Omni-ARMD 知识库发布，整合耐药基因组与临床药敏数据
Omni-ARMD: an integrated genomic and clinical knowledgebase bridging clinical phenotypes and molecular determinants of antimicrobial resistance
Omni-ARMD 是一个开放获取的耐药知识库，整合多来源基因组与临床数据，系统推断抗菌药物耐药的基因型—表型关系。研究团队用置信度加权的对数优势比富集框架，在物种—抗菌药物层面量化基因型与表型的关联，并汇总为跨域证据表示。当前版本收录来自 100 多万名患者的逾 1200 万条去标识微生物学记录，整理出超过 783 万条标准化药敏（AST）记录，并整合超过 36 万条基因—表型关联，覆盖 38 个物种、52 种抗菌药物和 375 个耐药基因。该库将超过 516 万条临床记录与基因组证据关联，匹配率 65.86%，物种—抗菌药物组合覆盖率为 2.61%。
来源：Nucleic Acids Research · doi.org
Antimicrobial resistance (AMR) is a major global health threat, yet its molecular determinants remain difficult to characterize in real-world settings, as genomic and clinical data are fragmented across resources. Existing databases typically separate gene-level mechanisms, curated genotype–phenotype associations, and large-scale clinical antimicrobial susceptibility testing (AST) data, limiting cross-scale interpretation. Here, we present Omni-ARMD, an open-access knowledgebase that integrates multi-source genomic and clinical data to systematically infer genotype–phenotype relationships in AMR. Omni-ARMD bridges large-scale clinical AST records and gene-level resistance evidence through a confidence-weighted log-odds enrichment framework, which quantifies genotype–phenotype associations at the organism–antimicrobial level and integrates these associations into aggregated cross-domain evidence representations. The current release includes over 12 million de-identified microbiology records from more than 1 million patients, harmonized to generate over 7.83 million standardized AST records. It also integrates over 0.36 million gene-phenotype associations, spanning 38 organisms, 52 antimicrobials, and 375 resistance genes. Omni-ARMD links over 5.16 million clinical records to genomic evidence, achieving a 65.86% match rate and a 2.61% coverage of organism–antimicrobial pairs. Omni-ARMD provides interactive modules for clinical investigation, genomic evidence analysis, mechanistic interpretation, and artificial intelligence-assisted exploration, enabling integrative and data-driven discovery in AMR. Omni-ARMD is freely available at www.omniarmd.cn.