{
  "abstract": "We present Ontologizer 3, an easy-to-use cross-platform desktop application for Gene Ontology (GO) overrepresentation analysis. Ontologizer 3 offers two complementary methods. The first is a frequentist approach that evaluates GO terms individually using a one-sided Fisher’s exact test, yielding term-level significance values. The second is a Bayesian approach that jointly evaluates terms using model-based gene set analysis (MGSA), yielding term-level posterior probabilities. Due to substantial overlap among annotated gene sets resulting from the GO’s hierarchical structure, the two methods produce different results. The frequentist approach tends to report a lengthy list of terms with strong annotation overlap, whereas, MGSA yields a parsimonious set of terms that explain the observed gene activity. Using simulated data with a known ground truth, we demonstrate that both methods reliably identify the causal term, but MGSA achieves substantially higher precision. Ontologizer 3 is implemented as a Tauri application with a Rust backend and an Angular frontend, presenting enriched terms in tabular and graphical form. The software is freely available under the MIT licence at https://github.com/P2GX/ontologizer-gui. Installation packages for Macintosh, Windows, and Debian-based Linux are available on the GitHub Releases page.",
  "abstract_shown": true,
  "affiliations": [
    "Berlin Institute of Health at Charité Universitätsmedizin , Luisenstr. 65, 10117, Berlin ,",
    "The Jackson Laboratory for Genomic Medicine , 10 Discovery Drive, 06032, Connecticut ,"
  ],
  "article_type": "brief report",
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  "author_total": 4,
  "authors": [
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      "name": "Lukas Ramlow",
      "orcid": "0000-0001-6089-0613"
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      ],
      "name": "Jasmin Scholtes"
    },
    {
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        0
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      "name": "Daniel Danis",
      "orcid": "0000-0003-0900-3411"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Peter N Robinson",
      "orcid": "0000-0002-0736-9199"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/ey51q42w5kqje.bib",
  "cited_by": 0,
  "doi": "10.1093/nargab/lqag131",
  "fulltext_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13728651/?tool=EBI",
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  "language": "eng",
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  "native_subjects": [
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      "heading",
      "Application Notes"
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      "Editor's Choice"
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  "pdf_url": "https://academic.oup.com/nargab/article-pdf/8/4/lqag131/72841871/lqag131.pdf",
  "pmcid": "PMC13728651",
  "pmid": "42979155",
  "published": "2026-11-03",
  "publisher": "Oxford University Press (OUP)",
  "ris": "https://research.draconitic.com/paper/ey51q42w5kqje.ris",
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      "url": "https://academic.oup.com/nargab/article/doi/10.1093/nargab/lqag131/9010724"
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    {
      "first_seen": "2026-11-04T15:20:46Z",
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    {
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      "url": "https://doi.org/10.1093/nargab/lqag131"
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  "subjects": [
    {
      "field": "biology",
      "origin": "issn:2631-9268",
      "subfield": "bioinformatics"
    }
  ],
  "title": "Ontologizer 3: a cross-platform desktop application for frequentist and Bayesian GO enrichment analysis",
  "title_text": "Ontologizer 3: a cross-platform desktop application for frequentist and Bayesian GO enrichment analysis",
  "type": "peer-reviewed",
  "updated_at": "2026-11-07T12:21:35Z",
  "url": "https://research.draconitic.com/paper/ey51q42w5kqje",
  "venue": "NAR Genomics and Bioinformatics",
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