PMC:7321036 / 102622-103260 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T18","span":{"begin":24,"end":31},"obj":"Body_part"}],"attributes":[{"id":"A18","pred":"fma_id","subj":"T18","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"Statistical analysis of protein abundance changes between control and infected runs were computed using peptide ion fragment data output from Spectronaut and processed using a pipeline of three functions from the R package MSstats (version 3.19.5) (Choi et al., 2014): function MSstats::SpectronauttoMSstatsFormat with default settings other than setting “removeProtein_with1Feature = TRUE”; function MSstats::dataProcess with default settings other than setting “censoredInt = 0,” “featureSubset = highQuality,” “remove_uninformative_feature_outlier = TRUE,” “clusters=7”; and function MSstats::groupComparison with all default settings."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T21","span":{"begin":104,"end":111},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T22","span":{"begin":174,"end":175},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"Statistical analysis of protein abundance changes between control and infected runs were computed using peptide ion fragment data output from Spectronaut and processed using a pipeline of three functions from the R package MSstats (version 3.19.5) (Choi et al., 2014): function MSstats::SpectronauttoMSstatsFormat with default settings other than setting “removeProtein_with1Feature = TRUE”; function MSstats::dataProcess with default settings other than setting “censoredInt = 0,” “featureSubset = highQuality,” “remove_uninformative_feature_outlier = TRUE,” “clusters=7”; and function MSstats::groupComparison with all default settings."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T95034","span":{"begin":24,"end":31},"obj":"Chemical"},{"id":"T79407","span":{"begin":104,"end":111},"obj":"Chemical"},{"id":"T77426","span":{"begin":112,"end":115},"obj":"Chemical"}],"attributes":[{"id":"A88602","pred":"chebi_id","subj":"T95034","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A89038","pred":"chebi_id","subj":"T79407","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A45459","pred":"chebi_id","subj":"T77426","obj":"http://purl.obolibrary.org/obo/CHEBI_24870"}],"text":"Statistical analysis of protein abundance changes between control and infected runs were computed using peptide ion fragment data output from Spectronaut and processed using a pipeline of three functions from the R package MSstats (version 3.19.5) (Choi et al., 2014): function MSstats::SpectronauttoMSstatsFormat with default settings other than setting “removeProtein_with1Feature = TRUE”; function MSstats::dataProcess with default settings other than setting “censoredInt = 0,” “featureSubset = highQuality,” “remove_uninformative_feature_outlier = TRUE,” “clusters=7”; and function MSstats::groupComparison with all default settings."}

{"project":"LitCovid-PubTator","denotations":[{"id":"2309","span":{"begin":70,"end":78},"obj":"Disease"}],"attributes":[{"id":"A2309","pred":"tao:has_database_id","subj":"2309","obj":"MESH:D007239"}],"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":"Statistical analysis of protein abundance changes between control and infected runs were computed using peptide ion fragment data output from Spectronaut and processed using a pipeline of three functions from the R package MSstats (version 3.19.5) (Choi et al., 2014): function MSstats::SpectronauttoMSstatsFormat with default settings other than setting “removeProtein_with1Feature = TRUE”; function MSstats::dataProcess with default settings other than setting “censoredInt = 0,” “featureSubset = highQuality,” “remove_uninformative_feature_outlier = TRUE,” “clusters=7”; and function MSstats::groupComparison with all default settings."}

{"project":"LitCovid-sentences","denotations":[{"id":"T894","span":{"begin":0,"end":638},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Statistical analysis of protein abundance changes between control and infected runs were computed using peptide ion fragment data output from Spectronaut and processed using a pipeline of three functions from the R package MSstats (version 3.19.5) (Choi et al., 2014): function MSstats::SpectronauttoMSstatsFormat with default settings other than setting “removeProtein_with1Feature = TRUE”; function MSstats::dataProcess with default settings other than setting “censoredInt = 0,” “featureSubset = highQuality,” “remove_uninformative_feature_outlier = TRUE,” “clusters=7”; and function MSstats::groupComparison with all default settings."}

{"project":"2_test","denotations":[{"id":"32645325-24794931-20773114","span":{"begin":262,"end":266},"obj":"24794931"}],"text":"Statistical analysis of protein abundance changes between control and infected runs were computed using peptide ion fragment data output from Spectronaut and processed using a pipeline of three functions from the R package MSstats (version 3.19.5) (Choi et al., 2014): function MSstats::SpectronauttoMSstatsFormat with default settings other than setting “removeProtein_with1Feature = TRUE”; function MSstats::dataProcess with default settings other than setting “censoredInt = 0,” “featureSubset = highQuality,” “remove_uninformative_feature_outlier = TRUE,” “clusters=7”; and function MSstats::groupComparison with all default settings."}