View this email in your browser

October 2014

Linking disease terminology with gene identifiers

New data bridge between ELIXIR and BBMRI prototype supports discovery of underlying causes of disease 

The team from the BioMedBridges use case on Integrating disease-related data and terminology from samples of different types have delivered a prototype linking ICD10/SNOMED CT concepts to Ensembl gene identifiers. With this project deliverable, the authors - Albert Pallejà Caro, Sune Frankild, David Westergaard, Pope Moseley and Søren Brunak - have produced a mapping between disease terminologies used to characterize patient conditions on one side and biobank samples and human gene identifies on the other.Linking biomolecular and biobank resources in this way and thus creating another data bridge between ELIXIR and BBMRI will enable systems biology analyses with the aim of finding the underlying causes of disease and, for example, also the molecular links between diseases and their comorbidities.

The detailed report on the deliverable can be downloaded here.

Life science data interoperability resources to combine efforts

Two workshops to kick off collaboration

In the life sciences, users are faced with a choice of multiple resources to facilitate and promote the use of standards, policies, models, identifiers, databases, tools, services, and ontologies. Some of these resources are well established while others are less mature and, although the scope of each is quite specific, there is potential overlap. To address this issue, which lies at the core of the BioMedBridges mission, the project has co-organised a series of workshops contributing to the harmonisation of the life science data interoperability landscape.

Representatives of, EDAM ontology, and the BioMedBridges Tools and Data Services Registry as well as the Standards Registry met during a knowledge exchange workshop on 1 October at EMBL-EBI in Hinxton. At the workshop, which followed the initial BioMedBridges standards workshop held in June in Amsterdam, participants identified areas of possible collaboration and coordination. Going deeper into the basis for successful integration, a workshop to agree on the development of a  common vocabulary to classify resources in the life sciences was held on 16 October in Brussels, collocated with the RDA-ESFRI workshop on data interoperability. The outcomes of the workshop, which was very well attended by representatives from a wide range of resources and disciplines, will be published in a summary in the near future.

Prototype of shape-matching software launched

User feedback welcome!

With the completion of a prototype of the shape-matching software, the BioMedBridges use case From cells to molecules - integrating structural data has completed a major milestone. In the first instance the prototype will perform volume matching on example datasets.The service is novel in providing access to volume data, a growing class of structural biology data. Development work on the prototype has clarified the requirements for the web-based shape-matching service, which is scheduled to be launched in March 2015.Feedback on the software from potential end users of the web-based service is welcome. Please contact Martyn Winn.A detailed report on the milestone is available here.

BioMedBridges "tool in the spotlight"

Imaging data management and interoperability with the XNAT server

Efforts on the BioMedBridges instance of XNAT were focused on lowering the barrier for users by making installation easier and providing documentation such as use agreements for shared imaging data
There is an increasing demand to incorporate imaging data into medical research, owing to the detailed information on anatomy, function, and pathology that techniques such as magnetic resonance imaging (MRI), computed tomography (CT), and ultrasound are able to provide. At the same time, medical research projects increasingly often involve a larger number of different medical centres. For example in epidemiological studies, patients or volunteers might be scanned at a medical centre closest to them while the data analysis takes place elsewhere. To exchange such imaging data and the derived results (for example organ volume measurements), researchers were previously often forced to resort to DVDs or FTP servers, with analyses carried out in different centres using different image processing tools. This way of working is often laborious and error-prone and does not allow for the sharing, reuse and/or repurposing of data.

XNAT (Extensible Neuroimaging Archive Toolkit, is an open source and highly extensible informatics platform for imaging research. In accordance with BioMedBridges objectives, Erasmus MC developed and deployed REST web services based on XNAT. The REST interface allows other applications (both web services and desktop applications) to embed data from medical imaging databases into XNAT and vice versa. Imaging data can be sent directly from a clinical workstation to the server and from there to a computing cluster to be analyzed; image-derived results can then automatically be stored in XNAT. In this way, a user-friendly data bridge for medical imaging trials is provided that enables the centralised sharing and analysis of imaging and image-derived data and which supports centralised correlative analysis between image-derived data and other types of data such as clinical data (e.g. disease status, age) and genetic data.

Via these new web services, three large datasets have been made available to a wide audience for research purposes, enabling both academic and industrial developers of image analysis software to validate their methods on these publicly available datasets. Moreover, in collaboration with EATRIS and BBMRI-ERIC, the web services were already applied in a multi-centre clinical study on imaging atherosclerosis, and they are currently implemented for use in a multi-centre study on vascular cognitive impairment. To simplify the installation of the XNAT imaging platform, a generic script was developed that largely automates the deployment. This script was made available to the community, in order to further promote the use of the XNAT imaging platform.

Find out more here or contact Stefan Klein of the BIGR group from the Erasmus University Medical Center, The Netherlands.

Upcoming events

SYMPOSIUM: Open bridges for life science data

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.

Further details will be made available here - until then, you can register here to receive updates!

Announcements and news 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.

Sign up

Would you like to subscribe to the BioMedBridges newsletter? Please sign up here. You can of course also unsubscribe from this list or update subscription preferences.
More information: