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Doc2Hpo: a web application for efficient and accurate HPO concept curation.
Cong Liu1, Fabricio Sampaio Peres Kury1, Ziran Li1
1Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA.
Nucleic Acids Research
|May 21, 2019
Summary
Doc2Hpo is a web tool that efficiently curates phenotype concepts from clinical text using the Human Phenotype Ontology (HPO). It reduces manual effort and improves accuracy for gene prioritization.
Area of Science:
- Biomedical Informatics
- Clinical Genomics
- Natural Language Processing
Background:
- Accurate phenotype concept curation from clinical text is crucial for genetic research and gene prioritization.
- Manual curation is time-consuming and prone to errors.
- Automated methods are needed to streamline this process.
Purpose of the Study:
- To introduce Doc2Hpo, an interactive web application for efficient phenotype concept curation.
- To enable automated concept normalization using the Human Phenotype Ontology (HPO).
- To facilitate the export of curated HPO concepts for gene prioritization.
Main Methods:
- Development of an interactive web application, Doc2Hpo.
- Implementation of automated concept extraction and normalization using HPO.
- Real-time editing capabilities for user-guided curation.
- Functionality for exporting HPO concepts.
Main Results:
- Doc2Hpo significantly reduces manual effort in HPO concept curation.
- The application achieves high accuracy in extracting and normalizing phenotype concepts.
- Interactive features enhance the efficiency and usability of the curation process.
Conclusions:
- Doc2Hpo offers an effective solution for phenotype concept curation from clinical text.
- The tool supports gene prioritization by providing accurate and efficient HPO concept extraction.
- Doc2Hpo is freely available, promoting its adoption in research and clinical settings.
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