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Overview of AIMS

Assay and Data Management System (AIMS) serves as the central repository for genomic, transcriptomic, proteomic and metabolomic experimental data produced by the MolPAGE Consortium. The primary purpose of the repository is to collect complete datasets (both raw and analysed data) accompanied by essential metadata. For each of the analytical techniques we carried out the data submission requirement analysis and outlined the minimal lists of parameters which were to be captured about each assay. Where a standard data exchange format and/or reporting requirements were available (e.g., MIAME recommendations and MAGE-ML), the data submission was designed with consideration of the existing standards.

The basic design principles and software environment of AIMS are similar to those of the Sample Management System. The data repository uses the Oracle database and is accessible through a web-based interface. It has similar system configuration tools and navigation structure.

Data model

The central classes and some attributes of the assay information management system are shown in the Figure. Central classes and some attributes of the assay information management system. Experimental parameters are assigned to assays and to groups of assays – Study Groups. Only aliquots captured within the Sample Information Management System can be used for creation of new assay entries

The AIMS’s architecture is based on two entities: “Assays” and “Study groups”, to which different experimental parameters are assigned. The “Assay” term represents a measurement performed on a given aliquot (e.g. a single hybridization in microarray technology). Data and protocol files are referenced from this entry. The content of a particular assay entry is technology-specific and depends on the metadata parameters for this technology. Each assay-entry belongs to a “study group” - a number of acquisitions which according to the investigator should be stored and analyzed together due to the underlying experiment design. A vast choice of options for the metadata submission and editing ensures that the time needed for the formatting and uploading the results and metadata is kept to a minimum. Similarly to PASSIM, AIMS does not only provide the means for data collection but also facilitates some simple searches and report generation.