A portable data format for laboratory data
Wolfgang Colsman and Rachel Uphill describe the work of
Allotrope Foundation in harmonising laboratory data formats
I
n 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, soſtware, and human input. Te 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 Te 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
The challenges of supporting a technical consortium
As described in the main article, Allotrope Foundation (
www.allotrope. org) 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
8 SCIENTIFIC COMPUTING WORLD
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 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
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