Draft content for handout that reflects the perspective of the foundation:
Background on the Allotrope Foundation in detail:
There is nothing like a language barrier to create inefficiency
And yet, that’s exactly the problem the pharmaceutical industry faces with laboratory data. Simply a condition of a constantly changing, science driven business with new and evolving technologies, the broad landscape of instrument & software providers has led to equally diverse data formats & systems to consume them. This means without parsing and translating all those formats, our instruments & software effectively speak different languages or dialects. The result is enormous inefficiencies in the form of:
• Tedious manual work and rework of data & documents by highly technical staff;
• Repeated experiments;
• A large portfolio of custom software solutions & patches to integrate data, to list a few.
“IF YOU WANT TO GO FAST, GO ALONE. IF YOU WANT TO GO FAR, GO TOGETHER.” – AFRICAN PROVERB
This problem, and the resulting inefficiencies & limitations, are common across the pharmaceutical industry, and yet each company independently toils & spends large sums of money to address it locally. These efforts are necessary, but are neither value added, nor in any way proprietary in the context of bringing new medicines to patients. Therefore, this problem should be solved in a precompetitive collaboration, across the community of stakeholders including pharma/biopharma companies, instrument and software providers, government institutions, and the scientific community at large.
Other technology communities have faced a similar moment in their evolution, and banded together to create standards which have enabled functionality that now dominates everyday life (i.e. jpeg & mpeg formats, the world wide web, networking & IEEE standards). Discovering new medicines is enormously challenging scientifically. Now with a very visible focus on improving the efficiency of pharmaceutical R&D, and efforts to lower the cost of new medicines as a component of healthcare costs, the moment has arrived for the industry to embrace a pre-competitive approach to solving problems that help all involved to be more successful. Similar efforts have emerged in Clinical and Biomedical information technologies (ref).
THE ALLOTROPE FOUNDATION*
On June 4, 2012, representatives from a number of pharmaceutical companies met to discuss challenges & potential solutions related to laboratory data management. The attendees, whose expertise ranged from information technology to chemometrics & analytical testing to drug discovery & product development, agreed to form an unincorporated, not-for-profit association, The Allotrope Foundation, to address these challenges. The Foundation will build a framework consisting of open document standards, an open metadata repository & open source class libraries – using existing standards and tools as appropriate. Eleven companies so far have joined the Foundation (Abbott, Amgen, Baxter, Boehringer Ingelheim, BMS, Eisai, EMD Serono, GSK, Merck, Pfizer and Vertex), and others are considering membership. Starting in 2013, the Allotrope Foundation’s initiative will be funded for a three-year term, beginning with the hiring of external partners to work closely with subject matter experts from member companies to build a framework for the analytical laboratory.
A HOLISTIC APPROACH IS NEEDED TO CATALYZE THE SHIFT TO A COMMON LANGUAGE: THE FRAMEWORK
Without adoption, a data standard alone is an abstract, esoteric idea that cannot alone create change. What’s required is a more holistic approach, a framework including information standards for experimental data, the meta-data associated with those data and the workflows that create and use data, and a toolkit, in the form of software, that enables the instrument & software providers to integrate the standards into their platforms
The Framework will consist of three interacting components:
• Open document standards based on XML, JSON or other formats that support structured data.
• Open metadata repositories containing dictionaries to provide accurate metadata input into numerous laboratory systems
• Open source class libraries that will produce and consume content from components 1 and 2 above.
In addition, a cutting-edge, proof-of-concept (PoC) application will be built using the Framework. As a primary objective, the PoC Application will be designed to demonstrate the power and advantages of using the Framework. Additionally, the PoC Application will be an essential component of a real-world test bed that will be used to test and optimize the usability of the Framework during its development.
* Allotropy is a property of some chemical elements to exist in two or more different forms (fr. Wikipedia). Examples include the allotropes of carbon– graphite, diamond, nanotubes, and fullerenes. The framework that the Allotrope Foundation builds will comprise “elemental” pieces that can be combined and integrated in different forms to create a multitude of software solutions.