ArticleJournal of biomedical semantics2017
Investigations on factors influencing HPO-based semantic similarity calculation.
Article in Journal of biomedical semantics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Mitochondrial DNA disease discovery through evaluation of genotype and phenotype data: The Solve-RD experience.American journal of human genetics · 2025Article
- Pheno-Ranker: a toolkit for comparison of phenotypic data stored in GA4GH standards and beyond.BMC bioinformatics · 2024Article
- Predicting disease-related phenotypes using an integrated phenotype similarity measurement based on HPO.BMC systems biology · 2019Article
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3 authors.
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Abstract
backgroundAlthough disease diagnosis has greatly benefited from next generation sequencing technologies, it is still difficult to make the right diagnosis purely based on sequencing technologies for many diseases with complex phenotypes and high genetic heterogeneity. Recently, calculating Human Phenotype Ontology (HPO)-based phenotype semantic similarity has contributed a lot for completing disease diagnosis. However, factors which affect the accuracy of HPO-based semantic similarity have not been evaluated systematically.
resultsIn this study, we proposed a new framework called HPOFactor to evaluate these factors. Our model includes four components: (1) the size of annotation set, (2) the evidence code of annotations, (3) the quality of annotations and (4) the coverage of annotations respectively.
conclusionsHPOFactor analyzes the four factors systematically based on two kinds of experiments: causative gene prediction and disease prediction. Furthermore, semantic similarity measurement could be designed based on the characteristic of these factors.
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