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Using Human Phenotype Ontology for Phenotypic Analysis of Clinical Notes
Feichen Shen1, Liwei Wang1, Hongfang Liu1
1Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.
Studies in Health Technology and Informatics
|January 4, 2018
Summary
This study explored using the Human Phenotype Ontology (HPO) to standardize phenotypic abnormalities in clinical notes. HPO aids in translating genetic information into observable characteristics for better disease understanding.
Area of Science:
- Clinical informatics
- Genomics
- Medical terminology
Background:
- Phenotypes represent observable traits of organisms.
- Translating genotype to phenotype is crucial for understanding human diseases.
- Standardized vocabularies are needed for computable phenotypic data.
Purpose of the Study:
- To investigate the utility of the Human Phenotype Ontology (HPO) for annotating phenotypic information within the clinical domain.
- To assess the feasibility of applying HPO to a large-scale clinical notes corpus.
Main Methods:
- Utilized a corpus of 12.8 million clinical notes.
- Data was collected from 729,000 patients between 2010 and 2015.
- Employed HPO as a standardized vocabulary for annotation.
Main Results:
- Successfully annotated phenotypic information using HPO.
- Demonstrated the potential of HPO in a real-world clinical data setting.
- Highlighted the value of standardized terminologies for clinical data.
Conclusions:
- HPO is a valuable tool for standardizing and annotating phenotypic abnormalities in clinical notes.
- Leveraging HPO can enhance the translation between genotype and phenotype.
- This approach supports improved data analysis and clinical research.
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