title: PhenDisco: phenotype discovery system for the database of genotypes and phenotypes.
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.
authors.affiliation: Division of Biomedical Informatics, University of California San Diego, La Jolla, California, USA.
authors.forename: Son
authors.initials: S
authors.lastname: Doan
authors.forename: Ko-Wei
authors.initials: KW
authors.lastname: Lin
authors.forename: Mike
authors.initials: M
authors.lastname: Conway
authors.forename: Lucila
authors.initials: L
authors.lastname: Ohno-Machado
authors.forename: Alex
authors.initials: A
authors.lastname: Hsieh
authors.forename: Stephanie Feudjio
authors.initials: SF
authors.lastname: Feupe
authors.forename: Asher
authors.initials: A
authors.lastname: Garland
authors.forename: Mindy K
authors.initials: MK
authors.lastname: Ross
authors.forename: Xiaoqian
authors.initials: X
authors.lastname: Jiang
authors.forename: Seena
authors.initials: S
authors.lastname: Farzaneh
authors.forename: Rebecca
authors.initials: R
authors.lastname: Walker
authors.forename: Neda
authors.initials: N
authors.lastname: Alipanah
authors.forename: Jing
authors.initials: J
authors.lastname: Zhang
authors.forename: Hua
authors.initials: H
authors.lastname: Xu
authors.forename: Hyeon-Eui
authors.initials: HE
authors.lastname: Kim
mesh_terms: D000465:Algorithms; D030541:Databases, Genetic / Q000592:standards; D055106:Genome-Wide Association Study; D005838:Genotype; D006801:Humans; D007256:Information Systems; D010641:Phenotype; D013358:Subject Headings
keywords: DBGAP; GWAS; Information Retrieval; Natural Language Processing; Phenotype Standardization; Text Mining