laboratory informatics


standard data formats should be overseen by a recognised standards body, such as ISO, IUPAC or ASTM, under the auspices of which AnIML is being developed. ‘As well as offering the necessary expertise to underpin development of a data format, a standards body provides both credibility and some assurance of longevity, and helps to ensure a level playing field for all stakeholders, including vendors and end users, academia and governmental bodies. Stakeholders need to have an equal voice, and a standards body can ensure that the development process is fair and truly consensual.’ Te challenge isn’t just about developing


harmonised data formats for recording, storing and reporting data that comes out of mass spec and chromatography devices or next generation sequencers, stresses Andrew Anderson, vice president of innovation at ACD/Labs. ‘Tey must focus equally, and in parallel, on standardising taxonomies and other data that we put into the system, so that experiments can be reproduced on any vendor’s instrumentation. Users need to describe the critical quality attributes of their method, in that data standard also.’ Taxonomies need to be sufficiently broad


to cover a wide range of instrument types, and flexible enough to encompass new instrumentation and experimental procedures, adds Graham McGibbon, manager of scientific solutions and partnerships at ACD/Labs. ‘Taking FTIR spectroscopy as an example, then there will be a set of acquisition settings that are common to every FTIR instrument, whoever the vendor. It is relatively easy to include these settings as a matter of routine in a digital file alongside the recorded


THERE IS ONE


POTENTIAL STUMBLING BLOCK THAT MIGHT ALSO HINDER RAPID UPTAKE


results, so that when someone comes to repeat the experiment, they have all the necessary settings and metadata.’ Te situation becomes more complicated when


you have some particular instrument-specific or vendor-specific settings that fall outside of the standard set of instrument data, and which may cause an experiment to yield different results if not included. ‘Tis would be particularly important if, for example, you want to build a library of FTIR spectra. Unless you have those certain acquisition settings, instrument-specific metadata and any other common metadata required to configure other vendors’ machines identically, you will need to carry out all your analyses on the same instruments. Importantly for that purpose, this doesn’t mean one needs each and every piece of parameter metadata from


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every instrument, but that some will be needed, and creating a standardised terminology for those is a key facilitator. Since a standard should allow for analytical instrument innovation, one must also plan how such a standard will be able to update changes without creating either problems of version, or other incompatibilities.’ ACD/Labs is an Allotrope Foundation partner,


and is encouraged by the progress of the initiative and its approach, Anderson suggests. ‘Allotrope is starting with its members; most mission- critical activities, and trying to build end-to-end digital systems that will minimise reliance on abstraction moments – when you have to rely on human intervention to move data from one system to another, or between different areas of a decision support platform. Rather than try and boil the ocean, Allotrope is building from a position of need. Te aim is to attempt to include – along with its standardisation of output data format – taxonomies/ontologies, methods and procedures, as well the flexibility to learn from specific examples and then adjust to more general situations. Achieving the ultimate goal of building an open format standard will require input and collaboration from and between all stakeholders – including the instrument developers and vendors, end users, and intermediaries such as ourselves and other informatics soſtware developers.’ And, with a standardised data format, users are


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able to retrieve original raw data or converted files easily, and to respond much more promptly and effectively to requests from colleagues, regulatory or legal bodies, Barrington-Light notes. ‘Te data sharing and recall capabilities of the system can aid development of new ways of reanalysing samples, and developing predictive models that are impossible when the information is scattered across the company in individual workstations and multiple disparate formats. ‘Te development of truly open standards will


take this even further, to enable scientists to make connections between data sets that aren’t possible today.’ Achieve all that and you could potentially


foresee a future in which soſtware systems make decisions, as well as provide the data that allows those decisions to be made, McGibbon continues. ‘With standardised formats for inputting and extracting data, it becomes feasible for soſtware to generate, interpret and make critical development or business decisions based on initially heterogeneous data. ‘But this will only be possible if we can utilise


data comprehensively, seamlessly and without any loss of context –and that requires ongoing development and implementation of sufficiently granular, flexible standard data formats that they can handle data from any experimental, analytical or decision-support systems.l


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