IMI projects generate a lot of data, particularly the ones that deal in translational research (those that ‘translate’ basic science into medical practice). Such projects depend on knowledge management (KM) capabilities that allow researchers to work with primary study data (generated themselves) and secondary study data (generated by others). Lacking a common KM platform, IMI projects were investing in individual solutions, causing wasteful and redundant overhead costs, while also risking the legacy of the data they generate. Though there are many KM platforms on the market, commercial solutions don’t suit the requirements of research projects that are publicly funded, that have multiple partners, or that wish to allow open access to datasets.
The consortium delivered a knowledge management software platform called eTRIKS that is now available to IMI and non-IMI researchers. They created and deployed a host of analytics applications known as eTRIKS Labs, as well as a variety of best practices, guides and standards and other documentation. The consortium’s assets are mostly available under open licenses and the application of best practices continues through the work of the eTRIKS commercial spinoff, Information Technology for Translational Medicine (ITTM), the eTRIKS Data Sciences Network and the many adopters of eTRIKS’ technologies.
eTRIKS supported over 60 projects by the end of the collaboration (with an initial goal to support 40). At the final meeting in September 2019, it was noted that several additional research groups had utilised eTRIKS’ software and best practices, bringing the known project engagements up to 70. (eTRIKS personnel have not formally tracked use of the eTRIKS project assets since the end of 2017, although some insights were gained throughout the eTRIKS extension through to end 2018 and until the project ended.)
In order to make an ‘open’ platform, eTRIKS translational research information platform is based on tranSMART, an open-source data warehouse designed to store large amounts of clinical data from clinical trials and basic research. eTRIKS released five major platform versions during the course of the project. The consortium split the work into different streams that covered hosting, software development, deployment, analytics, data curation, mapping, testing, as well as data standards and ethical data use.
The consortium also deployed and hosted the publicly-accessible open access eTRIKS Public Platform which houses about 200 curated clinical studies from a wide variety of disease areas. Those interested in using the eTRIKS platform were invited to use the public platform as a testing and training environment and were provided with a variety of support documents for helping to use the platform.
The project resulted in a number of modular applications and tools that could be used to perform data analysis, exploitation and visualisation. eTRIKS Labs arose out of a desire to brand the applications and make them available to the wider research community. All eTRIKS Labs are open license. Sample apps/tools include eTRIKS Analysis Environment (eAE), a high-performance compute grid scheduler; SmartR, which provides a dynamic and interactive way of visualising and analysing data within tranSMART; SNF, a novel computational method for genomic data integration; and Patient Input Platform, a discussion game framework to assist patients and legislators in navigating the risks and benefits of consenting their individual health data.
Standards Starter Pack
Data standards are the rules by which data are described and recorded. In order to share, exchange, and understand data, consistent standards are essential. The Standards Starter Pack was developed by the consortium to document best practices for optimising the quality and usability of data loaded to the eTRIKS platform. Intended for project leaders and data managers, it provides a review of biomedical data standards as well as guidelines on which standards platforms are best suited for specific research plans. The Standards Starter Pack documents were made available for all IMI projects to promote consistency in data handling and to raise awareness of the advantages of applying consistent standards across translational research projects.
Achievements & News
A number of IMI’s projects are making valuable contributions to the global effort to tackle COVID-19. The contributions include knowledge, tools and expertise, and while some come from projects in the infectious disease field, projects working in other areas, such as data management and Alzheimer’s disease, are also stepping up to the plate.###
One of the most prominent projects here is ZAPI, which brings together some of the world’s top virologists with the goal of delivering a platform and technologies to facilitate a rapid response to disease outbreaks. One of the diseases chosen by ZAPI as a case study is MERS (Middle East Respiratory Syndrome), which, like COVID-19, is caused by a coronavirus. Many of ZAPI’s results and outputs are proving valuable in the fight to tackle COVID-19.
Other projects contributing actively to COVID-19 research are: COMBACTE (providing access to a clinical trial network specialised in infectious disease studies); EHDEN (harmonising clinical data to facilitate reuse and advance research) and HARMONY (creating a COVID-19 data initiative). Elsewhere, tools developed through the AETIONOMY and PHAGO projects have been adapted for use in a new COVID-19 knowledge space.
In its open access guidelines for projects working on COVID-19, the European Commission flags up the eTRIKS standards starter pack and the DO>IT informed consent forms for clinical research as useful resource. Finally, the c4c project has compiled a set of resources on COVID-19 for children and families.
Find out more
- Read the full news article
IMI’s eTRIKS project will hold a meeting on bioinformatics and translational research in Barcelona, Spain on 15-16 May 2017. The datasets that are generated today are complex, and involve many different types of data. The consequence is that the integration of multiple types expertise is necessary. ###Over the last 4 years, the eTRIKS project has helped 41 translational research projects to get more value out of their data. During that time, it has become apparent that many scientists are simply not aware about the data infrastructure that is available for translational research. With that in mind, the two main themes of the meeting are:
- understanding the landscape of bioinformatics infrastructure and how to reduce fragmentation;
- giving translational researchers the knowledge and the tools they need to collaborate on making sense of translational research data faster.
At the event, data scientists and translational researchers will work together to build a common understanding of today’s research data challenges. The aim is to find ways to help fulfil the promise of better health through the optimal use of data. The event will therefore be of significant value to anyone involved in research data or in developing tools to manage research data.
Registration is free via the event webpage
IMI projects not only deliver great results, but sometimes also inspire the creation of spin-off projects, providing indirect economic benefits. The latest proof of that is ITTM (Information Technology for Translational Medicine, S.A.), a Luxembourg company, which was built on the knowledge and expertise gained during the eTRIKS project. ###While working on eTRIKS, researchers from the University of Luxembourg realised that there is really high demand for cleaning, filtering, hosting and standardising data in the pharmaceutical sector. Those services were outside the scope of the eTRIKS project which mainly focuses on providing an open source platform for knowledge management. So, the Luxembourg partners involved in the project started a new company, ITTM. ‘The expertise we gained during eTRIKS regarding curation and standardisation of data are the building blocks of ITTM’s service offers,’ said Reinhard Schneider, Head of the Bioinformatics Core facility at the University of Luxembourg’s Centre for Systems Biomedicine. ‘In addition we were lucky to get the POST group of Luxembourg as a strategic investor. They own big very secure data centres, which gives ITTM a very professional hosting infrastructure.’
IMI projects gather vast amounts of data during their lifespan, and once they end, there is usually the question – how to ensure that this data becomes available to the public, benefiting society in the long run? Thanks to the work of the Luxembourg Centre of Systems Biomedicine (LCSB) at the University of Luxembourg and their involvement in IMI’s eTRIKS project, now there is a solution.### The LCSB, one of eTRIKS project partners, was appointed by the Luxembourg state to host the latest node of ELIXIR, a European network for the sharing of scientific data. While eTRIKS provides projects with an open-source platform for knowledge management, ELIXIR provides an infrastructure, a kind of a highway system, which integrates research data from all corners of Europe and ensures a seamless service provision that is easily accessible to all. Luxembourg is the newest member in a network of 18 European countries and they are also the first node of ELIXIR, which will become a data repository for translational research, the interdisciplinary branch of the biomedical field. The inspiration to specialise in translational data came from IMI’s eTRIKS project, said Reinhard Schneider, Head of the Bioinformatics Core facility at the University of Luxembourg’s Centre for Systems Biomedicine, who is also involved in eTRIKS. 'The sustainability of eTRIKS is now secured,' he added. 'All IMI projects which will open their data are welcome to deposit their data on the Luxembourg ELIXIR node.'
IMI’s knowledge management project eTRIKS has created a ‘standards starter pack’ to raise awareness of, and provide guidance on, data standards in clinical, genomic and translational data management.### Data standards are vital tools in data management, as they make it easier to load data into knowledge management platforms and compare it to other datasets that have applied the same standards. Until now, information on standardisation was fragmented; the new starter pack provides a comprehensive, easy to navigate map of standardisation efforts. As such, it is designed primarily for data managers, data curators and scientists concerned with the long term impact and visibility, reproducibility, reuseability of their work.
The landscape of data standardisation is constantly evolving, as new techniques are developed and new therapeutic areas covered. For this reason, eTRIKS aims to release twice-yearly updates of its starter pack. Furthermore, the team is working on companion documents as well as curation support tools to facilitate implementation of the recommended standards.
Meanwhile, eTRIKS is keen to receive feedback on the current version of the standards starter pack.
IMI data management project eTRIKS will hold a community meeting in Amsterdam on 22 October. The event represents an excellent opportunity to learn about the eTRIKS project and the services it offers to IMI and other projects. A highlight of the event will be a review of how eTRIKS works with the IMI project ABIRISK. ###ABIRISK’s goal is to enhance our understanding of safety issues surrounding medicines based on biological molecules such as proteins and monoclonal antibodies. eTRIKS has set up a specific tranSMART tool for ABIRISK partners, onto which ABIRISK data has been curated, uploaded, stored and analysed. The meeting will also mark the launch of the eTRIKS Labs, an online space where new projects will be made available for review and feedback. According to the project, eTRIKS Labs will make it easier to co-create tools, services, training and guidelines for translational research.
- Register here
Severe asthma is often difficult to manage and many patients are unresponsive to treatment. IMI’s U-BIOPRED project aims to make severe asthma diagnosis and treatment more personalised by creating ‘handprints’ that identify sub-phenotypes of asthma.### The eTRIKS project has been working with U-BIOPRED by deploying analytical techniques to help them in their research, in order to create an environment where the diverse ‘big data’ sets can be compared and analysed. “eTRIKS provides gel without which we could be floating in pools of excess data with no direction,” said Professor Ian Adcock at Imperial College. “U-BIOPRED is using these data to produce at least 60 publications to advance the understanding of the complex causes and subtypes of severe asthma. The eTRIKS/tranSMART platform is a key ingredient to making this happen.”
- Read the press release
IMI’s eTRIKS project is inviting IMI and other projects to use its data curation services for public studies. eTRIKS’s goal is to promote the effective management and sharing of translational research information for IMI projects.### Public data repositories provide access to large amounts of data, but getting full value from them can be difficult. eTRIKS uses the open source tranSMART tool to provide access to different types of biological and clinical data in a well-structured environment. The project places a special emphasis on data cleaning and standardisation to deliver high data quality and improve cross-study compatibility.
IMI’s eTRIKS project will hold its first community meeting entitled Translational Research Knowledge Management in Action in Barcelona, Spain on 31 January 2014. Registration is open and free via the event web page.###
Ewan Birney of the European Bioinformatics Institute (EBI) will give the keynote speech on EMBL-EBI and Elixir: the importance of a life science data infrastructure. The agenda also includes presentations on the challenges faced and solutions from projects supported by eTRIKS, as well as the launch of the eTRIKS public server and platform 1.1.1. One of the key benefits for attendees is the opportunity to shape the future of eTRIKS.
- To stay up to date with eTRIKS, sign up to their blog and newsletter
IMI project eTRIKS is making progress towards its goal of turning the tranSMART knowledge management and analysis platform into an open system that can be readily adapted to diverse translational research needs.### At a recent workshop, 40 people from 12 organisations reviewed the state of the art in the area and set out a roadmap for the development of the platform. Describing tranSMART as ‘a great opportunity for all stakeholders’, eTRIKS academic lead Yi-Ke Guo of Imperial College London said: ‘We are in the midst of a transition from a vender-owned, pharmaceutical company centric application to an open platform centred on the common needs of all translational research stakeholders.’ The key decision coming out of the meeting was the revision of the core of transMART into a set of pluggable components or ‘legos’. This will allow different projects and users to configure tranSMART to fit their needs.
- More information on the workshop can be found in an eTRIKS blog post.
- Sign up to receive the latest updates on the project by filling in the form to the right of the blog text.
IMI’s eTRIKS project has launched a new version of its open, sustainable translational research informatics / knowledge management platform TransMART.### The update is important because it includes the replacement of a proprietary component with an open source component, and so will allow the project to build on inputs from the wider development community. Using open source software instead of proprietary software will result in savings of some €350 000 in licensing fees over five years for projects using eTRIKS’s services. Elsewhere, the project has already delivered three webinars on TransMART and launched a LinkedIn group to provide updates on the project’s activities and encourage debates on issues relating to data and knowledge management.
ParticipantsShow participants on map
- Astrazeneca AB, Södertälje, Sweden
- Bayer Aktiengesellschaft, Leverkusen, Germany
- Eli Lilly And Company LTD, Basingstoke, United Kingdom
- F. Hoffmann-La Roche AG, Basel, Switzerland
- Glaxosmithkline Research And Development LTD., Brentford, Middlesex, United Kingdom
- H. Lundbeck As, Valby, Denmark
- Janssen Pharmaceutica Nv, Beerse, Belgium
- Merck Kommanditgesellschaft Auf Aktien, Darmstadt, Germany
- Pfizer Limited, Sandwich, Kent , United Kingdom
- Sanofi-Aventis Recherche & Developpement, Chilly Mazarin, France
Universities, research organisations, public bodies, non-profit groups
- Association Eisbm, Vourles, France
- Cdisc Europe Foundation Fondation, Brussels, Belgium
- Centre National De La Recherche Scientifique Cnrs, Paris, France
- Imperial College Of Science Technology And Medicine, London, United Kingdom
- Universite Du Luxembourg, Esch-sur-Alzette, Luxembourg
- University of Oxford, Oxford, United Kingdom
Small and medium-sized enterprises (SMEs)
- Biosci Consulting Bvba, Maasmechelen, Belgium
Non EFPIA companies
- ID Business Solutions Limited, Guildford, United Kingdom
|Name||EU funding in €|
|Association Eisbm||306 400|
|Biosci Consulting Bvba||1 385 279|
|Cdisc Europe Foundation Fondation||464 382|
|Centre National De La Recherche Scientifique Cnrs||2 713 493|
|Imperial College Of Science Technology And Medicine||3 403 140|
|Universite Du Luxembourg||2 037 124|
|Total Cost||10 309 818|