ArticleAmerican journal of human genetics2015
The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.
Article in American journal of human genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 119 papers, 2 of them syntheses that pooled it.
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Who cites it
119 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Computational resources associating diseases with genotypes, phenotypes and exposures.Briefings in bioinformatics · 2019Pooled it
- Natural language processing systems for capturing and standardizing unstructured clinical information: A systematic review.Journal of biomedical informatics · 2017Pooled it
- Transcriptome-Based Classification of Resected Pancreatic Ductal Adenocarcinoma Enhances Prognostic Modelling Accuracy of Overall Survival Following Adjuvant Treatment.International journal of cancer · 2026Article
- Systematic identification of rare disease patients in electronic health records enables evaluation of clinical outcomes.Scientific reports · 2026Article
- Application of knowledge graphs in rare disease research.Frontiers in public health · 2026Review
- PERADIGM: Phenotype embedding similarity-based rare disease gene mapping.PLoS genetics · 2025Article
- Improving computational drug repositioning through multi-source disease similarity networks.Scientific reports · 2025Article
- Impact of Preexisting Rare Diseases on COVID-19 Severity, Reinfection, and Long COVID, and the Modifying Effects of Vaccination and Antiviral Therapy: A Retrospective Study from the N3C Data Enclave.medRxiv : the preprint server for health sciences · 2025Article
- A Copernican revolution of multigenic analysis: A retrospective study on clinical exome sequencing in unclear genetic disorders.Computational and structural biotechnology journal · 2024Article
- Predicting gene disease associations with knowledge graph embeddings for diseases with curtailed information.NAR genomics and bioinformatics · 2024Article
- Electronic health record signatures identify undiagnosed patients with common variable immunodeficiency disease.Science translational medicine · 2024Article
- PheSeq, a Bayesian deep learning model to enhance and interpret the gene-disease association studies.Genome medicine · 2024Article
- Text mining for contexts and relationships in cancer genomics literature.Bioinformatics (Oxford, England) · 2024Article
- The impact of the Turkish population variome on the genomic architecture of rare disease traits.Genetics in medicine open · 2024Article
- AI-based tools for the diagnosis and treatment of rare neurological disorders.Nature reviews. Neurology · 2023Article
- Identification and validation of subclusters of papillary thyroid carcinoma based on Human Phenotype Ontology.Gland surgery · 2023Article
- Ontology-driven and weakly supervised rare disease identification from clinical notes.BMC medical informatics and decision making · 2023Article
- Enriching representation learning using 53 million patient notes through human phenotype ontology embedding.Artificial intelligence in medicine · 2023Article
- Automated prioritization of sick newborns for whole genome sequencing using clinical natural language processing and machine learning.Genome medicine · 2023Article
- IMPROVE-DD: Integrating multiple phenotype resources optimizes variant evaluation in genetically determined developmental disorders.HGG advances · 2023Article
59 more citing papers are in PubMed but not listed here.
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Authors and funding
19 authors.
Funding
Abstract
The Human Phenotype Ontology (HPO) is widely used in the rare disease community for differential diagnostics, phenotype-driven analysis of next-generation sequence-variation data, and translational research, but a comparable resource has not been available for common disease. Here, we have developed a concept-recognition procedure that analyzes the frequencies of HPO disease annotations as identified in over five million PubMed abstracts by employing an iterative procedure to optimize precision and recall of the identified terms. We derived disease models for 3,145 common human diseases comprising a total of 132,006 HPO annotations. The HPO now comprises over 250,000 phenotypic annotations for over 10,000 rare and common diseases and can be used for examining the phenotypic overlap among common diseases that share risk alleles, as well as between Mendelian diseases and common diseases linked by genomic location. The annotations, as well as the HPO itself, are freely available.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.