ISA Infrastructure for Managing Experimental Metadata

The Investigation / Study / Assay (ISA) is a general purpose open source infrastructure with which to manage (collect, describe, store and communicate) metadata (i.e. sample characteristics, technologies used, type of measurements made) from complex studies employing a combination of technologies.

NEW: Download the ISA infrastructure overview, presented at ISMB 2009

Rationale

Today’s researchers can perform biological, biomedical and environmental studies where the same material is run through a wide range of assays, comprising several ‘omics (genomics, transcriptomics, proteomics and metabol/nomics) and conventional technologies, in combination.For example, consider a multi-assay study looking at the effect of a compound on a number of subjects by characterizing the metabolic profile of their urine (i.e. by mass spectroscopy), measuring protein and gene expression in the liver (i.e. by mass spectrometry and DNA microarrays, respectively), and conducting conventional analysis (i.e. histology).

To enable researchers to correctly interpret the complex data sets that result, and the conclusions drawn, it is necessary to report and record contextualizing experimental metadata at an appropriate level of granularity, using common terminologies and format.

Infrastructure Elements's Overview

To help managing the report of experimental metadata, we have developed the following ISA infrastructure’s elements:

ISA-Tab format to support the submission and exchange of the metadata and to render, in an effective way other XML -based metadata in user-friendly readable, common format. ISA-Tab has been developed in synergy with related, domain-specific effort, such as: MAGE TAB, FuGE, PSI and biomedical formats such as SDTM, complementing and extending where necessary. The decision on how to regulate its use (i.e. enforcing completion of mandatory fields or use of a controlled terminology) is beyond the scope of the ISA-Tab proposal, and are the focus of related effort, as as MIBBI and OBO Foundry. For further details, refer to the full specification documentation Release Candidate 1, ISA-TAB v1 (Nov 2008), view several examples files and read the first workshop report paper.

ISA-Tools, implementing ISA-Tab format and leveraging on MIBBI and OBO Foundry synergistic activities. The tools include the following a set of open source software components, which can work independently, or as unified system:

 

 

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