specific detection of the viral genome by RT-qPCR. The latter comprises a reverse transcriptase (RT) step, which translates the viral RNA into DNA, followed by a semiquantitative DNA polymerase chain reaction using oligonucleotides specific for the viral cDNA (qPCR). As a result, a short piece of the viral genome is strongly amplified and then is detected by a sequence-specific oligonucleotide probe labeled with a fluorescent dye."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T5","span":{"begin":371,"end":374},"obj":"Chemical"},{"id":"T6","span":{"begin":407,"end":410},"obj":"Chemical"},{"id":"T7","span":{"begin":443,"end":459},"obj":"Chemical"},{"id":"T8","span":{"begin":609,"end":624},"obj":"Chemical"},{"id":"T9","span":{"begin":625,"end":630},"obj":"Chemical"},{"id":"T10","span":{"begin":646,"end":661},"obj":"Chemical"},{"id":"T11","span":{"begin":658,"end":661},"obj":"Chemical"}],"attributes":[{"id":"A5","pred":"chebi_id","subj":"T5","obj":"http://purl.obolibrary.org/obo/CHEBI_16991"},{"id":"A6","pred":"chebi_id","subj":"T6","obj":"http://purl.obolibrary.org/obo/CHEBI_16991"},{"id":"A7","pred":"chebi_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/CHEBI_7754"},{"id":"A8","pred":"chebi_id","subj":"T8","obj":"http://purl.obolibrary.org/obo/CHEBI_7754"},{"id":"A9","pred":"chebi_id","subj":"T9","obj":"http://purl.obolibrary.org/obo/CHEBI_50406"},{"id":"A10","pred":"chebi_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/CHEBI_51121"},{"id":"A11","pred":"chebi_id","subj":"T11","obj":"http://purl.obolibrary.org/obo/CHEBI_37958"}],"text":"The SARS-CoV-2 diagnostic pipeline that has proven to be successful and that is currently used in many test centers consists of three steps: collecting nasopharyngeal or oropharyngeal swab specimens, isolation of total RNA, and specific detection of the viral genome by RT-qPCR. The latter comprises a reverse transcriptase (RT) step, which translates the viral RNA into DNA, followed by a semiquantitative DNA polymerase chain reaction using oligonucleotides specific for the viral cDNA (qPCR). As a result, a short piece of the viral genome is strongly amplified and then is detected by a sequence-specific oligonucleotide probe labeled with a fluorescent dye."}

{"project":"LitCovid-PubTator","denotations":[{"id":"87","span":{"begin":4,"end":14},"obj":"Species"},{"id":"88","span":{"begin":443,"end":459},"obj":"Chemical"},{"id":"89","span":{"begin":609,"end":624},"obj":"Chemical"}],"attributes":[{"id":"A87","pred":"tao:has_database_id","subj":"87","obj":"Tax:2697049"},{"id":"A88","pred":"tao:has_database_id","subj":"88","obj":"MESH:D009841"},{"id":"A89","pred":"tao:has_database_id","subj":"89","obj":"MESH:D009841"}],"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":"The SARS-CoV-2 diagnostic pipeline that has proven to be successful and that is currently used in many test centers consists of three steps: collecting nasopharyngeal or oropharyngeal swab specimens, isolation of total RNA, and specific detection of the viral genome by RT-qPCR. The latter comprises a reverse transcriptase (RT) step, which translates the viral RNA into DNA, followed by a semiquantitative DNA polymerase chain reaction using oligonucleotides specific for the viral cDNA (qPCR). As a result, a short piece of the viral genome is strongly amplified and then is detected by a sequence-specific oligonucleotide probe labeled with a fluorescent dye."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T25","span":{"begin":270,"end":272},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T26","span":{"begin":310,"end":323},"obj":"http://purl.obolibrary.org/obo/GO_0003968"},{"id":"T27","span":{"begin":310,"end":323},"obj":"http://purl.obolibrary.org/obo/GO_0003899"},{"id":"T28","span":{"begin":325,"end":327},"obj":"http://purl.obolibrary.org/obo/GO_0001171"}],"text":"The SARS-CoV-2 diagnostic pipeline that has proven to be successful and that is currently used in many test centers consists of three steps: collecting nasopharyngeal or oropharyngeal swab specimens, isolation of total RNA, and specific detection of the viral genome by RT-qPCR. The latter comprises a reverse transcriptase (RT) step, which translates the viral RNA into DNA, followed by a semiquantitative DNA polymerase chain reaction using oligonucleotides specific for the viral cDNA (qPCR). As a result, a short piece of the viral genome is strongly amplified and then is detected by a sequence-specific oligonucleotide probe labeled with a fluorescent dye."}

{"project":"LitCovid-sentences","denotations":[{"id":"T32","span":{"begin":0,"end":278},"obj":"Sentence"},{"id":"T33","span":{"begin":279,"end":495},"obj":"Sentence"},{"id":"T34","span":{"begin":496,"end":662},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"The SARS-CoV-2 diagnostic pipeline that has proven to be successful and that is currently used in many test centers consists of three steps: collecting nasopharyngeal or oropharyngeal swab specimens, isolation of total RNA, and specific detection of the viral genome by RT-qPCR. The latter comprises a reverse transcriptase (RT) step, which translates the viral RNA into DNA, followed by a semiquantitative DNA polymerase chain reaction using oligonucleotides specific for the viral cDNA (qPCR). As a result, a short piece of the viral genome is strongly amplified and then is detected by a sequence-specific oligonucleotide probe labeled with a fluorescent dye."}