SDRF2GRAPH: a visualization tool of a spreadsheet-based description of experimental processes

BMC Bioinformatics. 2009 May 7:10:133. doi: 10.1186/1471-2105-10-133.


Background: As larger datasets are produced with the development of genome-scale experimental techniques, it has become essential to explicitly describe the meta-data (information describing the data) generated by an experiment. The experimental process is a part of the meta-data required to interpret the produced data, and SDRF (Sample and Data Relationship Format) supports its description in a spreadsheet or tab-delimited file. This format was primarily developed to describe microarray studies in MAGE-tab, and it is being applied in a broader context in ISA-tab. While the format provides an explicit framework to describe experiments, increase of experimental steps makes it less obvious to understand the content of the SDRF files.

Results: Here, we describe a new tool, SDRF2GRAPH, for displaying experimental steps described in an SDRF file as an investigation design graph, a directed acyclic graph representing experimental steps. A spreadsheet, in Microsoft Excel for example, which is used to edit and inspect the descriptions, can be directly input via a web-based interface without converting to tab-delimited text. This makes it much easier to organize large contents of SDRF described in multiple spreadsheets.

Conclusion: SDRF2GRAPH is applicable for a wide range of SDRF files for not only microarray-based analysis but also other genome-scale technologies, such as next generation sequencers. Visualization of the Investigation Design Graph (IDG) structure leads to an easy understanding of the experimental process described in the SDRF files even if the experiment is complicated, and such visualization also encourages the creation of SDRF files by providing prompt visual feedback.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods*
  • Computer Graphics*
  • Databases, Genetic
  • Information Dissemination / methods
  • Information Storage and Retrieval / methods
  • Internet
  • Software*
  • User-Computer Interface