PMC:7321036 / 85216-85793 JSONTXT

Annnotations TAB JSON ListView MergeView

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7321036","sourcedb":"PMC","sourceid":"7321036","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7321036","text":"Raw mass spectrometry data from each DDA dataset were used to build separate libraries for DIA searches using the Pulsar search engine integrated into Spectronaut version 13.12.200217.43655 (Bruderer et al., 2015) by searching against a database of Uniprot Chlorocebus sequences (19,136 proteins, downloaded April 3, 2020) and 29 SARS-CoV-2 protein sequences translated from genomic sequence downloaded from GISAID (accession EPI_ISL_406596, downloaded April 7, 2020) with two mutations (G22661T Spike V367F and G26144T ORF3a G251V) detected by RNASeq analysis of virus stocks.","tracks":[{"project":"LitCovid-PMC-OGER-BB","denotations":[{"id":"T186","span":{"begin":232,"end":268},"obj":"NCBITaxon:9606"},{"id":"T187","span":{"begin":375,"end":425},"obj":"SP_6;NCBITaxon:9606"},{"id":"T188","span":{"begin":488,"end":549},"obj":"SO:0000704"}],"attributes":[{"subj":"T186","pred":"source","obj":"LitCovid-PMC-OGER-BB"},{"subj":"T187","pred":"source","obj":"LitCovid-PMC-OGER-BB"},{"subj":"T188","pred":"source","obj":"LitCovid-PMC-OGER-BB"}]},{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T619","span":{"begin":287,"end":295},"obj":"Body_part"},{"id":"T620","span":{"begin":341,"end":348},"obj":"Body_part"}],"attributes":[{"id":"A619","pred":"fma_id","subj":"T619","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A620","pred":"fma_id","subj":"T620","obj":"http://purl.org/sig/ont/fma/fma67257"},{"subj":"T619","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T620","pred":"source","obj":"LitCovid-PD-FMA-UBERON"}]},{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T343","span":{"begin":91,"end":94},"obj":"Disease"},{"id":"T344","span":{"begin":330,"end":338},"obj":"Disease"}],"attributes":[{"id":"A343","pred":"mondo_id","subj":"T343","obj":"http://purl.obolibrary.org/obo/MONDO_0022963"},{"id":"A344","pred":"mondo_id","subj":"T344","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"subj":"T343","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T344","pred":"source","obj":"LitCovid-PD-MONDO"}]},{"project":"LitCovid-PD-CLO","denotations":[{"id":"T1188","span":{"begin":235,"end":236},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T1189","span":{"begin":564,"end":569},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"}],"attributes":[{"subj":"T1188","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T1189","pred":"source","obj":"LitCovid-PD-CLO"}]},{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T458","span":{"begin":37,"end":40},"obj":"Chemical"},{"id":"T460","span":{"begin":287,"end":295},"obj":"Chemical"},{"id":"T461","span":{"begin":341,"end":348},"obj":"Chemical"}],"attributes":[{"id":"A458","pred":"chebi_id","subj":"T458","obj":"http://purl.obolibrary.org/obo/CHEBI_28139"},{"id":"A459","pred":"chebi_id","subj":"T458","obj":"http://purl.obolibrary.org/obo/CHEBI_91207"},{"id":"A460","pred":"chebi_id","subj":"T460","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A461","pred":"chebi_id","subj":"T461","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"subj":"T458","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T460","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T461","pred":"source","obj":"LitCovid-PD-CHEBI"}]},{"project":"LitCovid-PubTator","denotations":[{"id":"1892","span":{"begin":520,"end":525},"obj":"Gene"},{"id":"1894","span":{"begin":496,"end":501},"obj":"Gene"},{"id":"1895","span":{"begin":330,"end":340},"obj":"Species"},{"id":"1896","span":{"begin":570,"end":576},"obj":"Species"},{"id":"1897","span":{"begin":257,"end":268},"obj":"Species"},{"id":"1902","span":{"begin":488,"end":495},"obj":"Mutation"},{"id":"1903","span":{"begin":502,"end":507},"obj":"Mutation"},{"id":"1904","span":{"begin":512,"end":519},"obj":"Mutation"},{"id":"1905","span":{"begin":526,"end":531},"obj":"Mutation"}],"attributes":[{"id":"A1892","pred":"tao:has_database_id","subj":"1892","obj":"Gene:43740569"},{"id":"A1894","pred":"tao:has_database_id","subj":"1894","obj":"Gene:43740568"},{"id":"A1895","pred":"tao:has_database_id","subj":"1895","obj":"Tax:2697049"},{"id":"A1896","pred":"tao:has_database_id","subj":"1896","obj":"Tax:3724"},{"id":"A1897","pred":"tao:has_database_id","subj":"1897","obj":"Tax:60711"},{"id":"A1902","pred":"tao:has_standard_notation","subj":"1902","obj":"g.22661G\u003eT"},{"id":"A1903","pred":"tao:has_standard_notation","subj":"1903","obj":"p.V367F"},{"id":"A1904","pred":"tao:has_standard_notation","subj":"1904","obj":"g.26144G\u003eT"},{"id":"A1905","pred":"tao:has_standard_notation","subj":"1905","obj":"p.G251V"},{"subj":"1892","pred":"source","obj":"LitCovid-PubTator"},{"subj":"1894","pred":"source","obj":"LitCovid-PubTator"},{"subj":"1895","pred":"source","obj":"LitCovid-PubTator"},{"subj":"1896","pred":"source","obj":"LitCovid-PubTator"},{"subj":"1897","pred":"source","obj":"LitCovid-PubTator"},{"subj":"1902","pred":"source","obj":"LitCovid-PubTator"},{"subj":"1903","pred":"source","obj":"LitCovid-PubTator"},{"subj":"1904","pred":"source","obj":"LitCovid-PubTator"},{"subj":"1905","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-sentences","denotations":[{"id":"T769","span":{"begin":0,"end":577},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T769","pred":"source","obj":"LitCovid-sentences"}]},{"project":"2_test","denotations":[{"id":"32645325-25724911-20773110","span":{"begin":208,"end":212},"obj":"25724911"}],"attributes":[{"subj":"32645325-25724911-20773110","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"LitCovid-PMC-OGER-BB","color":"#ec93e6","default":true},{"id":"LitCovid-PD-FMA-UBERON","color":"#93ecd8"},{"id":"LitCovid-PD-MONDO","color":"#ecbe93"},{"id":"LitCovid-PD-CLO","color":"#a493ec"},{"id":"LitCovid-PD-CHEBI","color":"#9bec93"},{"id":"LitCovid-PubTator","color":"#ec93b5"},{"id":"LitCovid-sentences","color":"#93cfec"},{"id":"2_test","color":"#e9ec93"}]}]}}