laboratory informatics
biological pathway data on a public database, and also to databases informing about the genes that might be activating that pathway.’ Customers of Te Edge are primarily in the
experimental biology sector, working in areas including in vitro/in vivo pharmacology, ADME and DMPK. ‘Although these are well-established disciplines, there are really very few data standards for this space, and it is a struggle to get systems talk to one another. We expend a lot of effort to build in the ability to capture, structure and store results in a single database that allows users to access multidimensional experimental and analytical data, and interpret it all in context.’ One way of speeding the development and
uptake of data standards is to get involved in the development of such standards, Lemon points out. ‘We have worked with initiatives such as the Pistoia Alliance, and others, to bring our understanding and experience into this space. Te industry must collectively look at the needs from the perspective of the end users. Te pharma companies and laboratories don’t purchase soſtware and then find the instrumentation that can run with that soſtware. End users purchase instrumentation first, and expect it to work with their existing infrastructure.’ Te need for data standards may therefore
THERE IS STILL SOME
RESISTANCE [TO STANDARD DATA FORMATS] BY A FEW HARDWARE MANUFACTURERS
management are encouraging the development and adoption of data standards, Denny-Gouldson stresses. ‘We are not an instrument vendor or a provider of soſtware that analyses, reanalyses, or does specific science. From our perspective it is actually better if we get a data standard in an open format, because then we don’t have to use specific and bespoke connectors to get the data out. Wherever possible, we use open formats to store and publish data, even if that format is something as simple as a CSV file. We have supported AnIML for the last six or seven years, and we are also a partner of the Allotrope Foundation. In the
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big utopian view of the world, all data would be generated in a standard open format. Tis would also make it easier for niche providers to make their soſtware or instrumentation more saleable. What you don’t want, however, is to have so many standard data formats that you essentially end up with just another collection that throws up a different set of cross-communication issues.’ If we can get data standards adopted by
instrument and soſtware manufacturers, then adding or changing analytical instruments would feasibly be a fairly simple plug and play exercise that doesn’t require major changes to your soſtware system, adds Andrew Lemon, CEO at Te Edge Soſtware Consultancy. ‘It really boils down to interoperability. Data standards won’t just make in house or collaborative data more usable in an analytical or experimental setting. Tey will also allow researchers tomake use of public databases more effectively. In the experimental biology sector, for example, data standards will feasibly make it possible for a researcher to relate their own analytical results to
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seem obvious but, while efforts to develop and adopt data standards such as AnIML in the analytical chemistry space have been encouraging, equivalent moves in the bioanaytical space are lagging behind, Lemon suggests. ‘In my experience end users working in this sector aren’t really aware of data standards. Yet the ability to output data from all these technologies in one format would significantly help to streamline research.’ A true open data standard will structure data
at the point of capture, so that any part or all of the information – including any metadata around that information – can be extracted intact. ‘Right now we still have to rely on file formats that can be exchanged, but they are just a way of exporting data so that users in different departments or different organisations can read it. A lot of data is thrown out in the process of supplying pieces of information in a format that can be easily transported. Te only way to retrieve lost information is to go back to the raw data files.’ Tere’s nothing wrong with sending data
in a PDF or a Word document, so long as you can easily go back to the database from which it was generated and extract more complete information, Lemon adds. ‘And if all the information in that database is in the same format, then you have the potential to search and mine analytical data from multiple instrument types.’ Tere is one potential stumbling block that might also hinder the rapid uptake of data
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