PhenDisco: phenotype discovery system for the database of genotypes and phenotypes.

TitlePhenDisco: phenotype discovery system for the database of genotypes and phenotypes.
Publication TypeJournal Article
Year of Publication2013
AuthorsDoan S, Lin K-W, Conway M, Ohno-Machado L, Hsieh A, Feupe S F, Garland A, Ross MK, Jiang X, Farzaneh S, Walker R, Alipanah N, Zhang J, Xu H, Kim H-E
JournalJ Am Med Inform Assoc
Date Published2013 Sep 3
ISSN1527-974X
Abstract

The database of genotypes and phenotypes (dbGaP) developed by the National Center for Biotechnology Information (NCBI) is a resource that contains information on various genome-wide association studies (GWAS) and is currently available via NCBI's dbGaP Entrez interface. The database is an important resource, providing GWAS data that can be used for new exploratory research or cross-study validation by authorized users. However, finding studies relevant to a particular phenotype of interest is challenging, as phenotype information is presented in a non-standardized way. To address this issue, we developed PhenDisco (phenotype discoverer), a new information retrieval system for dbGaP. PhenDisco consists of two main components: (1) text processing tools that standardize phenotype variables and study metadata, and (2) information retrieval tools that support queries from users and return ranked results. In a preliminary comparison involving 18 search scenarios, PhenDisco showed promising performance for both unranked and ranked search comparisons with dbGaP's search engine Entrez. The system can be accessed at http://pfindr.net.

DOI10.1136/amiajnl-2013-001882
PubMed URLhttp://www.ncbi.nlm.nih.gov/pubmed/23989082?dopt=Abstract
PMCPMC3912702
Alternate JournalJ Am Med Inform Assoc
PubMed ID23989082
Track(s): 
Biomedical Informatics