PubMed:32654489 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PubMed/sourceid/32654489","sourcedb":"PubMed","sourceid":"32654489","source_url":"https://www.ncbi.nlm.nih.gov/pubmed/32654489","text":"Repurpose Open Data to Discover Therapeutics for COVID-19 Using Deep Learning.\nThere have been more than 2.2 million confirmed cases and over 120 000 deaths from the human coronavirus disease 2019 (COVID-19) pandemic, caused by the novel severe acute respiratory syndrome coronavirus (SARS-CoV-2), in the United States alone. However, there is currently a lack of proven effective medications against COVID-19. Drug repurposing offers a promising route for the development of prevention and treatment strategies for COVID-19. This study reports an integrative, network-based deep-learning methodology to identify repurposable drugs for COVID-19 (termed CoV-KGE). Specifically, we built a comprehensive knowledge graph that includes 15 million edges across 39 types of relationships connecting drugs, diseases, proteins/genes, pathways, and expression from a large scientific corpus of 24 million PubMed publications. Using Amazon's AWS computing resources and a network-based, deep-learning framework, we identified 41 repurposable drugs (including dexamethasone, indomethacin, niclosamide, and toremifene) whose therapeutic associations with COVID-19 were validated by transcriptomic and proteomics data in SARS-CoV-2-infected human cells and data from ongoing clinical trials. Whereas this study by no means recommends specific drugs, it demonstrates a powerful deep-learning methodology to prioritize existing drugs for further investigation, which holds the potential to accelerate therapeutic development for COVID-19.","tracks":[{"project":"sentences","denotations":[{"id":"T1","span":{"begin":0,"end":78},"obj":"Sentence"},{"id":"T2","span":{"begin":79,"end":325},"obj":"Sentence"},{"id":"T3","span":{"begin":326,"end":410},"obj":"Sentence"},{"id":"T4","span":{"begin":411,"end":525},"obj":"Sentence"},{"id":"T5","span":{"begin":526,"end":662},"obj":"Sentence"},{"id":"T6","span":{"begin":663,"end":916},"obj":"Sentence"},{"id":"T7","span":{"begin":917,"end":1278},"obj":"Sentence"},{"id":"T8","span":{"begin":1279,"end":1523},"obj":"Sentence"},{"id":"T1","span":{"begin":0,"end":78},"obj":"Sentence"},{"id":"T2","span":{"begin":79,"end":325},"obj":"Sentence"},{"id":"T3","span":{"begin":326,"end":410},"obj":"Sentence"},{"id":"T4","span":{"begin":411,"end":525},"obj":"Sentence"},{"id":"T5","span":{"begin":526,"end":662},"obj":"Sentence"},{"id":"T6","span":{"begin":663,"end":916},"obj":"Sentence"},{"id":"T7","span":{"begin":917,"end":1278},"obj":"Sentence"},{"id":"T8","span":{"begin":1279,"end":1523},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T1","pred":"source","obj":"sentences"},{"subj":"T2","pred":"source","obj":"sentences"},{"subj":"T3","pred":"source","obj":"sentences"},{"subj":"T4","pred":"source","obj":"sentences"},{"subj":"T5","pred":"source","obj":"sentences"},{"subj":"T6","pred":"source","obj":"sentences"},{"subj":"T7","pred":"source","obj":"sentences"},{"subj":"T8","pred":"source","obj":"sentences"},{"subj":"T1","pred":"source","obj":"sentences"},{"subj":"T2","pred":"source","obj":"sentences"},{"subj":"T3","pred":"source","obj":"sentences"},{"subj":"T4","pred":"source","obj":"sentences"},{"subj":"T5","pred":"source","obj":"sentences"},{"subj":"T6","pred":"source","obj":"sentences"},{"subj":"T7","pred":"source","obj":"sentences"},{"subj":"T8","pred":"source","obj":"sentences"}]},{"project":"NCBITAXON","denotations":[{"id":"T1","span":{"begin":166,"end":171},"obj":"OrganismTaxon"},{"id":"T2","span":{"begin":172,"end":196},"obj":"OrganismTaxon"},{"id":"T3","span":{"begin":238,"end":271},"obj":"OrganismTaxon"},{"id":"T4","span":{"begin":285,"end":293},"obj":"OrganismTaxon"},{"id":"T5","span":{"begin":1208,"end":1216},"obj":"OrganismTaxon"},{"id":"T6","span":{"begin":1228,"end":1233},"obj":"OrganismTaxon"}],"attributes":[{"id":"A1","pred":"db_id","subj":"T1","obj":"9606"},{"id":"A2","pred":"db_id","subj":"T2","obj":"2697049"},{"id":"A3","pred":"db_id","subj":"T3","obj":"694009"},{"id":"A4","pred":"db_id","subj":"T4","obj":"694009"},{"id":"A5","pred":"db_id","subj":"T5","obj":"694009"},{"id":"A6","pred":"db_id","subj":"T6","obj":"9606"},{"subj":"T1","pred":"source","obj":"NCBITAXON"},{"subj":"T2","pred":"source","obj":"NCBITAXON"},{"subj":"T3","pred":"source","obj":"NCBITAXON"},{"subj":"T4","pred":"source","obj":"NCBITAXON"},{"subj":"T5","pred":"source","obj":"NCBITAXON"},{"subj":"T6","pred":"source","obj":"NCBITAXON"}]},{"project":"mondo_disease","denotations":[{"id":"T1","span":{"begin":49,"end":57},"obj":"Disease"},{"id":"T2","span":{"begin":172,"end":196},"obj":"Disease"},{"id":"T3","span":{"begin":198,"end":206},"obj":"Disease"},{"id":"T4","span":{"begin":238,"end":271},"obj":"Disease"},{"id":"T5","span":{"begin":285,"end":295},"obj":"Disease"},{"id":"T6","span":{"begin":401,"end":409},"obj":"Disease"},{"id":"T7","span":{"begin":516,"end":524},"obj":"Disease"},{"id":"T8","span":{"begin":636,"end":644},"obj":"Disease"},{"id":"T9","span":{"begin":1143,"end":1151},"obj":"Disease"},{"id":"T10","span":{"begin":1208,"end":1218},"obj":"Disease"},{"id":"T11","span":{"begin":1514,"end":1522},"obj":"Disease"}],"attributes":[{"id":"A1","pred":"mondo_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A2","pred":"mondo_id","subj":"T2","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A3","pred":"mondo_id","subj":"T3","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A4","pred":"mondo_id","subj":"T4","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A5","pred":"mondo_id","subj":"T5","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A6","pred":"mondo_id","subj":"T6","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A7","pred":"mondo_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A8","pred":"mondo_id","subj":"T8","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A9","pred":"mondo_id","subj":"T9","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A10","pred":"mondo_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A11","pred":"mondo_id","subj":"T11","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"subj":"T1","pred":"source","obj":"mondo_disease"},{"subj":"T2","pred":"source","obj":"mondo_disease"},{"subj":"T3","pred":"source","obj":"mondo_disease"},{"subj":"T4","pred":"source","obj":"mondo_disease"},{"subj":"T5","pred":"source","obj":"mondo_disease"},{"subj":"T6","pred":"source","obj"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