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July 2014

New IT tools to change clinical research

Interactive workshop to see, discuss and evaluate

The first Clinical Research Informatics Solution Days organized by CRI/Medical University Duesseldorf (26-27 May in Duesseldorf) brought together experts, users and innovators from the clinical research domain. The interactive workshop, which was co-organized by ECRIN, BioMedBridges and other EU-funded projects (trANSFoRm, EHR4CR, p-medicine, ECRIN-IA), provided a unique opportunity to see, discuss and evaluate new IT tools in biomedical research. Although challenges still have to be overcome concerning for example the interoperability of tools and sustainability, it became obvious that these tools will soon change the way research is done. A similar workshop is planned for 2015. Please contact Töresin Karakoyun for details.

Enabling integration of phenotypic data

Cellular Microscopy Phenotype Ontology released

At the heart of the BioMedBridges project is the provision of infrastructure - including tools and services - to enable data interoperability. Simon Jupp, James Malone, Tony Burdett, Jean-Karim Heriche, Jan Ellenberg, Helen Parkinson and Gabriella Rustici from EMBL in Heidelberg and EMBL-European Bioinformatics Institute in Hinxton have published a paper on a new phenotype ontology. Previously, phenotypic data derived from high content screening had to be annotated using free-text, thus preventing the integration of independent datasets, including those generated in different biological domains such as cell lines, mouse and human tissues. To harmonize the annotation of cellular phenotypes the group developed the Cellular Microscopy Phenotype Ontology (CMPO), a species-neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations. Building a bridge between Euro-BioImaging, INFRAFRONTIER and EATRIS, CMPO is compatible with related ontology efforts, allowing for future cross-species integration of phenotypic data. It is intended to support researchers generating phenotypic data in annotating the phenotypes identified in their screens. The development of annotation tools to facilitate and support the annotation of phenotype terms with CMPO is underway.

The paper will be presented at the Phenotype day during the ISMB 2014 (July 11-15, Boston USA). More information on CMPO can be found here.

BioMedBridges prepares for the data deluge

Collaboration of life science and e-infrastructures

An initial BioMedBridges knowledge exchange workshop, held on 15-16 May in Hinxton and hosted by ELIXIR, provided a forum for the biomedical sciences research infrastructures (BMS RIs) to discuss their possible future service requirements with e‐infrastructure providers. The workshop addressed biological ‘big data’ and the challenges to be faced by the life sciences five years from now and further into the future. Topics of focus covered the storage, transfer and computation of biological data. Several BMS RIs had nominated technical representatives to participate in the workshop, which was attended by almost 30 participants overall, half from the biomedical science research infrastructures half from e-infrastructure and related initiatives. During the workshop, the BMS RI representatives provided a thorough overview of the diversity and types of data and their data-related needs. Read more about the results of the workshop and find the presentations.

Supporting researchers using sensitive data

Tools for handling data protection and ethical requirements

Organised by the BioMedBridges partners from TMF, technical staff, legal and ethics experts met on 30 June in Berlin to discuss how best to support life science researchers who need to use sensitive data and/or biosamples. Presentations outlined current and proposed EU data regulations, and synergies between existing resources that aid researchers in navigating various local, national, European and international legislation were explored. Participants learned about the guidance provided by the BBMRI legal wiki, the International Policy interoperability and data Access Clearinghouse (IPAC) and the Human Sample Exchange Regulation Navigator (hSERN), and the BioMedBridges tool for the assessment of legal and ethical requirements (see details below).The Resource Entitlement Management System (REMS) was also presented to explore whether, during the process of applying for access to certain datasets, a user might benefit from information on ethics and legal implications being provided.

The discussions reflected the complexity of the issue and highlighted the need to collaborate with each other, as each tool or resource covers a slightly different user group and provides a different level of resolution of the information provided to researchers. Ultimately, separate resources, maintained by the experts in the respective fields, may be needed while - in the longer-term -  harmonization and ease of use for the researcher are very desirable. Workshop participants agreed to continue the very useful discussions and establish initial interactions. More information on the workshop and presentations are available here (or contact Stephanie Suhr).

Standards and data harmonization: prerequisites to data integration

BioMedBridges workshop brings domain experts together

The workshop, hosted on 24-25 June by VUMC in Amsterdam, was attended by project partners and invited external experts from CDISC, and The aims of the workshop were to explore several aspects of standardisation, primarily:
  • Defining entity identifiers and identifiers best practice
  • Development of a standards registry which will document the standards in use within the biomedical sciences research infrastructures, facilitate data integration by matching data elements and integrate other resources within BioMedBridges and externally.
Presentations emphasized the importance of standards for biological data sharing and outlined the current standards landscape. Gap analyses were carried out in group sessions to identify common challenges faced in each field and how working solutions could be found through collaboration. A best practice document for identifiers is intended to be published later in the year. Based on the discussions, the standards registry developed within BioMedBridges will be integrated with existing resources such as,, the EDAM ontology and the BioMedBridges Service Registry. Information on key standards used in the biomedical sciences research infrastructure domains will be included as a priority and regular community input will be sought to keep the information up to date. Presentations given at the workshop are available online. For further information or to get involved, please contact Nathalie Conte.

BioMedBridges "tool in the spotlight"

The Legal & Ethical Requirements Assessment Tool and the Clinical Trials Information Mediator are being (co-) developed and implemented by the Clinical Research Informatics (CRI) group of Töresin Karakoyun.

Legal & Ethical Assessment Tool

Which legal and ethical requirements do researchers have to consider when they are going to use data from external sources? What about data protection, privacy, etc.?

As an individual researcher, it is almost impossible to be informed and knowledgeable about all of the issues involved, especially when this is not their daily business as is the case for many biomedical researchers. At the same time, consultation of experts in order to get this information can be a time consuming process. To support researchers faced with this situation and help them navigate this extremely complex landscape, BioMedBridges partners have developed the Legal and Ethical Assessment Tool.

How does it work? The tool was developed to support researchers in identifying legal and ethical requirements around sharing data and using them in new contexts. Central for the tool is its workflow: users are guided by a structured query process in which they are asked about specific data characteristics such as data type (e.g. metadata, text data, images, genetic data, biosamples or biosample associated data), extent of disclosure (pseudonymous versus anonymous), or the level of restrictions imposed on data use. At the end, the tool filters and displays rules, regulations and corresponding solutions that are important for the scenario specified.

Clinical Trials Information Mediator

Currently, finding related entries in different databases is often a time consuming task that has to be performed manually. The Clinical Trials Information Mediator supports researchers working in the personalized medicine area with this by providing insight into the effect of drugs on patients based on clinical trials data and genomic information.

What does it do? The Clinical Trials Information Mediator offers clinical trials data from over a graphical user interface and a RESTful web-service. The tool is a free to use web service which enables integration of data and information from different biomedical databases that were not linked before.

Next release: In the near future, this tool will support researchers by linking publications, genes, and drugs to clinical trials data. It will then also support the researcher by finding clinical trials data with related publications from PubMed automatically.

Find out more!

Legal and ethical requirements assessment tool: check it out here or contact Töresin Karakoyun, Murat Sariyar or Benjamin Braasch.

Clinical Trials Information Mediator: Check out this web based tool here or contact Töresin Karakoyun or Benjamin Braasch.

Upcoming events


Building the bio-connectome: open data infrastructure to accelerate innovation


17-19 November 2015, Wellcome Trust Genome Campus, Hinxton, UK

This international symposium will provide a forum to discuss recent advances in infrastructure to support data sharing and interoperability in the biological, medical, translational and clinical domains. Recent developments to address some of the most important challenges will be presented. Open to the entire life science community, plenary sessions and interactive workshops will provide ample room to discuss data challenges and opportunities in the life sciences now and in future.

Details - including information on how to register - will be made available here.

Other events

Announcements from the biomedical science research infrastructures

Are we missing an event or do you want to share your events with the BioMedBridges community? Please contact the BioMedBridges inreach/outreach team.

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