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迈向小鼠数据库整合——小鼠功能基因组学中两个用例的解决方案定义与实施

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

作者信息

Gruenberger Michael, Alberts Rudi, Smedley Damian, Swertz Morris, Schofield Paul, Schughart Klaus

机构信息

Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK.

出版信息

BMC Res Notes. 2010 Jan 22;3:16. doi: 10.1186/1756-0500-3-16.

DOI:10.1186/1756-0500-3-16
PMID:20205870
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC2826352/
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.

摘要

背景

整合众多不同生物数据库中的信息是生物医学研究中的一项重大挑战。为了明确问题和需求，并探索小鼠功能基因组学中数据库整合的策略，我们咨询了生物学家用户群体，并针对两个用户定义的用例实施了解决方案。

结果

我们组织了研讨会、会议，并通过问卷调查来确定小鼠功能基因组学中生物学家数据库用户的需求。结果，开发了两个可用于推动未来小鼠数据库设计或扩展的用例。在此，我们展示这些用例并描述一些针对它们的初步计算解决方案。以基因为中心的用例“MUSIG-Gen”的应用程序从基因名称列表开始，以类似“购物车”的方式从多个分布式数据库收集广泛的数据类型。这种迭代的用户驱动方法是对用户，尤其是那些没有计算生物学背景的用户强烈请求的回应。以表型为中心的用例“MUSIG-Phen”的应用程序基于类似的概念，从表型描述开始检索相关基因的信息。

结论

创建的用例及其原型软件实现应有助于更好地定义生物学家对数据库整合的需求，并可作为未来针对终端用户生物学家的生物信息学解决方案的起点。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa52/2826352/b6f39e780354/1756-0500-3-16-8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa52/2826352/07e456411e54/1756-0500-3-16-1.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa52/2826352/07e456411e54/1756-0500-3-16-1.jpg
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本文引用的文献

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Solutions for data integration in functional genomics: a critical assessment and case study.功能基因组学中的数据整合解决方案：批判性评估与案例研究
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Data curation + process curation=data integration + science.数据管理 + 流程管理 = 数据整合 + 科学。
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