Abstract
BackgroundMicroRNAs (miRNAs) are endogenous small RNAs that play a key role in post-transcriptional regulation of gene expression in animals and plants. The number of known miRNAs has increased rapidly over the years. The current release (version 14.0) of miRBase, the central online repository for miRNA annotation, comprises over 10.000 miRNA precursors from 115 different species. Furthermore, a large number of decentralized online resources are now available, each contributing with important miRNA annotation and information.ResultsWe have developed a software framework, designated here as miRMaid, with the goal of integrating miRNA data resources in a uniform web service interface that can be accessed and queried by researchers and, most importantly, by computers. miRMaid is built around data from miRBase and is designed to follow the official miRBase data releases. It exposes miRBase data as inter-connected web services. Third-party miRNA data resources can be modularly integrated as miRMaid plugins or they can loosely couple with miRMaid as individual entities in the World Wide Web. miRMaid is available as a public web service but is also easily installed as a local application. The software framework is freely available under the LGPL open source license for academic and commercial use.ConclusionmiRMaid is an intuitive and modular software platform designed to unify miRBase and independent miRNA data resources. It enables miRNA researchers to computationally address complex questions involving the multitude of miRNA data resources. Furthermore, miRMaid constitutes a basic framework for further programming in which microRNA-interested bioinformaticians can readily develop their own tools and data sources.
Highlights
MicroRNAs are endogenous small RNAs that play a key role in post-transcriptional regulation of gene expression in animals and plants
First of all, miRMaid is a software framework aiming at easing the manual workload for researchers when doing computational analyses involving miRNA data. miRMaid provides a uniform, intuitive and flexible application interface that is independent of programming language. miRMaid is designed to live as a public service as well as being installed locally
The local installation is recommended when a more data extensive analysis is needed. miRMaid is open-source software and users can contribute to the framework through the public source code repository or they can develop a miRMaid plugin that can be shared with the rest of the community
Summary
We have developed a software framework, designated here as miRMaid, with the goal of integrating miRNA data resources in a uniform web service interface that can be accessed and queried by researchers and, most importantly, by computers. miRMaid is built around data from miRBase and is designed to follow the official miRBase data releases. MiRMaid is built around data from miRBase and is designed to follow the official miRBase data releases. We have developed a software framework, designated here as miRMaid, with the goal of integrating miRNA data resources in a uniform web service interface that can be accessed and queried by researchers and, most importantly, by computers. It exposes miRBase data as inter-connected web services. MiRMaid constitutes a basic framework for further programming in which microRNA-interested bioinformaticians can readily develop their own tools and data sources
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