{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T12:44:38Z","timestamp":1791895478581,"version":"4.3.4"},"reference-count":0,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T00:00:00Z","timestamp":1791849600000},"content-version":"am","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>We asked whether the natural language used to name Gene Ontology (GO) Biological Process terms encodes hierarchical position in the GO directed acyclic graph.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Semantic representations of term names, combined with UMAP visualization and k-means clustering (k=20) recovered biologically coherent semantic groups whose depth distributions differed strongly (Kruskal\u2013Wallis H=5244, p&amp;lt;10\u2212300; \u03b72=0.217). Term-name length increased with depth (Pearson r=0.34, Spearman \u03c1=0.37; slope \u22483.2 letters per level), and this positive scaling held under shortest-, longest-, and average-path depth definitions. Vocabulary entropy followed a bell-shaped diversification\u2013specialization 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\u2013hierarchical association.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>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).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag768","type":"journal-article","created":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T11:37:20Z","timestamp":1791891440000},"source":"Crossref","is-referenced-by-count":0,"title":["Letters and Biological Process: Linguistic Structure Encodes Hierarchical Depth in the Gene Ontology"],"prefix":"10.1093","author":[{"given":"Sadiya","family":"Ahmad","sequence":"first","affiliation":[{"name":"Iowa State University Department of Computer Science, , Ames, IA 50011,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,10,13]]},"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btag768\/71904174\/btag768.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btag768\/71904174\/btag768.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T11:45:53Z","timestamp":1791891953000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article\/doi\/10.1093\/bioinformatics\/btag768\/8913739"}},"subtitle":[],"editor":[{"given":"Daisuke","family":"Kihara","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,10,13]]},"references-count":0,"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btag768","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,13]]},"article-number":"btag768"}}