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A portable data format for laboratory data

In the world of scientific computing, data is paramount. Nowhere is this truer than in the pharmaceutical/biopharmaceutical industry. Modern laboratories generate massive volumes of data from a wide variety of proprietary instruments, software, and human input. The path to delivering new medicines to patients begins with data generated from experimental testing and measurement, continues through the stages of aggregating and organising data into scientific information, and culminates with sharing and collaboration to create actionable scientific knowledge. Driving scientific data through its lifecycle is tedious, time-consuming, and a distraction from the real work of scientists; the associated inefficiencies are a major factor in long, expensive, product development cycles. More importantly there are significant challenges imposed by the current informatics environment that create friction in the process of using data for decision making and insight.

Drivers for integration

The importance of researcher productivity to overall business objectives has long been acknowledged in the pharmaceutical industry. While current trends in laboratory informatics place high priority on the optimisation of data handling and usage as the way to help scientists be most effective, successful implementation of this practice within the industry is still quite challenging. To address this, a group of pharma and biopharma companies launched Allotrope Foundation – an industry consortium specifically focused on the development of advanced technology solutions for handling data in R&D, with an initial focus on analytical chemistry.

Addressing real needs in R&D

From the outset, Allotrope Foundation has focused on the reality of the scientist’s day-to-day work, which is largely spent in collecting, organising, and formatting data for downstream applications. Out of Allotrope’s analysis emerged the first set of technical requirements for a significantly different paradigm for data management solutions, which include the ability to capture and represent in a standard format experimental data generated by any analytical device in the laboratory; the ability to record in a standard vocabulary more complete metadata related to each test and measurement event; and very importantly, the ability to transport that data for sharing beyond the boundaries of the originating devices and laboratories.

The route to platform independence

Allotrope Foundation’s strategy is to take a vendor-agnostic approach to the design of a holistic ‘framework’ for laboratory data. To take on the task of implementing this solution, Allotrope Foundation hired Osthus, a software services firm known internationally for its systems integration expertise. Soon thereafter, the Allotrope Framework went from an ambitious aspiration to a reality. Following extensive evaluation of technologies and standards, and proof-of-concept work with Allotrope Subject Matter Experts (SMEs), the Osthus team brought forward a design focused on the data itself – creating a unified, common data representation that can handle output from any laboratory instrument, and that is portable, allowing use by software applications independently of those instruments.

The end result is an advanced data structure called the Allotrope Data Format (ADF). It features the ability to store machine-generated datasets of unlimited size in a single file, organised as n-dimensional arrays to ensure that the details of the most complex data are recorded. The ADF is capable of storing the metadata describing each test and measurement event as well. The ADF is portable, allowing easy file transfer and use across operating system and vendor platforms.

Simple and elegant

The Allotrope Framework itself is a software toolkit that enables the manufacturers of analytical equipment and commercial software vendors to render their machine output in the ADF. As more vendors adopt the ADF, the readily accessible and easily usable data generated by their software will eliminate much of the friction that exists in collaborative efforts by teams of scientists and the organisations they work with. The Framework coupled with the ADF indeed presents several advantages over other integration techniques:

  • Broad data accessibility. The ADF creates a comprehensive and extensible data representation, eliminating the need for specific vendor-to-vendor technology integration. That will make it easier to access and share the data output from any vendor’s equipment or software.
  • Multi-channel application development. ADF files will be usable as input to a new generation of software applications for desktop systems, cloud-based application architectures, the web, and mobile operating systems, enabling an architecture that separates data from applications, and lowering the barrier for introducing new innovations.
  • Simpler data integration. For in-house software development teams, the Allotrope Framework will significantly lower the costs and effort for integration between new applications or workflows. The standard format of the data and representation of the metadata provide a level of interoperability that enables a ‘best-of-breed’ solution to laboratory IT infrastructure.

Reduction to practice

The technical feasibility of the ADF and Framework architecture has been established and Allotrope member companies are using them in their internal laboratory informatics solutions. These implementations by early adopters provide important real-world testing and feedback to the continuing development of the Framework and enable the members to learn from one another’s experience. The collaborative model, where costs are shared and the approach benefits from a collective intelligence of industry-leading companies, has enabled an extensible, sustainable solution to an industry-wide problem that would be out of reach for any one company. The benefits of that Framework are now within reach of any company or institution that joins Allotrope and takes the path to adoption.

More recently, it’s become clear that neither these challenges, nor potential solutions, are unique to the pharmaceutical business. In fact they generalise to the application of analytical chemistry in any R&D setting, including agrochemical, food, consumer products, etc. Allotrope has hosted four ‘Cross-Industry Workshops’ to introduce the concepts and approaches to a wider audience, provide an update on progress, and help map the Allotrope deliverable to attendees’ business needs in other sectors. The next opportunity for the wider community of IT professionals supporting laboratory informatics to learn, discuss, and assess whether the Framework should be part of their IT solution architecture will be 16 September 2015 in Chicago, USA


Wolfgang Colsman is chief technology officer of Osthus. Rachel Uphill was enterprise/information architect at GlaxoSmithKline.

Any correspondence regarding this article should be directed to: James M. Vergis, Allotrope Foundation Secretariat, Drinker Biddle & Reath LLP, 1500 K St, NW, Washington DC 20005-1209, USA.

Editor’s note: This article arose as a result of a conversation between Rachel Uphill and the Editor at the Paperless Lab Academy in Barcelona, earlier this year. Sadly, Rachel Uphill has since passed away after a short and sudden illness. Her colleagues write that, from the formative stages of Allotrope, she helped shape the goals and direction of the Foundation, drawing from passion and experience to challenge concepts, provide insight, and keep the challenges in clear view. She will be missed for her quick intellect and the warmth and light spirit with which she shared it.

As described in the main article, Allotrope Foundation ( is an international consortium of pharmaceutical and biotechnology companies founded in 2012 to build an innovative Framework that addresses the data management problems faced by the modern analytical laboratory.

A key to the success of the Foundation is that the Framework is being developed through collaboration, utilising the collective knowledge resources of its members. To achieve its goals, such a consortium must have clear objectives, rules of governance, transparent mechanisms for managing its budget, capability to process financial transactions, efficient project management rooted in an in-depth understanding of the subject matter, and seamless processes for executing big and small decisions, as well as other business components. To enable a time-efficient, productive, and legally compliant collaboration, the Foundation engaged a team of professionals from the Pharmaceutical Practice Group of the legal firm Drinker Biddle & Reath LLP (DBR) to serve as Secretariat.

The Secretariat’s goal is to support the participants in advancing the Foundation’s mission – and to do so from a neutral perspective, on time, within budget, and in compliance with the law. The Foundation is governed by its Board of Directors and the Secretariat draws upon the broad knowledge and experience of DBR staff to provide the Board, and the Foundation as a whole, with scientific, technical, regulatory, administrative, logistical, or legal support.

For example: Allotrope Foundation’s mission involves a detailed review of existing standards, taxonomies, approaches to metadata, and the creation of a software code. While the Foundation’s subject matter experts (SMEs) can provide input on their user needs and experiences, they have neither sufficient time nor sufficient expertise to research all available standards from the perspective of the Framework architecture or to write the code. Early on, therefore, the Foundation developed a Request for Information, then issued Request for Proposals, interviewed a number of software firms, and eventually hired one of them (Osthus) as the Framework Architect. An individual pharmaceutical company might have a special department overseeing and coordinating all these activities, culminating in the company’s legal department preparing and negotiating the contract. In a collaboration of independent companies, each with its own ‘user specifications’ and preferences, the role of managing all inputs and executing the collective decision falls to the Secretariat.

While part of a law firm, the DBR Pharma Group is a multidisciplinary team. It consists not only of attorneys proficient in consortia management, antitrust law and compliance, corporate law, and other specialised areas, but also scientists with extensive experience in both industry consortia and the pharmaceutical industry, and project assistants with expertise in project management, events planning, and financial book keeping. The Secretariat is independent from bio/pharma and instrument/software vendors and, as such, acts as a neutral party for Allotrope Foundation. This impartiality places the Secretariat in the best position to manage the Foundation’s projects on a day-to-day basis; facilitate consensus-building among all participating members as well as between the Foundation and external stakeholders; enable steady progress; anonymise input when necessary; and ensure consistent applications of policies set by the Foundation.

Throughout the Allotrope project, the staff scientists within the Secretariat (Science Advisors) help prepare materials for Allotrope Foundation meetings, peer-reviewed publications and technical reports; establish and maintain the website, online collaborative tools and member directories; attend to minutes, agendas, and other record-keeping; publish internal and external newsletters; interact with external agencies on behalf of the Foundation; carry out requested research; conduct confidential surveys and data gathering; construct and maintain databases; oversee collaborative development and joint testing. In addition, the Science Advisors along with DBR Regulatory Affairs professionals facilitate work on regulatory matters, which are crucial for pharmaceutical/biotech and other industries subject to government regulation.

One of the critical needs of any consortium is appropriate legal counsel. Legal services are needed to ensure compliance with national, international, federal, and local laws, covering issues ranging from antitrust compliance (intended to prevent anticompetitive behaviour), to tax and privacy laws, to licensing and patents, to trademarking and copyright laws, and others. In the context of Allotrope Foundation, where the stakeholders include a wide range of entities (pharma/biotech companies, instrument and software vendors, regulators, other industries using analytical instrumentation, academic and non-profit research centres, etc.) and where the output (the Framework) is intended to be directly implementable in companies’ laboratories and vendors’ instruments, scrupulous attention to legal aspects throughout the development and implementation of the Framework is particularly important. Such counsel is provided by the Secretariat, increasing the overall efficiency in terms of time responsiveness and resource use, since the attorneys are integrated in the Secretariat team serving all aspects of the Foundation.

In summary, Allotrope Foundation was formed to pool resources, expertise, and perspectives of various stakeholders. Engaging a neutral, experienced, multidisciplinary team such as the Secretariat was important to the Foundation from the very beginning from both a tactical and strategic point of view. Beyond providing the services and expertise described above, the Secretariat facilitated and supported the Foundation’s incubation within the International Consortium for Innovation and Quality in Pharmaceutical Development (IQ), helping to bring together like minded individuals, building consensus and ultimately achieving the critical mass to launch Allotrope Foundation.

Svetlana Lyapustina, Terrence P. Tougas, and James M. Vergis are Science Advisors in Allotrope Foundation Secretariat


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