The ISA infrastructure: from experimental planning to data publication and case studies in toxicology
The ISA infrastructure: from experimental planning to data publication
ISA stands for Investigation/Study/Assay and it is an infrastructure (http://isa-tools.org) composed of the generic and tabular ISA-TAB format and a set of software tools facilitating the management of bioscience experimental data . The format supports the description of multi-omic experiments and each software tool in the infrastructure facilitates one or more tasks related to data management in the life sciences, environmental or biomedical domains. The ISAcreator tool supports experimental planning based on design of experiments concepts and the description of the investigation, including protocols and assays. It can be configured to, for example, comply with minimum information checklists and to use certain ontologies for annotation by using the ISAconfigurator tool. There are also tools for storage and querying (BioInvestigation Index manager, web application and database), for interfacing with data analysis platforms (Risa for R/Bioconductor, GenomeSpace, Galaxy) and for conversion to multiple formats, including those required by public repositories (e.g. MAGE-TAB for ArrayExpress, PRIDE-XML for PRIDE) and the Resource Description Framework (RDF) for use in Semantic Web/Linked Data applications. Data publication platforms such as Nature Publishing Group Scientific Data and BioMed Central GigaScience database support the ISA-TAB format.
The community of users and collaborators is grouped under the ISA commons (http://isacommons.org) and its members belong to academic and industrial organisations worldwide working in a wide range of domains. In the systems toxicology and toxicogenomics domains, the ToxBank Data Warehouse  relies on the ISA-TAB format and the OpenTox standards.
This presentation will describe the ISA infrastructure and provide specific examples of its advantages, with focus on the the toxicology domain.
 Rocca-Serra et al. ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. Bioinformatics 2010.
 Kohonen et al. The ToxBank Data Warehouse: Supporting the Replacement of In Vivo Repeated Dose Systemic Toxicity Testing. Molecular Informatics. 2013