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To investigate\u00a0the toxicological mechanisms of air pollutants and their health effects, we developed R\u2010APEX, a knowledge graph (KG) platform integrating data from 24 biomedical databases and over 800 peer\u2010reviewed publications. The complete KG contains 91,661 nodes and 10,550,809 edges, encompassing 11 entity categories and 75 relation types. R\u2010APEX maps both curated and predicted associations, presented via interactive visualization. It leverages knowledge graph embedding (KEG) techniques to predict relationships between pollutants, genes, and diseases. These predictive capabilities support customized analyes for research needs, facilitating insight into how air pollutants contribute to human diseases, and aiding treatment discovery. Futhermore, R\u2010APEX enables multidimensional analysis hypothesis generation, and the development of research plans. It servers as a valuable resource for academic researchers exploring\u00a0 complex links between air pollution and biological systems, which supporting the validation of predictive models. All data and the platform are freely available at https:\/\/rapex.prophetdb.org, with the source code hosted on GitHub at https:\/\/github.com\/open\u2010prophetdb\/biomedgps\u2010data.<\/jats:p>","DOI":"10.1002\/aisy.202500036","type":"journal-article","created":{"date-parts":[[2025,5,11]],"date-time":"2025-05-11T14:24:17Z","timestamp":1746973457000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["R\u2010APEX: A Knowledge Graph\u2013Based Platform for the Elucidation of the Toxicological Mechanisms of Ambient Particulate Matter"],"prefix":"10.1002","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3933-1814","authenticated-orcid":false,"given":"Zhixing","family":"Zhu","sequence":"first","affiliation":[{"name":"Shanghai Engineering Research Center for Big Data in Pediatric Precision Medicine Center for Biomedical Informatics Shanghai Children's Hospital; School of Medicine Shanghai Jiao Tong University  Shanghai 200062 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2550-3910","authenticated-orcid":false,"given":"Jingcheng","family":"Yang","sequence":"additional","affiliation":[{"name":"Greater Bay Area Institute of Precision Medicine  115 Jiaoxi Road Guangzhou 511458 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaofei","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Epidemiology and Statistics, School of Public Health Guilin Medical University  Guangxi 541199 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhijie","family":"Zheng","sequence":"additional","affiliation":[{"name":"Cardiac Intensive Care Unit (CICU) Children's Hospital of Zhejiang University School of Medicine  Hangzhou 310057 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3281-9104","authenticated-orcid":false,"given":"Georgi Z.","family":"Genchev","sequence":"additional","affiliation":[{"name":"Center of Excellence in Computational Molecular Biology Faculty of Medicine Chulalongkorn University  Bangkok 10330 Thailand"},{"name":"Center for Artificial Intelligence in Medicine Faculty of Medicine Chulalongkorn University  Bangkok 10330 Thailand"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuchen","family":"Ye","sequence":"additional","affiliation":[{"name":"Department of Research Department of Pathology Shanghai University of Medicine &amp; Health Sciences Affiliated Zhoupu Hospital  1500 Zhouyuan Road Shanghai 201318 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8529-8886","authenticated-orcid":false,"given":"Liang","family":"Liu","sequence":"additional","affiliation":[{"name":"Clinical Research Unit Institute of Clinical Science Zhongshan Hospital of Fudan University  Shanghai 200032 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2862-5497","authenticated-orcid":false,"given":"Zihan","family":"Ran","sequence":"additional","affiliation":[{"name":"Department of Research Department of Pathology Shanghai University of Medicine &amp; Health Sciences Affiliated Zhoupu Hospital  1500 Zhouyuan Road Shanghai 201318 China"},{"name":"Inspection and Quarantine Department The College of Medical Technology Shanghai University of Medicine &amp; Health Sciences  279 Zhouzhu Road Shanghai 201318 China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2025,5,11]]},"reference":[{"key":"e_1_2_11_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(17)32345-0"},{"key":"e_1_2_11_3_1","doi-asserted-by":"publisher","DOI":"10.3389\/fpubh.2020.00014"},{"key":"e_1_2_11_4_1","first-page":"789","volume":"28","author":"Meo S. 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