laboratory informatics ➤


suggests. ‘We have been particularly interested to see how the platform is also being exploited at the clinical level, by physicians, to help direct diagnosis and treatment for individual patients. It’s not what the soſtware was designed for, but we do know that a number of hospitals are using Pathway Studio as a clinical tool.’ Complementing Pathway Studio, Elsevier


offers a comprehensive text mining portal, which allows users to identify every paper in the publisher’s dataset that mentions a specific protein, drug, gene, or even cell type or disease, and also to build content sets for further modeling and analysis. ‘You can mine full texts as well as abstracts, and this oſten identifies research on a drug target or gene that might otherwise have been missed.’


Intuitive and user friendly Te ultimate goal is to use underlying information to map as many common identifiers as possible, but in an intuitive and user-friendly way, Hodgkinson notes. ‘We have, for example, invested huge amounts of time building a taxonomy around many different cell types, so that users don’t have to type 20 different keywords to ensure that their search covers every synonym that may commonly be used for one cell type. Our goal is to provide the tools that will help researchers and clinicians derive the


IT’S NOT JUST IN- HOUSE RESEARCH THAT IS CREATING VAST QUANTITIES OF BIOLOGICAL DATA


maximum useful information from existing molecular, cellular, translational and clinical research, and to help them find whether published data have been reproduced or validated and so whether they are reliable.’ At the end of the day, utilising


experimental data in the context of existing data is largely about predicting cause and effect, rather than providing definitive answers. But herein lies another big data problem. How do you search for and filter out reliable, reproducible studies and experimental results, either to corroborate new results and drive the direction of disease, target or drug R&D, or even to instruct patient diagnosis and therapy at the clinical level? Tis is an important concept, Hodgkinson stresses. Te ability to identify and therefore


18 SCIENTIFIC COMPUTING WORLD @scwmagazine l www.scientific-computing.com


discard less safe experimental data is a key requirement for researchers who are siſting through published research. ‘How to ensure the providence, reliability and reproducibility of data is an issue that comes up time and time again. What we can or can’t trust? Our tools allow users to identify easily how long ago research was conducted, and whether it has ever been replicated, when and by whom.’


Making accurate predictions Te higher the quality and relevance of prior data, the more likely it is that predictions based on it will be accurate. ‘Tis is going to be an exciting area moving forwards,’ Hodgkinson continues. ‘How do we get to the point where we can really start to build a reliable inference base that allows researchers to make confident predictions.’ Elsevier continues to work to provide new


functionality to its tools, and is also working with a number of genomics providers on further platform integration. ‘Trough these collaborations we hope to make it possible for researchers to step directly back and forth between Pathway Studio and bioinformatics tools, such as Illumina’s BaseSpace Correlation Engine,’ for example, Hodgkinson suggests. Users identify their


genes and proteins of interest, and can then take them directly into Pathway Studio to see which other disease processes and pathways may be linked. It’s an area of development that we are accelerating to allow users to combine our platform with their bioinformatics tools directly.’


Distributed research Te move towards distributed research is shaping the industry and market for bioinformatics-related tools, comments Jens Hoefens, director of informatics at PerkinElmer. ‘Many large pharma companies are outsourcing research to contract research organisations (CROs) and collaborating with academics and biotechs. Tere is a huge need for informatics solutions that can support cross- organisation management, utilisation and analysis of NGS, high content screening and other sources of bioinformatics data, as they are generated by different instrumentation and migrated between partners in varying formats.’ Tis means that you have technical


challenges not only with respect to giving and controlling access to information, but also with respect to ensuring that the soſtware is easy to use, Hoefens continues. ➤


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