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/10033/620698
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
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.
Citation:
BMC Research Notes. 2010 Jan 22;3(1):16
Issue Date:
22-Jan-2010
URI:
http://dx.doi.org/10.1186/1756-0500-3-16; http://hdl.handle.net/10033/620698
Type:
Journal Article
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.accessioned2017-01-13T09:51:23Z-
dc.date.available2017-01-13T09:51:23Z-
dc.date.issued2010-01-22en
dc.identifier.citationBMC Research Notes. 2010 Jan 22;3(1):16en
dc.identifier.urihttp://dx.doi.org/10.1186/1756-0500-3-16en
dc.identifier.urihttp://hdl.handle.net/10033/620698-
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.titleTowards the integration of mouse databases - definition and implementation of solutions to two use-cases in mouse functional genomicsen
dc.typeJournal Articleen
dc.language.rfc3066enen
dc.rights.holderGruenberger et al.en
dc.date.updated2015-09-04T08:31:01Zen
All Items in HZI are protected by copyright, with all rights reserved, unless otherwise indicated.