PMC:7574920 / 56142-56737 JSONTXT

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{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7574920","sourcedb":"PMC","sourceid":"7574920","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7574920","text":"For classification of samples by LAMP-sequencing, reads were assigned to wells and counted using custom scripts. A read was considered as a match to SARS-CoV-2 N gene if at least one of three short sequences (~13 nt, marked orange in fig. S4A) not covered by RT-LAMP primers was found in the read, otherwise it was counted as unmatched. Sequencing reads were grouped by UMI and by position of the matched sequence with the aim of removing PCR duplicates. A sample was considered if more than 200 total UMIs were observed and called positive if more than 10,000 virus-matching UMIs were observed.","tracks":[{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T196","span":{"begin":162,"end":166},"obj":"Body_part"}],"attributes":[{"id":"A196","pred":"fma_id","subj":"T196","obj":"http://purl.org/sig/ont/fma/fma74402"},{"subj":"T196","pred":"source","obj":"LitCovid-PD-FMA-UBERON"}]},{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T106","span":{"begin":149,"end":157},"obj":"Disease"}],"attributes":[{"id":"A106","pred":"mondo_id","subj":"T106","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"subj":"T106","pred":"source","obj":"LitCovid-PD-MONDO"}]},{"project":"LitCovid-PD-CLO","denotations":[{"id":"T453","span":{"begin":113,"end":114},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T454","span":{"begin":138,"end":139},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T455","span":{"begin":162,"end":166},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T456","span":{"begin":423,"end":426},"obj":"http://purl.obolibrary.org/obo/PR_000001343"},{"id":"T457","span":{"begin":455,"end":456},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T458","span":{"begin":561,"end":566},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"}],"attributes":[{"subj":"T453","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T454","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T455","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T456","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T457","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T458","pred":"source","obj":"LitCovid-PD-CLO"}]},{"project":"LitCovid-PubTator","denotations":[{"id":"392","span":{"begin":160,"end":161},"obj":"Gene"},{"id":"393","span":{"begin":149,"end":159},"obj":"Species"}],"attributes":[{"id":"A392","pred":"tao:has_database_id","subj":"392","obj":"Gene:43740575"},{"id":"A393","pred":"tao:has_database_id","subj":"393","obj":"Tax:2697049"},{"subj":"392","pred":"source","obj":"LitCovid-PubTator"},{"subj":"393","pred":"source","obj":"LitCovid-PubTator"}],"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_"}]},{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T299","span":{"begin":259,"end":261},"obj":"http://purl.obolibrary.org/obo/GO_0001171"}],"attributes":[{"subj":"T299","pred":"source","obj":"LitCovid-PD-GO-BP"}]},{"project":"LitCovid-sentences","denotations":[{"id":"T404","span":{"begin":0,"end":112},"obj":"Sentence"},{"id":"T405","span":{"begin":113,"end":336},"obj":"Sentence"},{"id":"T406","span":{"begin":337,"end":454},"obj":"Sentence"},{"id":"T407","span":{"begin":455,"end":595},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T404","pred":"source","obj":"LitCovid-sentences"},{"subj":"T405","pred":"source","obj":"LitCovid-sentences"},{"subj":"T406","pred":"source","obj":"LitCovid-sentences"},{"subj":"T407","pred":"source","obj":"LitCovid-sentences"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"LitCovid-PD-FMA-UBERON","color":"#d2ec93","default":true},{"id":"LitCovid-PD-MONDO","color":"#ec93ec"},{"id":"LitCovid-PD-CLO","color":"#93ecd2"},{"id":"LitCovid-PubTator","color":"#ecb893"},{"id":"LitCovid-PD-GO-BP","color":"#9e93ec"},{"id":"LitCovid-sentences","color":"#a1ec93"}]}]}}