Modeling and Managing Experimental Data Using FuGE

Want to share your umpteen multi-omics data sets and experimental protocols with one common format? Encourage collaboration! Speak a common language! Share your work! How, you might ask? With FuGE!

In 2007, FuGE version 1 was released (website, Nature Biotechnology paper). FuGE allows biologists and bioinformaticians to describe any life science experiment using a single format, making collaboration and repeatability of experiments easier and more efficient. However, if you wanted to start using FuGE, until now it was difficult to know where to start. Do you use FuGE as it stands? Do you create an extension of FuGE that specifically meets your needs? What do the developers of FuGE suggest when taking your first steps using it? This paper focuses on best practices for using FuGE to model and manage your experimental data. Read this paper, and you’ll be taking your first steps with confidence!

ResearchBlogging.org

Want to share your umpteen multi-omics data sets and experimental protocols with one common format? Encourage collaboration! Speak a common language! Share your work! How, you might ask? With FuGE, and this latest paper (citation at the end of the post) tells you how.

In 2007, FuGE version 1 was released (website, Nature Biotechnology paper). FuGE allows biologists and bioinformaticians to describe any life science experiment using a single format, making collaboration and repeatability of experiments easier and more efficient. However, if you wanted to start using FuGE, until now it was difficult to know where to start. Do you use FuGE as it stands? Do you create an extension of FuGE that specifically meets your needs? What do the developers of FuGE suggest when taking your first steps using it? This paper focuses on best practices for using FuGE to model and manage your experimental data. Read this paper, and you’ll be taking your first steps with confidence!

[Aside: Please note that I am one of the authors of this paper.]

What is FuGE? I’ll leave it to the authors to define:

The approach of the Functional Genomics Experiment (FuGE) model is different, in that it attempts to generalize the modeling constructs that are shared across many omics techniques. The model is designed for three purposes: (1) to represent basic laboratory workflows, (2) to supplement existing data formats with metadata to give them context within larger workflows, and (3) to facilitate the development of new technology-specific formats. To support (3), FuGE provides extension points where developers wishing to create a data format for a specific technique can add constraints or additional properties.

A number of groups have started using FuGE, including MGED, PSI (for GelML and AnalysisXML), MSI, flow cytometry, RNA interference and e-Neuroscience (full details in the paper). This paper helps you get a handle on how to use FuGE by presenting two running examples of capturing experimental metadata in the fields of flow cytometry and proteomics of flow cytometry and gel electrophoresis. Part of Figure 2 from the paper is shown on the right, and describes one section of the flow cytometry FuGE extension from FICCS.

The flow cytometry equipment created as subclasses of the FuGE equipment class.
The flow cytometry equipment created as subclasses of the FuGE equipment class.

FuGE covers many areas of experimental metadata including the investgations, the protocols, the materials and the data. The paper starts by describing how protocols are designed in FuGE and how those protocols are applied. In doing so, it describes not just the protocols but also parameterization, materials, data, conceptual molecules, and ontology usage.

Examples of each of these FuGE packages are provided in the form of either the flow cytometry or the GelML extensions. Further, clear scenarios are provided to help the user determine when it is best to extend FuGE and when it is best to re-use existing FuGE classes. For instance, it is best to extend the Protocol class with an application-specific subclass when all of the following are true: when you wish to describe a complex Protocol that references specific sub-protocols, when the Protocol must be linked to specific classes of Equipment or Software, and when specific types of Parameter must be captured. I refer you to the paper for scenarios for each of the other FuGE packages such as Material and Protocol Application.

The paper makes liberal use of UML diagrams to help you understand the relationship between the generic FuGE classes and the specific sub-classes generated by extensions. A large part of the paper is concerned expressly with helping the user understand how to model an experiment type using FuGE, and also to understand when FuGE on its own is enough. But it also does more than that: it discusses the current tools that are already available for developers wishing to use FuGE, and it discusses the applicability of other implementations of FuGE that might be useful but do not yet exist. Validation of FuGE-ML and the storage of version information within the format are also described. Implementations of FuGE, including SyMBA and sysFusion for the XML format and ISA-TAB for compatibility with a spreadsheet (tab-delimited) format, are also summarised.

I strongly believe that the best way to solve the challenges in data integration faced by the biological community is to constantly strive to simply use the same (or compatible) formats for data and for metadata. FuGE succeeds in providing a common format for experimental metadata that can be used in many different ways, and with many different levels of uptake. You don’t have to use one of the provided STKs in order to make use of FuGE: you can simply offer your data as a FuGE export in addition to any other omics formats you might use. You could also choose to accept FuGE files as input. No changes need to be made to the underlying infrastructure of a project in order to become FuGE compatible. Hopefully this paper will flatten the learning curve associated for developers, and get them on the road to a common format. Just one thing to remember: formats are not something that the end user should see. We developers do all this hard work, but if it works correctly, the biologist won’t know about all the underpinnings! Don’t sell your biologists on a common format by describing the intricacies of FuGE to them (unless they want to know!), just remind them of the benefits of a common metadata standard: cooperation, collaboration, and sharing.

Jones, A., Lister, A.L., Hermida, L., Wilkinson, P., Eisenacher, M., Belhajjame, K., Gibson, F., Lord, P., Pocock, M., Rosenfelder, H., Santoyo-Lopez, J., Wipat, A., & Paton, N. (2009). Modeling and Managing Experimental Data Using FuGE OMICS: A Journal of Integrative Biology, 2147483647-13 DOI: 10.1089/omi.2008.0080