LABORATORY INFORMATICS GUIDE 2014 | STANDARDS ➤


stretching over four decades. As laboratories become progressively ‘paperless’, progress towards a fully integrated environment will depend on overcoming the limitations posed by the current lack of data standards. Organisations such as the Pistoia Alliance,


the Allotrope Foundation, and the Consortium for Standardisation in Lab Automation (SiLA) have recognised and taken action to address the issue from the standpoint of ‘industry associations’. As Peter Boogaard explains in the previous


article, the Allotrope Foundation (www. allotrope.org) is an international association of biotech and pharmaceutical companies that are collaborating to build a common laboratory information framework for an interoperable means of generating, storing, retrieving, transmitting, analysing, and archiving laboratory data, as well as higher- level business objects such as study reports and files of regulatory submissions. In a recent press release, Allotrope Foundation announced its partnership with Osthus to build the framework, which will have three interacting components: 1. Open document standards based on XML, JSON or other formats that support structured data;


2. Open metadata repositories containing dictionaries to provide accurate metadata input into laboratory systems;


3. Open-source class libraries that will produce and consume content from the first and second components; The Pistoia Alliance (www.pistoiaalliance. org) is a global, non-profit, precompetitive alliance of life science companies, vendors, publishers, and academic groups that is aiming to lower barriers to innovation by improving the interoperability of R&D business processes. The Pistoia Alliance is trying to identify the root causes of inefficiencies in R&D and to develop best practices and pilot technology. Pistoia is not a standards group, but the membership recognises that their organisations are tackling common precompetitive problems – aggregating, accessing, and sharing data that is essential to innovation, but provides little competitive advantage. The ELN project (ELN Query Standard) initiated by the Pistoia Alliance has ground to a halt, but could be revisited if there were sufficient interest amongst members. However, there is good progress with the release of the HELM (Hierarchical Editing Language for Macromolecules), a standard open source


12 | www.scientific-computing.com/lig2014


tools for biomolecular representation. The consortium for Standardization in Lab


Automation (SiLA, www.sila-standard.org) is developing and introducing new interface and data management standards to allow the rapid integration of lab automation systems. SiLA is a not-for-profit membership corporation with a global footprint and is open to institutions, corporations, and individuals active in the life science lab automation industry. Leading system manufacturers, software suppliers, system integrators and Pharma/Biotech corporations have joined the SiLA consortium and participate in and contribute to different technical work groups.


academic, government, and vendor communities. It is far too soon to estimate what the


industry associations will achieve, and there is a risk that the industry may end up with a multitude of standards. The diversity of laboratory types, the wide range of different data generators spanning different technologies and vendor communities, and the range of informatics’ tools all conspire to add enormous complexity to the challenge. Furthermore there is the need to agree not only the technical format of a data standard, but also the ontologies and vocabularies for relevant laboratory data elements. It is not unusual to find misunderstandings of data definitions within a single company, let alone across an industry! Where will the laboratory informatics


The long history of incremental


adoption of laboratory technologies has left a legacy of proprietary


approaches to interfacing laboratory and business systems


In addition to the strategic activity of these


industry associations, the most prominent initiative in developing a data interchange standard is AnIML (animl.sourceforge.net). AnIML is a standardised XML data format that can be used for storing and sharing experiment data. It is suitable for a wide range of scientific disciplines. Its origins are in the analytical chemistry, but the scope has been extended to include biological data. AnIML documents can capture laboratory


workflows and results, irrespective of the instrument or measurement technique used. To achieve this, AnIML provides a generic data-container that permits the storage of sample information, method information, measurement results, instruments and software used, as well as workflow information that ties experiments and samples together. AnIML is being developed by the ASTM E13.15 subcommittee on analytical data, which consists of volunteers from industrial,


community stand if and when data interchange standards emerge? Firstly, laboratory integration would become easier, cheaper, and more effective. However, the long history of incremental adoption of laboratory technologies has left a legacy of proprietary approaches to interfacing laboratory and business systems. A data standard would be dependent on industry-wide agreement, approval by various regulatory bodies and other interested parties, and the willingness of the vendor community to cooperate. As strong as the business case may be, the task is therefore far from straightforward and has no guarantee of success. However, there may be another approach,


which will not be driven by the informatics community itself, but which may develop through the adoption of emerging technologies. The development of an ‘internet of things’ – where every ‘thing’ is uniquely identified and seamlessly connected into the information network – will depend on the adoption of data and communication standards to facilitate data capture, connectivity, and interoperability. So, if every piece of laboratory equipment


that generates data can have its own IP address and can be linked seamlessly into the networks, a truly integrated business ecosystem that incorporates laboratory data and information management becomes possible. The relentless evolution of new technologies


offers the hope that if all else fails, then the trends in integration, sharing and collaboration in the consumer world may provide the basis and incentive to address requirements in the laboratory. l John Trigg is director of phaseFour Informatics.


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