Towards the integration of mouse databases - definition and implementation of solutions to two use-cases in mouse functional genomics.
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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.
CitationTowards the integration of mouse databases - definition and implementation of solutions to two use-cases in mouse functional genomics. 2010, 3 (1):16notBMC Res Notes
AffiliationDepartment of Infection Genetics, Helmholtz Centre for Infection Research & University of Veterinary Medicine Hannover, Inhoffenstr, 7, D-38124 Braunschweig, Germany. firstname.lastname@example.org.
JournalBMC research notes
The following license files are associated with this item:
- Atlas - a data warehouse for integrative bioinformatics.
- Authors: Shah SP, Huang Y, Xu T, Yuen MM, Ling J, Ouellette BF
- Issue date: 2005 Feb 21
- Solutions for data integration in functional genomics: a critical assessment and case study.
- Authors: Smedley D, Swertz MA, Wolstencroft K, Proctor G, Zouberakis M, Bard J, Hancock JM, Schofield P
- Issue date: 2008 Nov
- The Gaggle: an open-source software system for integrating bioinformatics software and data sources.
- Authors: Shannon PT, Reiss DJ, Bonneau R, Baliga NS
- Issue date: 2006 Mar 28
- Mitochondrial Disease Sequence Data Resource (MSeqDR): a global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities.
- Authors: Falk MJ, Shen L, Gonzalez M, Leipzig J, Lott MT, Stassen AP, Diroma MA, Navarro-Gomez D, Yeske P, Bai R, Boles RG, Brilhante V, Ralph D, DaRe JT, Shelton R, Terry SF, Zhang Z, Copeland WC, van Oven M, Prokisch H, Wallace DC, Attimonelli M, Krotoski D, Zuchner S, Gai X, MSeqDR Consortium Participants., MSeqDR Consortium participants: Sherri Bale, Jirair Bedoyan, Doron Behar, Penelope Bonnen, Lisa Brooks, Claudia Calabrese, Sarah Calvo, Patrick Chinnery, John Christodoulou, Deanna Church,., Rosanna Clima, Bruce H. Cohen, Richard G. Cotton, IFM de Coo, Olga Derbenevoa, Johan T. den Dunnen, David Dimmock, Gregory Enns, Giuseppe Gasparre,., Amy Goldstein, Iris Gonzalez, Katrina Gwinn, Sihoun Hahn, Richard H. Haas, Hakon Hakonarson, Michio Hirano, Douglas Kerr, Dong Li, Maria Lvova, Finley Macrae, Donna Maglott, Elizabeth McCormick, Grant Mitchell, Vamsi K. Mootha, Yasushi Okazaki,., Aurora Pujol, Melissa Parisi, Juan Carlos Perin, Eric A. Pierce, Vincent Procaccio, Shamima Rahman, Honey Reddi, Heidi Rehm, Erin Riggs, Richard Rodenburg, Yaffa Rubinstein, Russell Saneto, Mariangela Santorsola, Curt Scharfe,., Claire Sheldon, Eric A. Shoubridge, Domenico Simone, Bert Smeets, Jan A. Smeitink, Christine Stanley, Anu Suomalainen, Mark Tarnopolsky, Isabelle Thiffault, David R. Thorburn, Johan Van Hove, Lynne Wolfe, and Lee-Jun Wong.
- Issue date: 2015 Mar
- The Mouse Genome Database (MGD): updates and enhancements.
- Authors: Blake JA, Eppig JT, Bult CJ, Kadin JA, Richardson JE, Mouse Genome Database Group.
- Issue date: 2006 Jan 1