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

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 impor...

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Autores principales: Doan, Son, Lin, Ko-Wei, Conway, Mike, Ohno-Machado, Lucila, Hsieh, Alex, Feupe, Stephanie Feudjio, Garland, Asher, Ross, Mindy K, Jiang, Xiaoqian, Farzaneh, Seena, Walker, Rebecca, Alipanah, Neda, Zhang, Jing, Xu, Hua, Kim, Hyeon-Eui
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BMJ Publishing Group 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3912702/
https://www.ncbi.nlm.nih.gov/pubmed/23989082
http://dx.doi.org/10.1136/amiajnl-2013-001882
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author Doan, Son
Lin, Ko-Wei
Conway, Mike
Ohno-Machado, Lucila
Hsieh, Alex
Feupe, Stephanie Feudjio
Garland, Asher
Ross, Mindy K
Jiang, Xiaoqian
Farzaneh, Seena
Walker, Rebecca
Alipanah, Neda
Zhang, Jing
Xu, Hua
Kim, Hyeon-Eui
author_facet Doan, Son
Lin, Ko-Wei
Conway, Mike
Ohno-Machado, Lucila
Hsieh, Alex
Feupe, Stephanie Feudjio
Garland, Asher
Ross, Mindy K
Jiang, Xiaoqian
Farzaneh, Seena
Walker, Rebecca
Alipanah, Neda
Zhang, Jing
Xu, Hua
Kim, Hyeon-Eui
author_sort Doan, Son
collection PubMed
description 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.
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spelling pubmed-39127022014-02-04 PhenDisco: phenotype discovery system for the database of genotypes and phenotypes Doan, Son Lin, Ko-Wei Conway, Mike Ohno-Machado, Lucila Hsieh, Alex Feupe, Stephanie Feudjio Garland, Asher Ross, Mindy K Jiang, Xiaoqian Farzaneh, Seena Walker, Rebecca Alipanah, Neda Zhang, Jing Xu, Hua Kim, Hyeon-Eui J Am Med Inform Assoc Brief Communication 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. BMJ Publishing Group 2014-01 2013-08-29 /pmc/articles/PMC3912702/ /pubmed/23989082 http://dx.doi.org/10.1136/amiajnl-2013-001882 Text en Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions This is an Open Access article distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 3.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See: http://creativecommons.org/licenses/by-nc/3.0/
spellingShingle Brief Communication
Doan, Son
Lin, Ko-Wei
Conway, Mike
Ohno-Machado, Lucila
Hsieh, Alex
Feupe, Stephanie Feudjio
Garland, Asher
Ross, Mindy K
Jiang, Xiaoqian
Farzaneh, Seena
Walker, Rebecca
Alipanah, Neda
Zhang, Jing
Xu, Hua
Kim, Hyeon-Eui
PhenDisco: phenotype discovery system for the database of genotypes and phenotypes
title PhenDisco: phenotype discovery system for the database of genotypes and phenotypes
title_full PhenDisco: phenotype discovery system for the database of genotypes and phenotypes
title_fullStr PhenDisco: phenotype discovery system for the database of genotypes and phenotypes
title_full_unstemmed PhenDisco: phenotype discovery system for the database of genotypes and phenotypes
title_short PhenDisco: phenotype discovery system for the database of genotypes and phenotypes
title_sort phendisco: phenotype discovery system for the database of genotypes and phenotypes
topic Brief Communication
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3912702/
https://www.ncbi.nlm.nih.gov/pubmed/23989082
http://dx.doi.org/10.1136/amiajnl-2013-001882
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