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March 2014

ISBE and MIRRI join

BioMedBridges fulfills its promise as research infrastructures mature

Two othe three newest biomedical sciences research infrastructures on the ESFRI roadmap, ISBE for systems biology and MIRRI for microbial resources, joined the BioMedBridges consortium as Associate Partners during the project's 2014 Annual General Meeting in Florence, Italy.

Richard Kitney, ISBE Coordinator: “We look forward to working closely with BioMedBridges to develop synergies across the landscape of the biomedical sciences research infrastructures.” Erko Stackebrandt, Coordinator of MIRRI, added: “It is very important for MIRRI to explore synergies with other biological and medical research infrastructures and we look forward to contributing to BioMedBridges particularly to help deliver interoperability of high quality data to facilitate the generation of knowledge and drive innovation in the life sciences.”

Also during the AGM, the BioMedBridges steering committee agreed that the INFRAFRONTIER Research Infrastructure, BioMedBridges partner since the start of the project, will in future be represented in the project by its legal entity, the INFRAFRONTIER GmbH.

INFRAFRONTIER GmbH Director Martin Hrabé de Angelis explained: "Bringing in the INFRAFRONTIER GmbH as a formal partner was a logical step for us. It contributes to our efforts to shape the European Research Area in the field of life sciences research infrastructures.”

"The joining of ISBE and MIRRI as Associate Partners and of the INFRAFRONTIER GmbH as project partner mark important milestones both for the BioMedBridges project and the biomedical sciences research infrastructures as a whole" said Professor Janet Thornton, BioMedBridges Coordinator. “It demonstrates that the landscape of biomedical sciences research infrastructures in Europe is maturing as well as becoming more tightly integrated. BioMedBridges is fulfilling its important role in bringing together the very diverse communities and aligning them to a common goal: sharing and integrating the heterogeneous data in the life sciences so scientists can efficiently navigate and fully exploit data resources to tackle the grand societal challenges.”

BioMedBridges Second Annual General Meeting

Two days of scientific excellence and networking

Held in the stunning Italian city of Florence, the BioMedBridges Second Annual General Meeting took place earlier this month (10 - 11 March) at the historic Convitto della Calza.

Over 120 delegates from 13 different countries participated in the meeting
During the meeting, partners and external stakeholders reviewed and discussed the exciting science that drives the project and the momentous progress made on the innovative technical bridges built. Complimenting this, eleven external speakers - leading researchers in their respective fields, nominated by each of the biomedical sciences research infrastructures - presented their cutting-edge research and outlined the relevance of BioMedBridges in this context.

Dipak Kalra (University College London and EHR4CR), nominated by BioMedBridges partner infrastructure ECRIN, described the requirements of electronic health record architectures and systems needed to ensure the robust long-term preservation of clinical information. Kalra outlined the invaluable role of the EHR4CR Protocol Feasibility Services in preventing costly protocol amendments during clinical trials and the EHR4CR Patient Recruitment Services, which integrate a unique information flow to enable efficient patient identification and recruitment. Several of the BioMedBridges partners are also involved in the EHR4CR, ensuring the efficient exploitation of solutions produced in both projects.
Richard Frackowiak of the Human Brain Project uses a combination of bioinformatics tools and data mining techniques to redefine brain disease diagnosis. He  addressed the importance of federating clinical data from hospital archives and proprietary databases, which requires strong protection of patient data throughout the Medical Informatics Workflow. There are important synergies between the Human Brain Project and BioMedBridges which representatives from both projects are actively investigating. (Presentation available here.)
On day two of the meeting, BioMedBridges project members gave presentations covering both the technical and use case specific aspects of the project. Helen Parkinson (EMBL-EBI/ELIXIR) demonstrated how the work done in the project adds value to the research infrastructures involved by supporting data exchange, integration and analysis through the application of common standards across domains.
Cath Brooksbank (EMBL-EBI/ELIXIR) emphasized the importance of "completing the circle" of technical development through user training and user experience workshops. The resources developed within the project, including ‘living’ documentation and online training modules, are designed ot support this approach.
With numerous networking sessions, workshops, demonstrations and poster presentations interspersed across both days, the BioMedBridges Second Annual General Meeting provided invaluable opportunities for project members, external speakers and committee members to establish new technical and social bridges. 
Presentations, posters and photos from the meeting are available.
External speakers. First row from left: Tim Brooks (Public Health England, for ERINHA), Catherine Boyen (Station Biologique de Roscoff, for EMBRC), Anna Tramontano (University of Rome, for INSTRUCT), Janet Thornton (BioMedBridges Coordinator, EMBL-EBI), Robert Gentleman (Genentech, for ELIXIR). Second row from left: Hanns Haering (University of Tuebingen, for INFRAFRONTIER), P. Friedl (Radboud University Nijmegen/Anderson Cancer Center Houston, for Euro-BioImaging), Wiebe Kooistra (EMBRC), Olli Kallioniemi (FIMM, for EATRIS), Dipak Kalra (University College London, for ECRIN).

First periodic report published

At the end of February, BioMedBridges published its first periodic report, covering the first two years of the project from January 2012 to December 2013. The report, which includes detailed information on the technical infrastructure supporting data interoperability developed by the project partners, is available from the project website.

Supporting data sharing

Under the umbrella of BioMedBridges, the biomedical sciences research infrastructures involved in the project plus AnaEE, ISBE and MIRRI as well as LifeWatch developed a document on the Principles of data management and sharing at European Research Infrastructures. The document makes key recommendations on how data management and sharing via the research infrastructures can be supported and describes the technical requirements underlying openly available data. The detailed recommendations and the background and context for data management and sharing at the RIs are described in the full version of the document, which can be downloaded here.

Tool in the spotlight

A new recurring item in the BioMedBridges Newsletter will be “Tool in the spotlight”. Each time another tool that is developed or extended under the BioMedBridges flag will be highlighted. In this issue we will focus on UniChem, a tool developed by Jon Chambers and John Overington at EMBL-EBI.

Why UniChem?

There are many different databases containing data on small molecules. These databases have different but overlapping communities of users, many of whom profit from being able to search for the same molecule in related databases and from being able to easily navigate to these other databases. UniChem provides a simple mechanism to interlink between a very large number of different chemistry databases, removing duplication of effort and ensuring that users have access to up to date information in the most efficient way.

Moving from identical compounds to 'equivalent' compounds

UniChem was originally developed two years ago as part of the FP7-funded EU-OPENSCREEN preparatory phase project. Initially, the tool only returned identical compounds listed in other resources. The contribution from BioMedBridges has now extended UniChem with a connectivity search function that allows the user to find not only exact matches of their chemical structure but also 'equivalent' structures that have the same atom connectivity while differing in stereochemistry or isotopic composition, or which exist in a different salt form. In this way, the UniChem resolver finds and links 60 million related molecules from 21 data sources worldwide, including information whether a specific compound has been patented in some form or what research has been done on it. This functionality facilitates research for example into the mechanism of action of an existing drug and its possible off-label uses and is particularly important in the development of new pharmaceuticals, where early candidate triage - filtering out compounds that are most worthwhile to pursue - can save significant amounts of time and money.

Find out more

  • Documentation from the BioMedBridges course on UniChem is available here
  • Go to the UniChem website

Upcoming events

You can find BioMedBridges at: Do you miss an event or do you want to share your events with the BioMedBridges community? Please contact the BioMedBridges inreach/outreach team.

BioMedBridges workshops

A workshop on standards involving representatives from all biomedical sciences research infrastructures is planned to be held in June 2014. Please get in touch if you are interested in attending or contributing.

BioMedBridges is planning a joint workshop with e-infrastructure representatives to discuss how underlying technical needs of the life sciences can be met. Interested? Get in touch.

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