MiMiR – an integrated platform for microarray data sharing, mining and analysis

Abstract

BackgroundDespite considerable efforts within the microarray community for standardising data format, content and description, microarray technologies present major challenges in managing, sharing, analysing and re-using the large amount of data generated locally or internationally. Additionally, it is recognised that inconsistent and low quality experimental annotation in public data repositories significantly compromises the re-use of microarray data for meta-analysis. MiMiR, the Microarray data Mining Resource was designed to tackle some of these limitations and challenges. Here we present new software components and enhancements to the original infrastructure that increase accessibility, utility and opportunities for large scale mining of experimental and clinical data.ResultsA user friendly Online Annotation Tool allows researchers to submit detailed experimental information via the web at the time of data generation rather than at the time of publication. This ensures the easy access and high accuracy of meta-data collected. Experiments are programmatically built in the MiMiR database from the submitted information and details are systematically curated and further annotated by a team of trained annotators using a new Curation and Annotation Tool. Clinical information can be annotated and coded with a clinical Data Mapping Tool within an appropriate ethical framework. Users can visualise experimental annotation, assess data quality, download and share data via a web-based experiment browser called MiMiR Online. All requests to access data in MiMiR are routed through a sophisticated middleware security layer thereby allowing secure data access and sharing amongst MiMiR registered users prior to publication. Data in MiMiR can be mined and analysed using the integrated EMAAS open source analysis web portal or via export of data and meta-data into Rosetta Resolver data analysis package.ConclusionThe new MiMiR suite of software enables systematic and effective capture of extensive experimental and clinical information with the highest MIAME score, and secure data sharing prior to publication. MiMiR currently contains more than 150 experiments corresponding to over 3000 hybridisations and supports the Microarray Centre's large microarray user community and two international consortia. The MiMiR flexible and scalable hardware and software architecture enables secure warehousing of thousands of datasets, including clinical studies, from microarray and potentially other -omics technologies.

Gene Expression Commons: An Open Platform for Absolute Gene Expression Profiling

“…In databases like Oncomine, Flymine [13], Ingenuity, EMAAS [14], MiMiR [15] and many others around the world, microarray data can be imported, queried and visualized for a selected gene across all analyses or for multiple genes in a selected analysis. However, none of these databases provide an analysis platform for absolute gene expression profiling.…”

Exploring the use of internal and externalcontrols for assessing microarray technical performance

“…These reports are included in the MiMiR database, together with the individual hybridization files and experimental ontology and annotation information [25,26]. …”

EMAAS: An extensible grid-based Rich Internet Application for microarray data analysis and management

“…MiMiR is a MIAME-compliant microarray data warehouse supporting over 200 research group at the MRC Clinical Science Centre/Imperial College and 2 international consortia [ 25 ]. MiMiR provides a secure environment for collection, capture, comprehensive and consistent experimental annotation and dissemination of data [ 26 ]. It is fully integrated with EMAAS through the EMAAS-MiMiR web interface, see Figure 3 for screenshots.…”