ArticlePloS one2015
HPOSim: an R package for phenotypic similarity measure and enrichment analysis based on the human phenotype ontology.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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38 citing papers in PubMed.
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- Drug Repurposing for Non-Alcoholic Fatty Liver Disease by Analyzing Networks Among Drugs, Diseases, and Genes.Metabolites · 2025Article
- Improving patient clustering by incorporating structured variable label relationships in similarity measures.BMC medical research methodology · 2025Article
- An AI-based approach driven by genotypes and phenotypes to uplift the diagnostic yield of genetic diseases.Human genetics · 2025Article
- Pheno-Ranker: a toolkit for comparison of phenotypic data stored in GA4GH standards and beyond.BMC bioinformatics · 2024Article
- IDeRare: a lightweight and extensible open-source phenotype and exome analysis pipeline for germline rare disease diagnosis.JAMIA open · 2024Article
- DiSMVC: a multi-view graph collaborative learning framework for measuring disease similarity.Bioinformatics (Oxford, England) · 2024Article
- PheSom: a term frequency-based method for measuring human phenotype similarity on the basis of MeSH vocabulary.Frontiers in genetics · 2023Article
- PhenoExam: gene set analyses through integration of different phenotype databases.BMC bioinformatics · 2022Article
- Approach to Cohort-Wide Re-Analysis of Exome Data in 1000 Individuals with Neurodevelopmental Disorders.Genes · 2022Article
- A Novel FrameshiftBiomedicines · 2022Article
- Gene-SCOUT: identifying genes with similar continuous trait fingerprints from phenome-wide association analyses.Nucleic acids research · 2022Article
- Clinical diagnosis of metabolic disorders using untargeted metabolomic profiling and disease-specific networks learned from profiling data.Scientific reports · 2022Article
- The similarity of inherited diseases (I): clinical similarity within the phenotypic series.BMC medical genomics · 2021Article
- SVInterpreter: A Comprehensive Topologically Associated Domain-Based Clinical Outcome Prediction Tool for Balanced and Unbalanced Structural Variants.Frontiers in genetics · 2021Article
- Phenotype-genotype comorbidity analysis of patients with rare disorders provides insight into their pathological and molecular bases.PLoS genetics · 2020Article
- Evaluation of standard and semantically-augmented distance metrics for neurology patients.BMC medical informatics and decision making · 2020Article
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4 authors.
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Abstract
backgroundPhenotypic features associated with genes and diseases play an important role in disease-related studies and most of the available methods focus solely on the Online Mendelian Inheritance in Man (OMIM) database without considering the controlled vocabulary. The Human Phenotype Ontology (HPO) provides a standardized and controlled vocabulary covering phenotypic abnormalities in human diseases, and becomes a comprehensive resource for computational analysis of human disease phenotypes. Most of the existing HPO-based software tools cannot be used offline and provide only few similarity measures. Therefore, there is a critical need for developing a comprehensive and offline software for phenotypic features similarity based on HPO.
resultsHPOSim is an R package for analyzing phenotypic similarity for genes and diseases based on HPO data. Seven commonly used semantic similarity measures are implemented in HPOSim. Enrichment analysis of gene sets and disease sets are also implemented, including hypergeometric enrichment analysis and network ontology analysis (NOA).
conclusionsHPOSim can be used to predict disease genes and explore disease-related function of gene modules. HPOSim is open source and freely available at SourceForge (https://sourceforge.net/p/hposim/).
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