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

2.50
Hdl Handle:
http://hdl.handle.net/10033/96658
Title:
Towards the integration of mouse databases - definition and implementation of solutions to two use-cases in mouse functional genomics.
Authors:
Gruenberger, Michael; Alberts, Rudi; Smedley, Damian; Swertz, Morris; Schofield, Paul; Schughart, Klaus ( 0000-0002-6824-7523 )
Abstract:
ABSTRACT: 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.
Affiliation:
Department of Infection Genetics, Helmholtz Centre for Infection Research & University of Veterinary Medicine Hannover, Inhoffenstr, 7, D-38124 Braunschweig, Germany. kls@helmholtz-hzi.de.
Citation:
Towards the integration of mouse databases - definition and implementation of solutions to two use-cases in mouse functional genomics. 2010, 3 (1):16notBMC Res Notes
Journal:
BMC research notes
Issue Date:
2010
URI:
http://hdl.handle.net/10033/96658
DOI:
10.1186/1756-0500-3-16
PubMed ID:
20205870
Type:
Article
Language:
null
ISSN:
1756-0500
Appears in Collections:
publications of the department infection genetics (INFG)

Full metadata record

DC FieldValue Language
dc.contributor.authorGruenberger, Michaelen
dc.contributor.authorAlberts, Rudien
dc.contributor.authorSmedley, Damianen
dc.contributor.authorSwertz, Morrisen
dc.contributor.authorSchofield, Paulen
dc.contributor.authorSchughart, Klausen
dc.date.accessioned2010-04-16T11:52:58Zen
dc.date.available2010-04-16T11:52:58Zen
dc.date.issued2010en
dc.identifier.citationTowards the integration of mouse databases - definition and implementation of solutions to two use-cases in mouse functional genomics. 2010, 3 (1):16notBMC Res Notesen
dc.identifier.issn1756-0500en
dc.identifier.pmid20205870en
dc.identifier.doi10.1186/1756-0500-3-16en
dc.identifier.urihttp://hdl.handle.net/10033/96658en
dc.description.abstractABSTRACT: 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.en
dc.languageENGen
dc.language.isonullen
dc.titleTowards the integration of mouse databases - definition and implementation of solutions to two use-cases in mouse functional genomics.en
dc.typeArticleen
dc.contributor.departmentDepartment of Infection Genetics, Helmholtz Centre for Infection Research & University of Veterinary Medicine Hannover, Inhoffenstr, 7, D-38124 Braunschweig, Germany. kls@helmholtz-hzi.de.en
dc.identifier.journalBMC research notesen

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