To collect investigation data in a consistent manner across the cluster, the ToxBank consortium selected to use ISAcreator, an open access tool (http://isatab.sourceforge.net/isahelp/ch03.html). ISAcreator provides a graphical user interface to create a consistently recorded series of data files that include the experimental design and information concerning the overall investigation, information on the experimental steps linked to both protocols as well as raw or processed data files.
The ISAcreator tool has been successfully used to generate data concerning a diverse series of experiments, including transcriptomics studies. The tool provides a series of forms for entering the information and can generate an archive of the entire investigation in the ISA-TAB format. This tool is essential for entering information in a consistent manner. The tool design as OSGI compliant framework, allows extending its functionality by developing custom ontology lookup plugins. SEURAT-1 specific resources (users and organizations as well as SEURAT-1 protocols and keywords) are integrated via a custom ToxBank plugin (https://github.com/ToxBank/toxbank-isa-plugin), utilizing ToxBank REST API client (https://github.com/ToxBank/toxbank-api-client ), and SEURAT specific ISAcreator installer. The following figure shows the ISAcreator user interface with fields that support integration with SEURAT-1 resources.
The ISA-TAB model allows experimental factors and other properties to be defined as ontology entries that require specific ontologies, facilitating the reuse of on-going ontology developments in bioinformatics. ChEBI and Unit Ontology are considered relevant for representing chemical compounds and measurement units; specific ontologies such as Cell Line Ontology will be identified and reused when designing templates for raw and processed biological data upload. SEURAT-1 allows the data to be annotated with entries from the keyword hierarchy, described in the section 3 of this document.
When the ISA-TAB document has been prepared in can be uploaded to the ToxBank Data Warehouse (TBDW). For a guide please see, Toxbank Guide.
Advanced Notes on comparison to other tools: The structure of an ISA-TAB archive is similar to the structure of the tables in a (normalized) relational database (RDBMS). Indeed, when converted to a Resource Description Format (RDF) an ISA-TAB archive could be used to build and populate an SQL database.
The structure of the archive is also similar to structure of the the R/Bioconductor eSet object. An eSet object consists of 1.) phenoData Contains variables describing sample 2.) assayData, contains matrices of values with equal dimensions, and with column number equal to nrow(phenoData), 3.) featureData Contains variables describing features (i.e., rows in assayData) unique to this experiment and 4.) experimentData, Contains details of experimental methods (Class: MIAME-class). Indeed, work is under way to enable creation of R/Bioconductor eSet objects directly from ISA-TAB archives (Risa-R/Bioconductor package).