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Towards the integration of mouse databases - definition and implementation of solutions to two use-cases in mouse functional genomics

BACKGROUND: The integration of information present in many disparate biological databases represents a major challenge in biomedical research. To define the problems and needs, and to explore strategies for database integration in mouse functional genomics, we consulted the biologist user community...

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Autores principales: Gruenberger, Michael, Alberts, Rudi, Smedley, Damian, Swertz, Morris, Schofield, Paul, Schughart, Klaus
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2826352/
https://www.ncbi.nlm.nih.gov/pubmed/20205870
http://dx.doi.org/10.1186/1756-0500-3-16
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author Gruenberger, Michael
Alberts, Rudi
Smedley, Damian
Swertz, Morris
Schofield, Paul
Schughart, Klaus
author_facet Gruenberger, Michael
Alberts, Rudi
Smedley, Damian
Swertz, Morris
Schofield, Paul
Schughart, Klaus
author_sort Gruenberger, Michael
collection PubMed
description BACKGROUND: The integration of information present in many disparate biological databases represents a major challenge in biomedical research. To define the problems and needs, and to explore strategies for database integration in mouse functional genomics, we consulted the biologist user community and implemented solutions to two user-defined use-cases. RESULTS: We organised workshops, meetings and used a questionnaire to identify the needs of biologist database users in mouse functional genomics. As a result, two use-cases were developed that can be used to drive future designs or extensions of mouse databases. Here, we present the use-cases and describe some initial computational solutions for them. The application for the gene-centric use-case, "MUSIG-Gen" starts from a list of gene names and collects a wide range of data types from several distributed databases in a "shopping cart"-like manner. The iterative user-driven approach is a response to strongly articulated requests from users, especially those without computational biology backgrounds. The application for the phenotype-centric use-case, "MUSIG-Phen", is based on a similar concept and starting from phenotype descriptions retrieves information for associated genes. CONCLUSION: The use-cases created, and their prototype software implementations should help to better define biologists' needs for database integration and may serve as a starting point for future bioinformatics solutions aimed at end-user biologists.
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spelling pubmed-28263522010-02-23 Towards the integration of mouse databases - definition and implementation of solutions to two use-cases in mouse functional genomics Gruenberger, Michael Alberts, Rudi Smedley, Damian Swertz, Morris Schofield, Paul Schughart, Klaus BMC Res Notes Research article BACKGROUND: The integration of information present in many disparate biological databases represents a major challenge in biomedical research. To define the problems and needs, and to explore strategies for database integration in mouse functional genomics, we consulted the biologist user community and implemented solutions to two user-defined use-cases. RESULTS: We organised workshops, meetings and used a questionnaire to identify the needs of biologist database users in mouse functional genomics. As a result, two use-cases were developed that can be used to drive future designs or extensions of mouse databases. Here, we present the use-cases and describe some initial computational solutions for them. The application for the gene-centric use-case, "MUSIG-Gen" starts from a list of gene names and collects a wide range of data types from several distributed databases in a "shopping cart"-like manner. The iterative user-driven approach is a response to strongly articulated requests from users, especially those without computational biology backgrounds. The application for the phenotype-centric use-case, "MUSIG-Phen", is based on a similar concept and starting from phenotype descriptions retrieves information for associated genes. CONCLUSION: The use-cases created, and their prototype software implementations should help to better define biologists' needs for database integration and may serve as a starting point for future bioinformatics solutions aimed at end-user biologists. BioMed Central 2010-01-22 /pmc/articles/PMC2826352/ /pubmed/20205870 http://dx.doi.org/10.1186/1756-0500-3-16 Text en Copyright ©2010 Gruenberger et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research article
Gruenberger, Michael
Alberts, Rudi
Smedley, Damian
Swertz, Morris
Schofield, Paul
Schughart, Klaus
Towards the integration of mouse databases - definition and implementation of solutions to two use-cases in mouse functional genomics
title Towards the integration of mouse databases - definition and implementation of solutions to two use-cases in mouse functional genomics
title_full Towards the integration of mouse databases - definition and implementation of solutions to two use-cases in mouse functional genomics
title_fullStr Towards the integration of mouse databases - definition and implementation of solutions to two use-cases in mouse functional genomics
title_full_unstemmed Towards the integration of mouse databases - definition and implementation of solutions to two use-cases in mouse functional genomics
title_short Towards the integration of mouse databases - definition and implementation of solutions to two use-cases in mouse functional genomics
title_sort towards the integration of mouse databases - definition and implementation of solutions to two use-cases in mouse functional genomics
topic Research article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2826352/
https://www.ncbi.nlm.nih.gov/pubmed/20205870
http://dx.doi.org/10.1186/1756-0500-3-16
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