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Pistoia focuses on ontologies, data warehousing and networks of alliances

Following its annual Spring European Conference, held at HP in Zurich last month, the Pistoia Alliance has announced a series of new initiatives, including one to map the ontologies being used in the life sciences; another to understand the complex landscape of alliances, foundations, partnerships and consortia in life sciences; and it is also now seeking funding to investigate the idea of a Standardised Data Warehouse for life science data.

The Pistoia Alliance is an international group of experts from the life-science industry. A not-for-profit body, it organises collaboration at the pre-competitive stage to address issues around aggregating, accessing, and sharing data that are essential to innovation, but provide little competitive advantage. In this way, it seeks to lower barriers to innovation in R&D. It was set up in 2009 by representatives of AstraZeneca, GSK, Novartis, and Pfizer who met at a conference in Pistoia, Italy, and its work is openly published.

The Ontologies Mapping project has been set up to create better tools and establish best practices for ontology management in life sciences R&D. Ontologies, as the term is used in the life sciences, are controlled vocabularies listing standardised terms to allow researchers to exploit large amounts of complex data in life sciences research. The project will see the Pistoia Alliance develop a set of standardised guidelines, tools, and services. The first phase of the Ontologies Mapping project will define the requirements for a standardised tool that will allow users to integrate, understand and analyse their data more effectively.

As part of the project, a community of interest will be set up to provide guidance. Once completed, any tool developed will be released free of charge under an open-source licence to the life sciences community. The project has been funded through the Pistoia Alliance’s membership and the first phase is expected to deliver results by the end of 2015.

Michael Braxenthaler, president of the Pistoia Alliance, said: ‘The use of ontologies in life sciences R&D is crucial to integrating and understanding the vast amounts of data that researchers must handle. However, with its increase in importance, there has been a corresponding rise in the number of tools and approaches, which can create confusion. Through this project we aim to create a standardised set of tools and guidelines which can be used by all life sciences companies and organizations.’

The launch of the Ontologies Mapping project builds on the success of the Pistoia Alliance’s other projects, HELM (Hierarchical Editing Language for Macromolecules) and the CSCS Expert Community (Controlled Substances Compliance Services), both of which have seen widespread adoption of their outputs throughout the life sciences industry.

The Alliance is also hoping to secure funding for a second project, so that it can look at the issue of a Standardised Data Warehouse. The genesis of this project was the realisation that every pharmaceutical research and development (R&D) organisation has its own internal database warehouse systems for storing summary data, each with a unique design. These tend to diverge, particularly in research and early development projects with in vivo data. In addition, the trend towards the development of biological drugs means that most pharma R&D Informatics groups must adapt or link their warehouses, which are optimised for small-molecule data, to accommodate these large-molecule activities. A further driver is the growing need to increase interoperability with collaborating partners through standard harmonised models for data warehouses used at the research and early development stage.

The purpose of the Standardised Data Warehouses (SDW) project will be to compare and contrast existing data warehouse systems used by Pistoia Alliance members in research and early development. The project will deliver standardised reference models and guidelines for best practice, whilst still allowing for adaptation to meet local requirements.

Of course, the Pistoia Alliance is not the only game in town. Amongst others, there is also the Allotrope Foundation, whose work was presented at the Paperless Lab Academy in Barcelona last month, as reported on the Scientific Computing World website, but that too, is only one of several. So complex is the landscape of alliances, foundations, partnerships and consortia in the life sciences world, with many organisations that may overlap in their aims or share a significant proportion of their membership, that Pistoia is undertaking another project to ‘map’ the alliances in life science research.

Ultimately, the aim is to reduce overlaps and duplication of effort. The result would be a detailed picture and decision tree that would allow the industry rapidly to identify who it should contact for each need that it has. Such a project would also allow the various alliances to identify their partners and competitors and work out how best to support each other and collaborate towards the common goal of improving science.

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