The international Open Bridges for Life-Science Data symposium, which took place 17-18 November on the Wellcome Genome Campus in Hinxton, attracted around 250 delegates from all over the world.
On 1 September 2015 the CORBEL cluster project started to establish common research infrastructure to support Europe's biomedical research community. CORBEL (Coordinated Research Infrastructures Building Enduring Life-science Services), which will also build on the output of BioMedBridges, is a four-year €14.5 million EU project that will harmonise user access to biological and medical technologies, biological samples and data services, required by cutting-edge biomedical research.
Offering a web service involves offering access to the processing capabilities of some software, some computational resource, and often access to some data. Doing so effectively involves not only getting the service right, but also ensuring that the terms on which it is offered support the intended use, without unacceptable exposure for the institution providing service.
Aims A growing number of web pages are offering advice on how to choose an open license for data or code. The advice they give is partly conflicting. This workshop is intended to get together the authors of such pages and others with expertise or experience in this area to clarify the choices. Among the issues to be discussed are:
Data is the lifeblood of science. Scientists produce data and analyse data, and service providers including research infrastructures (and e-infrastructures) provide facilities for data production and/or storage, sharing and reuse.
Metabolomics is one of the latest -omics sciences and there is a growing interest for its application in prognosis, diagnosis, patient stratification and personalized medicine. For this reason, biomedical research infrastructures are strongly interested in the development of this technology. Because metabolomics is multidisciplinary in nature, it could rapidly become an “experimental bridge” between the different communities served by the research infrastructures.
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.
A paper on the UniChem Widesearch - developed as one of the BioMedBridges data integration pilots by Jon Chambers and colleagues - was just published in the Journal of Cheminformatics.
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.
New data bridge between ELIXIR and BBMRI supports discovery of underlying causes of disease
THE WORKSHOP REPORT IS NOW AVAILABLE
17-18 November 2015, Wellcome Genome Campus, Hinxton, UK Join us to discuss the latest advances in the technical infrastructure behind large-scale data sharing in the life sciences, and the interoperability of data resources supporting biological, medical, translational and clinical research.
Collaboration of life science and e-infrastructures
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, BioSharing.org and identifiers.org. The aims of the workshop were to explore several aspects of standardisation, primarily:
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.
The workshop “Clinical Research Informatics Solution Days” will be held on 26-27 May in Duesseldorf, Germany. The workshop is jointly organised by ECRIN and other EU-funded projects including BioMedBridges to bring together experts, users and innovators from the clinical research domain. The workshop will provide an overview of available IT-tools and services for modern clinical studies. The tools and services will also be demonstrated in interactive hands-on sessions.
Photos and presentations from the second annual general meeting of the BioMedBridges partners and external experts and stakeholders, which took place on 10-11 March 2014 in Florence, Italy, are now available.
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 encouraged:
With a launch event in Brussels on 18 December, ELIXIR celebrated assuming its legal entity and entering its permanent phase after Estonia joined the United Kingdom, Sweden, Switzerland, the Czech Republic and the European Molecular Biology Laboratory (EMBL) in ratifying the Consortium Agreement.
The BioMedBridges Executive Steering Committee met on Friday, 13 December 2013 in Hinxton. The steering committee, hosted by ELIXIR, came together to review the achievements from the first half of the project and discuss the strategy and priorities for the second.
The interactive HandsOn Biobanks conference will take place on 21 – 22 November 2013 in the World Forum, The Hague and will zoom in on questions such as:
Shortly after its Inaugural Conference (find a short Highlights Report here), EATRIS received the status of an ERIC (European Research Infrastructure Consortium). This European legal status is intended to facilitate and support the work of international research infrastructures in Europe.
EU-OPENSCREEN is holding its 3rd stakeholder meeting on 20 November in Oslo, Norway. More information and how to register here.
Learn more about the Euro-BioImaging infrastructure model (one of the biomedical sciences research infrastructures involved in BioMedBridges) and about the next steps Euro-BioImaging is taking towards the implementation phase at this upcoming Stakeholder meeting. More information and how to register here.
The BBMRI-ERIC Inauguration Conference took place on 16 September 2013 in Graz, Austria. BBMRI, together with ELIXIR, coordinates the Standards Description and Harmonization work package (WP3) of BioMedBridges. The conference program highlighted how biobank data can be utilised within personalised medicine and provided a thorough overview of the BBMRI nodes in the research infrastructure's 14 member states. The importance of BBMRI's coordination efforts were stressed.
The scope of BioMedBridges and the Phenobridge Work Package (WP7) were discussed at a recent webinar titled "Databridges enhance access to research data in INFRAFRONTIER". The webinar (held in German) was part of a series on "Open Access to Research Data" hosted by the Helmholtz Association's Open Access Coordination Office. Information on the webinar and the presentation given are available here.
BioMedBridges participated in the ISMB/ECCB 2013 conference (18-23 July) in Berlin to introduce the project to the wider user community and to present the trial version of the tools registry. Many visitors signed up for the registry mailing lists.
BioMedBridges participated in the EATRIS launch event in Amsterdam, 4 June 2013. A full post conference report which will provide highlights from each presentation of event will soon be published on the EATRIS website.
In February-March 2013, BioMedBridges partners at STFC and EBI carried out a survey on shape/volume fitting in structural biology. There were over 40 responses and a summary of the results of the survey has now been released. The results will inform the development of a new service for the analysis and comparison of structural volume data.
BioMedBridges partner Helen Parkinson speaking at a webinar: "Current uses of and future directions for the Genome-Wide Association Studies Catalog", 18 July 2013. Registration now open for course: EMBL Advanced Course: Computational Aspects of High-Throughput Screening planning and analysis, EMBL Heidelberg, Germany, Monday 14 October - Wednesday 16 October 2013.