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Ontology, a growing discipline in the semantic web, enables hierarchical domain representation, thereby allowing finer data access to be achieved. Deep Learning (DL) supports pattern recognition in Electronic Health Records (EHR), which include patient demographics and diagnosis histories. Prescribing medications with minimal adverse effects is crucial, particularly for patients who require multiple drugs, as drug interactions can result in more complex conditions. This study introduces an integrated approach that combines Ontology with DL neural networks to improve prescription accuracy. This study proposes NexusOpti, a model featuring an Enhanced Gated Recurrent Unit (E-GRU) layer. To understand drug\u2013disease interactions, hierarchical data were extracted from the International Classification of Diseases (ICD) and Anatomical Therapeutic Chemical (ATC) ontologies. These structured data were processed using a self-attention mechanism to enhance the recommendation precision. This integration not only addresses data security concerns but also improves the accuracy of the medicine recommendations. The model was evaluated using key metrics such as the hit ratio and normalised discounted cumulative gain (NDCG). The NexusOpti model, incorporating the Enhanced Gated Recurrent Unit (E-GRU) layer, outperforms the existing GRU model in terms of NDCG and Hit Ratio metrics. 13% of improvement in performance was oberved to the comparison between NexusOpti with the E-GRU and the GRAM baseline model. These findings highlight the effectiveness of the model in advancing personalised, safer, and data-driven medication prescriptions.<\/jats:p>","DOI":"10.1038\/s41598-026-48044-x","type":"journal-article","created":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T08:25:55Z","timestamp":1785745555000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Precision pharmacology: deep learning infused ontological framework with E-GRU enhancement for tailored medicine prescriptions"],"prefix":"10.1038","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1847-1981","authenticated-orcid":false,"given":"Harichandra","family":"Khalingarajah","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9866-4045","authenticated-orcid":false,"given":"Asokan","family":"Vasudevan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5957-2906","authenticated-orcid":false,"given":"P.","family":"Abinaya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3227-4439","authenticated-orcid":false,"given":"T.","family":"Manonmani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2135-3051","authenticated-orcid":false,"given":"N.","family":"Raja","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,8,3]]},"reference":[{"key":"48044_CR1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1109\/JTEHM.2020.3040236","volume":"9","author":"G Tsang","year":"2020","unstructured":"Tsang, G., Zhou, S. 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