DATA INTERCHANGE STANDARDS: WHAT, WHY AND WHEN?
Standardisation is crucial in a world where sharing is increasingly commonplace, argues John Trigg
W
hy can ordinary consumers share their data when the laboratory informatics community cannot?
Sharing and collaboration are becoming second nature in the consumer world where the ability to communicate and transfer data over the web has become a routine part of everyday life; to the point where the terms ‘upload’ and ‘download’ are part of everyday vocabulary. A simple example is the ability to take a photograph on a camera phone, and immediately upload it to a photo- sharing site, or email it, or ‘message’ it or tweet it. The ability to do this is totally dependent on standards; the internet provides the infrastructure; wi-fi or telecoms provide the messaging; and the device (camera/phone) generates the data (photo) in a format that can be used by other applications. It’s a process everyone takes for granted, without having to worry about the data format of the photo and whether the recipient will be able to open it. It may be thought a simplistic example, particularly when compared to the complexity of laboratory systems that serve an extensive range of measurement and other services, but the underlying principle paints a vivid picture of how laboratory systems ought to be able to work together. Yet the laboratory informatics community
has been debating for decades the topic of standards for interchanging data, or more accurately the lack of such standards. On one side of the debate is a compelling argument that says laboratories will be able
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www.scientific-computing.com/lig2014
to work more efficiently and effectively if there are common standards for exchanging data. On the other side, the vendors argue that standards would constrain innovation in the development of tools for capturing and processing data. In the background is a more political viewpoint: proprietary data formats facilitate a commercial ‘lock-in’ for the vendors; and the adoption of open data standards would disrupt the marketplace, not only for the vendors, but also for the third-party systems’ integrators. Few people could argue against the
benefits of data standards. Laboratories would welcome the ability to acquire data and then process it, view it, store it, share
One of the consequences of the transition from paper to digital
technologies is that we are going into the unknown, and we will become totally dependent on technology
it, re-analyse it, and preserve it without the constraints of proprietary data-capture software and integration tools. The advantages include not only ease of use, but also the reduction in costs associated with third party and custom solutions to interface laboratory devices and systems. A less obvious benefit is the ability to archive data in a human-readable format over the long term. One of the consequences of the transition from paper to digital technologies is that we are going into the unknown,
and we will become totally dependent on technology in order to access electronic records. Basically we will no longer have any physical artefacts that represent our accumulated records of laboratory experimentation and their outcomes. It will all be digital; the IT industry has a poor track record when it comes to digital preservation. However, the long-term preservation
of electronic records does present one example of where a standard – PDF or PDF/A – has been adopted in the laboratory world. However, electronic document standards, such as PDF and PDF/A, have a very different purpose from that of data interchange standards. With regard to the write-up of an experiment, PDF or PDF/A can preserve a rendition of the data generated in the experiment, but does not preserve the data itself. In order to preserve the data and to maintain the capability to use and re-use it over the long term, then a data interchange standard is necessary. The transition from paper to electronic
lab notebooks created the need to be able to preserve, for several decades, the integrity, authenticity, and readability of experimental records to support business and scientific requirements. PDF and PDF/A both have ISO registration as open standards, and are typically used to provide the electronic rendition of the experimental ‘document’. The primary purpose is the preservation of a flat document, including the text, fonts, graphics, and other information
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