ArticleJAMIA open2023
Linking rare and common disease vocabularies by mapping between the human phenotype ontology and phecodes.
Article in JAMIA open, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Kernelized approach enables explainable gene prioritizations for complex traits.bioRxiv : the preprint server for biology · 2026Article
- Genetically supported drug target prioritization for rare diseases.Genome medicine · 2026Article
- Quantify unmet medical need across the disease landscape - A large language model-based methodology.PLoS medicine · 2026Article
- Residual allelic activity likely underlies the low rates of disease expression for predicted loss-of-function variants in population-scale biobanks.American journal of human genetics · 2025Article
- A scalable approach for genomic-first rare disorder detection in a healthcare-based population.American journal of human genetics · 2025Article
- Development of a genetic priority score to predict drug side effects using human genetic evidence.Nature communications · 2025Article
- Exclusion-based exome sequencing in critically ill adults 18-40 years old has a 24% diagnostic rate and finds racial disparities in access to genetic testing.American journal of human genetics · 2025Article
- Variants in BSN, encoding the presynaptic protein Bassoon, result in a distinct neurodevelopmental disorder with a broad phenotypic range.American journal of human genetics · 2025Article
- An interdisciplinary fetal neonatal neurology collaborative promotes integrative life-course brain health.Frontiers in neurology · 2025Review
- Implications of mappings between International Classification of Diseases clinical diagnosis codes and Human Phenotype Ontology terms.JAMIA open · 2024Article
- Expanding drug targets for 112 chronic diseases using a machine learning-assisted genetic priority score.Nature communications · 2024Article
- Universal Exome Sequencing in Critically Ill Adults: A Diagnostic Yield of 25% and Race-Based Disparities in Access to Genetic Testing.medRxiv : the preprint server for health sciences · 2024Article
- A deep learning transformer model predicts high rates of undiagnosed rare disease in large electronic health systems.medRxiv : the preprint server for health sciences · 2023Article
- Next-generation phenotyping: introducing phecodeX for enhanced discovery research in medical phenomics.Bioinformatics (Oxford, England) · 2023Article
- Linking rare and common disease vocabularies by mapping between the human phenotype ontology and phecodes.JAMIA open · 2023Article
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3 authors.
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Abstract
Enabling discovery across the spectrum of rare and common diseases requires the integration of biological knowledge with clinical data; however, differences in terminologies present a major barrier. For example, the Human Phenotype Ontology (HPO) is the primary vocabulary for describing features of rare diseases, while most clinical encounters use International Classification of Diseases (ICD) billing codes. ICD codes are further organized into clinically meaningful phenotypes via phecodes. Despite their prevalence, no robust phenome-wide disease mapping between HPO and phecodes/ICD exists. Here, we synthesize evidence using diverse sources and methods-including text matching, the National Library of Medicine's Unified Medical Language System (UMLS), Wikipedia, SORTA, and PheMap-to define a mapping between phecodes and HPO terms via 38 950 links. We evaluate the precision and recall for each domain of evidence, both individually and jointly. This flexibility permits users to tailor the HPO-phecode links for diverse applications along the spectrum of monogenic to polygenic diseases.
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