{
  "abstract": "Motivation: We asked whether the natural language used to name Gene Ontology (GO) Biological Process terms encodes hierarchical position in the GO directed acyclic graph.\n\nResults: Semantic representations of term names, combined with Uniform Manifold Approximation and Projection visualization and k-means clustering (k=20) recovered biologically coherent semantic groups whose depth distributions differed strongly (Kruskal–Wallis H=5244; p<10−300; η2=.217). Term-name length increased with depth (Pearson r = .34, Spearman ρ=0.37; slope =3.2 letters per level), and this positive scaling held under shortest-, longest-, and average-path depth definitions. Vocabulary entropy followed a bell-shaped diversification–specialization curve with an intermediate-depth peak (maximal at depth 4) that lies outside a Monte Carlo null envelope across most depths, and null-model tests supported a genuine linguistic–hierarchical association.\n\nAvailability and implementation: The go_lingdepth Python package, regenerated result tables, and figure-generation scripts are available at https://github.com/Sadiya-ISU/Letters-and-Biological-Process and archived on Zenodo (DOI: 10.5281/zenodo.21501473).",
  "abstract_shown": true,
  "affiliations": [
    "Department of Computer Science, Iowa State University , Ames, IA 50011,"
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 1,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Sadiya Ahmad"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/c0c0twnq4v9np.bib",
  "cited_by": 0,
  "doi": "10.1093/bioinformatics/btag768",
  "fulltext_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13718435/",
  "id": "c0c0twnq4v9np",
  "issns": [
    "1367-4803",
    "1367-4811"
  ],
  "landing_url": "https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btag768/8913739",
  "language": "en",
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "AcademicSubjects/SCI01060"
    ],
    [
      "heading",
      "Databases and Ontologies"
    ],
    [
      "heading",
      "Original Paper"
    ],
    [
      "openalex",
      "1312|Biomedical Text Mining and Ontologies"
    ]
  ],
  "openalex": "W7221720625",
  "pdf_url": "https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btag768/71904174/btag768.pdf",
  "pmcid": "PMC13718435",
  "pmid": "42867150",
  "published": "2026-10-13",
  "publisher": "Oxford University Press (OUP)",
  "ris": "https://research.draconitic.com/paper/c0c0twnq4v9np.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:19:38Z",
      "native_id": "10.1093/bioinformatics/btag768",
      "source": "crossref",
      "url": "https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btag768/8913739"
    },
    {
      "first_seen": "2026-11-02T12:22:28Z",
      "native_id": "PMC13718435",
      "source": "pmc",
      "url": "https://doi.org/10.1093/bioinformatics/btag768"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Biomedical Text Mining and Ontologies",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Letters and biological process: linguistic structure encodes hierarchical depth in the gene ontology",
  "title_text": "Letters and biological process: linguistic structure encodes hierarchical depth in the gene ontology",
  "type": "peer-reviewed",
  "updated_at": "2026-11-02T12:22:28Z",
  "url": "https://research.draconitic.com/paper/c0c0twnq4v9np",
  "venue": "Bioinformatics",
  "versions": []
}