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PhenDisco: phenotype discovery system for the database of genotypes and phenotypes
Son Doan1, Ko-Wei Lin, Mike Conway
1Division of Biomedical Informatics, University of California San Diego, La Jolla, California, USA.
Journal of the American Medical Informatics Association : JAMIA
|August 31, 2013
Summary
Phenotype discovery in large genetic databases like dbGaP is difficult due to non-standardized data. PhenDisco, a new system, standardizes phenotype information and improves search retrieval for genome-wide association studies (GWAS).
Area of Science:
- Genomics
- Bioinformatics
- Data Science
Background:
- The National Center for Biotechnology Information (NCBI) developed the database of genotypes and phenotypes (dbGaP) as a key resource for genome-wide association studies (GWAS).
- Accessing relevant GWAS data within dbGaP is challenging due to the non-standardized presentation of phenotype information.
- Existing search functionalities may not effectively retrieve studies based on specific phenotypic interests.
Purpose of the Study:
- To develop an improved information retrieval system for the dbGaP database.
- To address the challenge of finding relevant genome-wide association studies (GWAS) based on specific phenotypes.
- To enhance the usability and discoverability of phenotype data within dbGaP.
Main Methods:
- Development of PhenDisco, an information retrieval system comprising text processing and information retrieval tools.
- Phenotype variables and study metadata standardization using text processing.
- Implementation of query support and ranked result return functionalities for users.
Main Results:
- PhenDisco demonstrated promising performance in preliminary comparisons against dbGaP's Entrez search engine.
- The system showed effectiveness in both unranked and ranked search scenarios across 18 test cases.
- Standardization of phenotype data improved the ability to discover relevant studies.
Conclusions:
- PhenDisco offers a valuable solution for navigating and retrieving phenotype-specific GWAS data from dbGaP.
- The developed system enhances research efficiency by simplifying the discovery of relevant genetic studies.
- PhenDisco provides a standardized and effective approach to phenotype-based data retrieval in large genetic databases.
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