{
  "abstract": "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.",
  "abstract_shown": true,
  "affiliations": [
    "Zhongshan School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University , Shenzhen, Guangdong 518107 ,",
    "Department of Clinical Laboratory, The Seventh Affiliated Hospital, Sun Yat-sen University , Shenzhen, Guangdong 518107 ,",
    "State Key Laboratory of Anti-Infective Drug Discovery and Development; School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou, Guangdong 510006 ,",
    "Ministry of Education, Key Laboratory of Tropical Diseases Control (Sun Yat-sen University) , Guangzhou, Guangdong 510080 ,"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 8,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Hai Tang",
      "orcid": "0000-0002-8608-692X"
    },
    {
      "affs": [
        1
      ],
      "name": "Xiaoying Xie",
      "orcid": "0000-0002-6113-6505"
    },
    {
      "affs": [
        0
      ],
      "name": "Shikang Zheng",
      "orcid": "0009-0002-9170-9535"
    },
    {
      "affs": [
        0
      ],
      "name": "Lei Wang",
      "orcid": "0009-0003-6483-5568"
    },
    {
      "affs": [
        0
      ],
      "name": "Runtian Yao",
      "orcid": "0009-0006-5483-3667"
    },
    {
      "affs": [
        0,
        2
      ],
      "name": "Xin Ding",
      "orcid": "0000-0001-6993-3034"
    },
    {
      "affs": [
        0,
        3
      ],
      "name": "Guo-Bao Tian",
      "orcid": "0000-0001-6750-5482"
    },
    {
      "affs": [
        0
      ],
      "name": "Weizhong Li",
      "orcid": "0000-0002-9003-7733"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/5bztwr3tasnjw.bib",
  "cited_by": 0,
  "doi": "10.1093/nar/gkag1045",
  "fulltext_url": null,
  "id": "5bztwr3tasnjw",
  "issns": [
    "0305-1048",
    "1362-4962"
  ],
  "landing_url": "https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1045/9002506",
  "language": null,
  "licence": "CC-BY-NC-4.0",
  "licence_label": "CC BY-NC 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1313|Antibiotic Resistance in Bacteria"
    ]
  ],
  "openalex": "W7223907612",
  "pdf_url": "https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkag1045/72528742/gkag1045.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-27",
  "publisher": "Oxford University Press (OUP)",
  "ris": "https://research.draconitic.com/paper/5bztwr3tasnjw.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:18:50Z",
      "native_id": "10.1093/nar/gkag1045",
      "source": "crossref",
      "url": "https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1045/9002506"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "issn:0305-1048",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Omni-ARMD: an integrated genomic and clinical knowledgebase bridging clinical phenotypes and molecular determinants of antimicrobial resistance",
  "title_text": "Omni-ARMD: an integrated genomic and clinical knowledgebase bridging clinical phenotypes and molecular determinants of antimicrobial resistance",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:18:50Z",
  "url": "https://research.draconitic.com/paper/5bztwr3tasnjw",
  "venue": "Nucleic Acids Research",
  "versions": []
}