CISBAN Meetings & Conferences Standards

1st RSBI Workshop, 6-8 December 2007

Last week I attended the first RSBI (Reporting Structure for Biological Investigations) Workshop, carrying with me a multitude of hats. RSBI is a working group committed to the progression of standardization in multi-omics investigations. The purpose of the workshop was to examine and offer suggestions on the initial draft of ISA-TAB (more on that in a moment).

My first hat was a FuGE-user's hat, as the triumvirate of standards upon which RSBI is built is the Functional Genomics Experiment Model (FuGE), the Minimum Information for Biological and Biomedical Investigations (MIBBI) Project, and the Ontology for Biomedical Investigations (OBI). I was asked to give a current status update on FuGE itself, and on any communities that have already built extensions to FuGE. Andy Jones from Liverpool provided me with all of the hot-off-the-press information (my FuGE slides) – thanks Andy!

My second hat was a SyMBA-developer's hat. SyMBA uses FuGE to build a database and web front-end for storing data and experimental metadata. We use it in-house to store all of our large, high-throughput 'omics data. The use of FuGE in the system made it relevant for the workshop (my SyMBA slides, more SyMBA slides).

My final hat was a CISBAN-employee's hat. I work in the Wipat group there, and CISBAN is one of the "leading groups" involved in RSBI. As such, I was CISBAN's representative to the workshop.

The reason for the workshop, as stated earlier, was the evaluation of ISA-TAB, a proposed tabular format whose purpose is to provide a standard format for data and metadata submission into the formative BioMAP database at the EBI. ISA-TAB would have two uses:

  1. Humans: As a tabular format, it is quite easy for people to view and manipulate such templates within spreadsheet software such as Excel.
  2. Computers: As an interim solution only, ISA-TAB would be used as a computational exchange format until such time as each of the FuGE-based community extensions are complete for Metabolomics, Proteomics, and Transcriptomics. At this time, ISA-TAB would remain available for human use, but there would be a conversion step into "FuGE-ML".

The scope for ISA-TAB is large, and this was reflected in the attendees of the meeting. Representatives from ArrayExpress, Pride, and BioMAP were of course present, but also attending were people from the Metabolomics community, the MIACA project, toxico- and environmental genomics, and the FDA's NCTR.

A full write-up of the results of the workshop will soon be available online at the project's RSBI Google Group, so I'll leave it there. It was an exciting meeting, with fantastic food and even better discussions on getting public databases organized quickly for simple, straightforward multi-omics investigation data and metadata submission.

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By Allyson Lister

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