ArticleNucleic acids research2019
Doc2Hpo: a web application for efficient and accurate HPO concept curation.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed.
- PhenoSS: phenotype semantic similarity-based approach for rare disease prediction and patient clustering.Journal of the American Medical Informatics Association : JAMIA · 2026Article
- Harmonizing Multi-Institutional Clinical Documentation Using Natural Language Processing in Neurofibromatosis Type 1.Neurology. Clinical practice · 2026Observational
- RankVar: machine learning-based variant ranking and reinterpretation for rare genetic diseases.Genome medicine · 2026Article
- AutoPCR: automated phenotype concept recognition by prompting.Bioinformatics (Oxford, England) · 2026Article
- Note-Level Phenotyping of Multiple-Sclerosis Notes by a Large Language Model Achieves near Human-Level Agreement.Journal of clinical medicine · 2026Article
- Interpretable fine-tuned large language models facilitate making genetic test decisions for rare diseases.NPJ digital medicine · 2026Article
- PhenoSS: Phenotype semantic similarity-based approach for rare disease prediction and patient clustering.medRxiv : the preprint server for health sciences · 2026Article
- Clinical exome sequencing efficacy and phenotypic expansions involving non-isolated congenital anomalies of kidney and urinary tract (CAKUT+).European journal of human genetics : EJHG · 2025Article
- ClinFly: an all-in-one method to translate, de-identify, and summarize medical reports in HPO format.NAR genomics and bioinformatics · 2025Article
- Generative Models and Sentence Transformers for the Recognition and Normalization of Continuous and Discontinuous Phenotype Mentions: Model Development and Evaluation.JMIR medical informatics · 2025Article
- Improving automated deep phenotyping through large language models using retrieval-augmented generation.Genome medicine · 2025Article
- Automatic genetic phenotype normalization from dysmorphology physical examinations: an overview of the BioCreative VIII-Task 3 competition.Database : the journal of biological databases and curation · 2025Review
- A simplified retriever to improve accuracy of phenotype normalizations by large language models.Frontiers in digital health · 2025Article
- Enhancing human phenotype ontology term extraction through synthetic case reports and embedding-based retrieval: A novel approach for improved biomedical data annotation.Journal of pathology informatics · 2025Article
- Genetic landscape in undiagnosed patients with syndromic hearing loss revealed by whole exome sequencing and phenotype similarity search.Human genetics · 2025Article
- Phenotype driven molecular genetic test recommendation for diagnosing pediatric rare disorders.NPJ digital medicine · 2024Article
- PheNormGPT: a framework for extraction and normalization of key medical findings.Database : the journal of biological databases and curation · 2024Article
- Assessing the utility of large language models for phenotype-driven gene prioritization in the diagnosis of rare genetic disease.American journal of human genetics · 2024Article
- Fine-tuning large language models for rare disease concept normalization.Journal of the American Medical Informatics Association : JAMIA · 2024Article
- FastHPOCR: pragmatic, fast, and accurate concept recognition using the human phenotype ontology.Bioinformatics (Oxford, England) · 2024Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
We present Doc2Hpo, an interactive web application that enables interactive and efficient phenotype concept curation from clinical text with automated concept normalization using the Human Phenotype Ontology (HPO). Users can edit the HPO concepts automatically extracted by Doc2Hpo in real time, and export the extracted HPO concepts into gene prioritization tools. Our evaluation showed that Doc2Hpo significantly reduced manual effort while achieving high accuracy in HPO concept curation. Doc2Hpo is freely available at https://impact2.dbmi.columbia.edu/doc2hpo/. The source code is available at https://github.com/stormliucong/doc2hpo for local installation for protected health data.
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Registered trials
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.