OntoTiger: a platform of ontology-based application tools for integrative biomedical exploration.

Journal: Nucleic acids research
Published Date: Jul 7, 2025

Abstract

Biomedical ontologies, such as Gene Ontology (GO), Disease Ontology (DO), and the Human Phenotype Ontology (HPO), have been extensively applied to characterize molecular roles and their semantic relationships in biomedical research and clinical practice. Although numerous algorithms have been developed to quantify relationships between ontology terms or to explore molecular functions, the absence of a comprehensive tool to integrate these algorithms has limited effective ontology applications. To address this, we developed OntoTiger, a platform of Ontology-based application Tools for InteGrativE biomedical exploRation. OntoTiger combines >20 classic algorithms, supporting six prevalent molecular types as well as five widespread biomedical ontologies. The platform comprises four modules: (i) Annotation module, which qualifies the relationships between ontology terms and molecules; (ii) Similarity module, quantifying functional similarity between/across pairwise ontology terms or between molecules; (iii) Prediction module, characterizing the molecular roles from an ontological perspective; and (iv) Enrichment module, elucidating the potential biological significance of a particular list of molecules. OntoTiger provides a freely accessible, user-friendly web server dedicated to enabling one-stop ontology-based applications and is freely available at https://bio-computing.hrbmu.edu.cn/OntoTiger.

Authors

  • Haixiu Yang
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China.
  • Guoyou He
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, Heilongjiang, China.
  • Meiyi Zhang
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China.
  • Hongyu Fu
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China.
  • Guanzhi He
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, Heilongjiang, China.
  • Chao Wang
    College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, China.
  • Yangyang Liu
    Department of Cardiology, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China.
  • Sainan Zhang
    Lab of Biomechatronics and Intelligent Robotics, Department of Mechanical and Aerospace Engineering, North Carolina State University, Raleigh, NC, USA.
  • Tao Wang
    Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
  • Yongqun Oliver He
    University of Michigan Medical School, Ann Arbor, MI, USA.
  • Liang Cheng
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150001, China. liangcheng@hrbmu.edu.cn.

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