Papers Standards

BioSharing is Caring: Being FAIR

FAIR: Findable, Accessible, Interoperable, Reusable
Source: Scientific Data via March 16, 2016.

In my work for BioSharing, I get to see a lot of biological data standards. Although you might laugh at the odd dichotomy of multiple standards (rather than One Standard to Rule Them All), there are reasons for it. Some of those reasons are historical, such as a lack of cross-community involvement during inception of standards, and some are technical, such as vastly different requirements in different communities. The FAIR paper, published yesterday by Wilkinson et al. (and by a number of my colleagues at BioSharing) in Scientific Data, helps guide researchers towards the correct standards and databases by clarifying data stewardship and management requirements. If used correctly, a researcher can be assured that as long as a resource is FAIR, it’s fine.

This article describes four foundational principles—Findability, Accessibility, Interoperability, and Reusability—that serve to guide data producers and publishers as they navigate around these obstacles, thereby helping to maximize the added-value gained by contemporary, formal scholarly digital publishing. Importantly, it is our intent that the principles apply not only to ‘data’ in the conventional sense, but also to the algorithms, tools, and workflows that led to that data. All scholarly digital research objects—from data to analytical pipelines—benefit from application of these principles, since all components of the research process must be available to ensure transparency, reproducibility, and reusability.(doi:10.1038/sdata.2016.18)

This isn’t the first time curators, bioinformaticians and other researchers have shouted out the importance of being able to find, understand, copy and use data. But any help in spreading the message is more than welcome.


Need more help finding the right standard or database for your work? Visit BioSharing!

Further information:

Meetings & Conferences

Standards and infrastructure for managing experimental metadata (ISMB DAM SIG 2009)

Philippe Rocca-Serra, EBI

Metagenomics and metatranscriptomics experiments are growing in size and complexity. Gilbert et al PLoS One, 2008 is one example. There are many different domains of science, and the all share some common problems. Consistent reporting of the experimental metadata along with the resulting data has a positive and long-lasting impact on the value of collective scientific outputs. To help solve these problems, many communities have developed reporting standards covering minimal information to be reported about an experiment type (MIBBI).

At the EBI, there are separate submission systems for proteomics data, transcriptomics data, sequence data etc. This is frustrating for the researcher who may have all of this information in one experiment. Therefore, BII is being developed to simplify the submission process. More generally, work is underway to promote synergies among standards initiatives. The common efforts include: MIBBI for scope, FuGE and ISA-TAB for syntax, and OBO foundry ontologies and terminologies for semantics. There is a MIBBI talk later this week at ISMB by Chris Taylor.

There are a number of components that are part of the ISA infrastructure (for more information, see The isacreator configurator allows you to set metadata fields and allowed values; isacreator itself is used to describe and upload the experimental metadata (ontologies are accessed in real time via the ontology lookup services and BioPortal, and groups of samples are colour coded); isacreator has a nice visualisation of the various group types that gives you an overview of size and relative importance to other groups.

My thoughts: Firstly, you should know that I contributed to both the FuGE projects and the ISA-TAB projects, and helped develop the ISA-TAB specification. Therefore, I have an interest in this. Moving on… Overall, it really looks like isacreator is coming along nicely from its early incarnations. It looks nice, which is very important for user uptake. It also is compatible with FuGE (though development is still ongoing to increase compatibility, I think).

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Please note that this post is merely my notes on the presentation. They are not guaranteed to be correct, and unless explicitly stated are not my opinions. They do not reflect the opinions of my employers. Any errors you can happily assume to be mine and no-one else’s. I’m happy to correct any errors you may spot – just let me know!

Data Integration Meetings & Conferences

FuGE / ISA-TAB Workshop, Day 1

Today was the first day of the workshop – back at the good old EBI, though it isn't as recognizable as it used to be. Sure, there is the new EBI extension, but I am used to that now. However, they're renovating the inside of the old EBI building as well, reducing many of my friends to portakabin living over the winter months: better them than me!

Today definitely had an emphasis on the "work" part of "workshop". While a large part of the work on the XSLT for converting between FuGE and ISA-TAB is complete, some of the slightly stickier areas of the conversion are still being worked on. We spent today on trying to iron out some of the difficulties that arise from trying to convert the sort of rich tree structure that you get from the XML implementation of FuGE (FuGE-ML) into the flatter tabular format of ISA-TAB. Below are some of the more general ideas that we were throwing around as a result. (Some are more directly related to the conversion process than others – but all raise interesting points to me.)

  • One of the column names in the ISA-TAB Assay file is currently named "Raw Data File" in the 1.0 Specification. This caused a large amount of discussion as to what "raw" meant, and that many people would have a different idea of what a raw data file was. It was originally named this way to act as a foil against another (optional) column name, "Derived Data File". However, derived data files have a more precise definition in ISA-TAB – such a column can only be used to name files resulting from data transformations or processing. In the end, we are considering a name change, from "Raw Data File" to "Data File".
  • In the end, there will be a few simple ways to format your FuGE-ML files in a way that will aid the conversion into ISA-TAB. It would be useful to eventually produce a set of guidelines to aid in interoperability.
  • Some of the developers already using FuGE (myself included) are using the <Description> element within a FuGE-ML file as a way to allow our biologists to give a free-text description to both materials and data files. There is no specific element in these objects to add such information, and therefore the generic Description element is the best location. This isn't exactly as per FuGE best-practices, where the default Description elements are really only meant for private comments within a local FuGE implementation, and can normally be ignored by external bioinformaticians making use of your FuGE-ML. Such material and data descriptions can be copied into the ISA-TAB file as free text within the Comment[] columns, where what sits within the "[]" is the material or data identifier. We'll have to see if this idea turns out to be useful.
  • The main challenge in collapsing FuGE-ML into ISA-TAB is ensuring that the multi-level protocol application structures (for more information, see the GenericProtocolApplication and GenericProtocol objects within the FuGE Object Model) are correctly converted. We spent the majority of today trying to figure out an elegant way of doing this. We'll work on it again tomorrow, and will hopefully have a new version of the XSLT with a first-bash solution tomorrow evening!

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CISBAN Data Integration Meetings & Conferences Software and Tools Standards

Pre-workshop post on the FuGE / ISA-TAB Workshop, 8-9 December

Tomorrow is the first day of a two-day workshop set up to continue the integration process between the ISA-TAB format and the FuGE standard. (Well, technically, it starts tonight with a workshop dinner, where I'll get to catch up with the people in the workshop, many of whom I haven't seen since the MGED 11 meeting in Italy this past summer. Should be fun!)

ISA-TAB can be seen as the next generation of MAGE-TAB, a very popular format with biologists who need to get their data and metadata into a common format acceptable by public repositories such as ArrayExpress. ISA-TAB goes one step further, and does for tabular formats what FuGE does for object models and XML formats: that is, it is able to represent multi-omics experiments rather than just the transcriptomics experiments of MAGE-TAB. I encourage you to find out more about both FuGE and ISA-TAB by looking at their respective project pages. The FuGE group also has a very nice introduction to the model in their Nature Biotechnology article.

Each day I'll provide a summary of what's gone on at the workshop, which centers around the current status of both ISA-TAB and some relevant FuGE extensions, as well as the production of a seamless conversion from FuGE-ML to ISA-TAB and back again. ISA-TAB necessarily cannot handle as much detail as the FuGE model can (being limited by the tabular format), and therefore in the FuGE-ML to ISA-TAB direction, it is possible that it may not be entirely lossless. However, this workshop and all the work that's gone on around it aims to reconcile the two formats as much as possible. And, even though I have mentioned a caveat or two, this reconciliation is entirely possible: both ISA-TAB and FuGE share the same high-level structures. Indeed, ISA-TAB was created with FuGE in mind, to ensure that such a useful undertaking used all it could of the FuGE Object Model. It is important to remember that FuGE is an abstract model which can be converted into many formats, including XML. Because it is an abstract model, many projects can make use of its structures while maintaing whatever concrete format they wish.

Specific topics of the workshop include:

  • Advance and possibly finalize XSLT rendering of FUGE Documents into ISA-TAB. This includes the finishing-off of the generic FuGE XSL stylesheet.
  • Work on some of the extensions, including FCM, Gel-ML, and MAGE2. MAGE2 is the most interesting for me for this workshop, as I've heard that it's almost complete. This is the XML format that is a direct extension of the FuGE model, and will be very useful for bioinformaticians wishing to store, share and search their transcriptomics data using a multi-omics standard like FuGE.

Thanks to Philippe Rocca-Serra and Susanna-Assunta Sansone for the hard work they've done on the format specification, and for everyone who's coming today. It's a deliberately small group so that we can spend our time in technical discussion rather than in presentations. I'm a bit of a nut about data and metadata standards (and am in complete agreement with Frank over at peanutbutter on the triumverate of experimental standards) and so I love these types of meetings. It's going to be fun, and I'll keep you updated!

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