PMC:7073332 / 46655-47600 JSONTXT

{"project":"LitCovid-PubTator","denotations":[{"id":"1147","span":{"begin":126,"end":130},"obj":"Species"},{"id":"1148","span":{"begin":899,"end":903},"obj":"Species"}],"attributes":[{"id":"A1147","pred":"tao:has_database_id","subj":"1147","obj":"Tax:694448"},{"id":"A1148","pred":"tao:has_database_id","subj":"1148","obj":"Tax:694448"}],"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":"For each drug that was in both the CMAP data set and our drug–target network, we calculated an enrichment score (ES) for each HCoV signature data set based on previously described methods97 as follows:4 \\documentclass[12pt]{minimal} \t\t\t\t\\usepackage{amsmath} \t\t\t\t\\usepackage{wasysym} \t\t\t\t\\usepackage{amsfonts} \t\t\t\t\\usepackage{amssymb} \t\t\t\t\\usepackage{amsbsy} \t\t\t\t\\usepackage{mathrsfs} \t\t\t\t\\usepackage{upgreek} \t\t\t\t\\setlength{\\oddsidemargin}{-69pt} \t\t\t\t\\begin{document}$${\\mathrm {ES}} = \\left\\{ {\\begin{array}{*{20}{c}} {{\\mathrm{ES}_{\\mathrm{up}}} - {\\mathrm {ES}_{\\mathrm{down}}},{\\mathrm {sgn}}\\left( {{\\mathrm {ES}_{\\mathrm{up}}}} \\right)\\, \\ne \\,{\\mathrm {sgn}}\\left( {{\\mathrm {ES}_{\\mathrm{down}}}} \\right)} \\\\ {0,\\mathrm {else}} \\end{array}} \\right.$$\\end{document}ES=ESup−ESdown,sgnESup≠sgnESdown0,elseESup and ESdown were calculated separately for the up- and down-regulated genes from the HCoV signature data set using the same method."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T323","span":{"begin":113,"end":115},"obj":"http://purl.obolibrary.org/obo/CLO_0053755"},{"id":"T324","span":{"begin":479,"end":481},"obj":"http://purl.obolibrary.org/obo/CLO_0053755"},{"id":"T325","span":{"begin":529,"end":531},"obj":"http://purl.obolibrary.org/obo/CLO_0053755"},{"id":"T326","span":{"begin":560,"end":562},"obj":"http://purl.obolibrary.org/obo/CLO_0053755"},{"id":"T327","span":{"begin":614,"end":616},"obj":"http://purl.obolibrary.org/obo/CLO_0053755"},{"id":"T328","span":{"begin":645,"end":647},"obj":"http://purl.obolibrary.org/obo/CLO_0008149"},{"id":"T329","span":{"begin":683,"end":685},"obj":"http://purl.obolibrary.org/obo/CLO_0053755"},{"id":"T330","span":{"begin":772,"end":774},"obj":"http://purl.obolibrary.org/obo/CLO_0053755"},{"id":"T331","span":{"begin":884,"end":889},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"}],"text":"For each drug that was in both the CMAP data set and our drug–target network, we calculated an enrichment score (ES) for each HCoV signature data set based on previously described methods97 as follows:4 \\documentclass[12pt]{minimal} \t\t\t\t\\usepackage{amsmath} \t\t\t\t\\usepackage{wasysym} \t\t\t\t\\usepackage{amsfonts} \t\t\t\t\\usepackage{amssymb} \t\t\t\t\\usepackage{amsbsy} \t\t\t\t\\usepackage{mathrsfs} \t\t\t\t\\usepackage{upgreek} \t\t\t\t\\setlength{\\oddsidemargin}{-69pt} \t\t\t\t\\begin{document}$${\\mathrm {ES}} = \\left\\{ {\\begin{array}{*{20}{c}} {{\\mathrm{ES}_{\\mathrm{up}}} - {\\mathrm {ES}_{\\mathrm{down}}},{\\mathrm {sgn}}\\left( {{\\mathrm {ES}_{\\mathrm{up}}}} \\right)\\, \\ne \\,{\\mathrm {sgn}}\\left( {{\\mathrm {ES}_{\\mathrm{down}}}} \\right)} \\\\ {0,\\mathrm {else}} \\end{array}} \\right.$$\\end{document}ES=ESup−ESdown,sgnESup≠sgnESdown0,elseESup and ESdown were calculated separately for the up- and down-regulated genes from the HCoV signature data set using the same method."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T487","span":{"begin":9,"end":13},"obj":"Chemical"},{"id":"T488","span":{"begin":57,"end":61},"obj":"Chemical"},{"id":"T489","span":{"begin":113,"end":115},"obj":"Chemical"},{"id":"T490","span":{"begin":479,"end":481},"obj":"Chemical"},{"id":"T491","span":{"begin":529,"end":531},"obj":"Chemical"},{"id":"T492","span":{"begin":560,"end":562},"obj":"Chemical"},{"id":"T493","span":{"begin":614,"end":616},"obj":"Chemical"},{"id":"T494","span":{"begin":683,"end":685},"obj":"Chemical"},{"id":"T495","span":{"begin":772,"end":774},"obj":"Chemical"}],"attributes":[{"id":"A487","pred":"chebi_id","subj":"T487","obj":"http://purl.obolibrary.org/obo/CHEBI_23888"},{"id":"A488","pred":"chebi_id","subj":"T488","obj":"http://purl.obolibrary.org/obo/CHEBI_23888"},{"id":"A489","pred":"chebi_id","subj":"T489","obj":"http://purl.obolibrary.org/obo/CHEBI_73509"},{"id":"A490","pred":"chebi_id","subj":"T490","obj":"http://purl.obolibrary.org/obo/CHEBI_73509"},{"id":"A491","pred":"chebi_id","subj":"T491","obj":"http://purl.obolibrary.org/obo/CHEBI_73509"},{"id":"A492","pred":"chebi_id","subj":"T492","obj":"http://purl.obolibrary.org/obo/CHEBI_73509"},{"id":"A493","pred":"chebi_id","subj":"T493","obj":"http://purl.obolibrary.org/obo/CHEBI_73509"},{"id":"A494","pred":"chebi_id","subj":"T494","obj":"http://purl.obolibrary.org/obo/CHEBI_73509"},{"id":"A495","pred":"chebi_id","subj":"T495","obj":"http://purl.obolibrary.org/obo/CHEBI_73509"}],"text":"For each drug that was in both the CMAP data set and our drug–target network, we calculated an enrichment score (ES) for each HCoV signature data set based on previously described methods97 as follows:4 \\documentclass[12pt]{minimal} \t\t\t\t\\usepackage{amsmath} \t\t\t\t\\usepackage{wasysym} \t\t\t\t\\usepackage{amsfonts} \t\t\t\t\\usepackage{amssymb} \t\t\t\t\\usepackage{amsbsy} \t\t\t\t\\usepackage{mathrsfs} \t\t\t\t\\usepackage{upgreek} \t\t\t\t\\setlength{\\oddsidemargin}{-69pt} \t\t\t\t\\begin{document}$${\\mathrm {ES}} = \\left\\{ {\\begin{array}{*{20}{c}} {{\\mathrm{ES}_{\\mathrm{up}}} - {\\mathrm {ES}_{\\mathrm{down}}},{\\mathrm {sgn}}\\left( {{\\mathrm {ES}_{\\mathrm{up}}}} \\right)\\, \\ne \\,{\\mathrm {sgn}}\\left( {{\\mathrm {ES}_{\\mathrm{down}}}} \\right)} \\\\ {0,\\mathrm {else}} \\end{array}} \\right.$$\\end{document}ES=ESup−ESdown,sgnESup≠sgnESdown0,elseESup and ESdown were calculated separately for the up- and down-regulated genes from the HCoV signature data set using the same method."}

{"project":"LitCovid-sentences","denotations":[{"id":"T279","span":{"begin":0,"end":945},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"For each drug that was in both the CMAP data set and our drug–target network, we calculated an enrichment score (ES) for each HCoV signature data set based on previously described methods97 as follows:4 \\documentclass[12pt]{minimal} \t\t\t\t\\usepackage{amsmath} \t\t\t\t\\usepackage{wasysym} \t\t\t\t\\usepackage{amsfonts} \t\t\t\t\\usepackage{amssymb} \t\t\t\t\\usepackage{amsbsy} \t\t\t\t\\usepackage{mathrsfs} \t\t\t\t\\usepackage{upgreek} \t\t\t\t\\setlength{\\oddsidemargin}{-69pt} \t\t\t\t\\begin{document}$${\\mathrm {ES}} = \\left\\{ {\\begin{array}{*{20}{c}} {{\\mathrm{ES}_{\\mathrm{up}}} - {\\mathrm {ES}_{\\mathrm{down}}},{\\mathrm {sgn}}\\left( {{\\mathrm {ES}_{\\mathrm{up}}}} \\right)\\, \\ne \\,{\\mathrm {sgn}}\\left( {{\\mathrm {ES}_{\\mathrm{down}}}} \\right)} \\\\ {0,\\mathrm {else}} \\end{array}} \\right.$$\\end{document}ES=ESup−ESdown,sgnESup≠sgnESdown0,elseESup and ESdown were calculated separately for the up- and down-regulated genes from the HCoV signature data set using the same method."}

{"project":"2_test","denotations":[{"id":"32194980-21849665-19614271","span":{"begin":187,"end":189},"obj":"21849665"}],"text":"For each drug that was in both the CMAP data set and our drug–target network, we calculated an enrichment score (ES) for each HCoV signature data set based on previously described methods97 as follows:4 \\documentclass[12pt]{minimal} \t\t\t\t\\usepackage{amsmath} \t\t\t\t\\usepackage{wasysym} \t\t\t\t\\usepackage{amsfonts} \t\t\t\t\\usepackage{amssymb} \t\t\t\t\\usepackage{amsbsy} \t\t\t\t\\usepackage{mathrsfs} \t\t\t\t\\usepackage{upgreek} \t\t\t\t\\setlength{\\oddsidemargin}{-69pt} \t\t\t\t\\begin{document}$${\\mathrm {ES}} = \\left\\{ {\\begin{array}{*{20}{c}} {{\\mathrm{ES}_{\\mathrm{up}}} - {\\mathrm {ES}_{\\mathrm{down}}},{\\mathrm {sgn}}\\left( {{\\mathrm {ES}_{\\mathrm{up}}}} \\right)\\, \\ne \\,{\\mathrm {sgn}}\\left( {{\\mathrm {ES}_{\\mathrm{down}}}} \\right)} \\\\ {0,\\mathrm {else}} \\end{array}} \\right.$$\\end{document}ES=ESup−ESdown,sgnESup≠sgnESdown0,elseESup and ESdown were calculated separately for the up- and down-regulated genes from the HCoV signature data set using the same method."}