PMC:7642385 / 7373-8014 JSONTXT

{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/7642385","sourcedb":"PMC","sourceid":"7642385","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7642385","text":"We observed different relevance scores for the same pathogen, depending on the length of k-mers (Supplementary Figs. 1 and 2). For k = 6 we found that all viruses were in the upper half when ranking the relevance scores, while the viruses were in the lower half for k = 8. This was independent of the HLA-class epitopes (Supplementary Fig. 1 and 2).\nFigure 2 Some viruses and bacteria have peptides (k-mers) matching SARS-CoV-2 epitopes. The top 10 pathogen relevance scores were averaged over k = 6,7,8 amino acids for (a) HLA-I, and (b) HLA-II. Pathogen relevance score for each pathogen and k are presented in Supplementary Figs. 1 and 2.","divisions":[{"label":"label","span":{"begin":350,"end":358}}],"tracks":[{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T62","span":{"begin":301,"end":304},"obj":"Body_part"},{"id":"T63","span":{"begin":504,"end":515},"obj":"Body_part"},{"id":"T64","span":{"begin":524,"end":527},"obj":"Body_part"},{"id":"T65","span":{"begin":539,"end":542},"obj":"Body_part"}],"attributes":[{"id":"A62","pred":"fma_id","subj":"T62","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A63","pred":"fma_id","subj":"T63","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A64","pred":"fma_id","subj":"T64","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A65","pred":"fma_id","subj":"T65","obj":"http://purl.org/sig/ont/fma/fma84795"},{"subj":"T62","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T63","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T64","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T65","pred":"source","obj":"LitCovid-PD-FMA-UBERON"}]},{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T41","span":{"begin":417,"end":425},"obj":"Disease"}],"attributes":[{"id":"A41","pred":"mondo_id","subj":"T41","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"subj":"T41","pred":"source","obj":"LitCovid-PD-MONDO"}]},{"project":"LitCovid-PD-CLO","denotations":[{"id":"T72","span":{"begin":155,"end":162},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T73","span":{"begin":231,"end":238},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T74","span":{"begin":364,"end":371},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T75","span":{"begin":376,"end":384},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_2"},{"id":"T76","span":{"begin":390,"end":398},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T77","span":{"begin":521,"end":522},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T78","span":{"begin":536,"end":537},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"}],"attributes":[{"subj":"T72","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T73","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T74","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T75","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T76","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T77","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T78","pred":"source","obj":"LitCovid-PD-CLO"}]},{"project":"LitCovid-sentences","denotations":[{"id":"T51","span":{"begin":0,"end":126},"obj":"Sentence"},{"id":"T52","span":{"begin":127,"end":272},"obj":"Sentence"},{"id":"T53","span":{"begin":273,"end":349},"obj":"Sentence"},{"id":"T54","span":{"begin":350,"end":437},"obj":"Sentence"},{"id":"T55","span":{"begin":438,"end":546},"obj":"Sentence"},{"id":"T56","span":{"begin":547,"end":641},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T51","pred":"source","obj":"LitCovid-sentences"},{"subj":"T52","pred":"source","obj":"LitCovid-sentences"},{"subj":"T53","pred":"source","obj":"LitCovid-sentences"},{"subj":"T54","pred":"source","obj":"LitCovid-sentences"},{"subj":"T55","pred":"source","obj":"LitCovid-sentences"},{"subj":"T56","pred":"source","obj":"LitCovid-sentences"}]},{"project":"LitCovid-PubTator","denotations":[{"id":"155","span":{"begin":417,"end":427},"obj":"Species"},{"id":"157","span":{"begin":321,"end":347},"obj":"Gene"}],"attributes":[{"id":"A155","pred":"tao:has_database_id","subj":"155","obj":"Tax:2697049"},{"subj":"155","pred":"source","obj":"LitCovid-PubTator"},{"subj":"157","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_"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"LitCovid-PD-FMA-UBERON","color":"#db93ec","default":true},{"id":"LitCovid-PD-MONDO","color":"#93ecc1"},{"id":"LitCovid-PD-CLO","color":"#eca793"},{"id":"LitCovid-sentences","color":"#9398ec"},{"id":"LitCovid-PubTator","color":"#b2ec93"}]}]}}