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December 2014

Dear colleagues and friends,

As we are entering the final year of the BioMedBridges project, we can take a moment to celebrate what we have achieved so far. Looking back over the last issues of the newsletter, there is a lot to be proud of!

The project successfully passed its half-way point, which we celebrated in March at our Annual General Meeting in Florence, Italy, with three exciting days of networking and exchange of experiences with renowned experts and colleagues from related initiatives. Over the year, the project completed the first batch of major deliverables, including for example the Cellular Microscopy Phenotype Ontology (CMPO), the Legal and ethical requirements assessment tool, and the first pilots for semantic web integration, with more big deliverables due at the end of this month.

ISBE and MIRRI joined the project as Associate partners, and BBMRI-ERIC and INFRAFRONTIER are set to become full project partners - this is a major milestone in the development of the emerging research infrastructures.

Not least, the workshops held this year, either under the BioMedBridges umbrella or in collaboration with other projects and initiatives, have been hugely successful in reaching out and kick-starting collaborations between the biomedical sciences research infrastructures, with the wider life science community, and beyond. I encourage you to have a look at the workshop reports linked below.

Let's continue with the good work.

Wishing you and us all happy holidays and a very successful 2015,

Janet Thornton

Metadata Model and Mapping Registry

Request for feedback on first public beta


With the release of the first public BETA of the Metadata Model and Mapping registry, the standards work package of BioMedBridges is reaching a major deliverable. The registry complements great resources such as Biosharing.org, which maps the landscape of community developed standards in the life sciences. However, once suitable standards have been identified, users typically need to manually explore technical documentation to uncover the full details needed to assess whether they are fit for purpose. Using a simple Google search, the Metadata Model and Mapping registry enables researchers to find (standard) data models, formats, (biobank) data dictionaries, guidelines, and templates, and to compare their data elements and relationships in a uniform way. In future releases the registry will be enhanced with semantic search capabilities and by integration of the BiobankConnect mapping tool. This initiative is part of the broader movement to promote findability, accessibility, integration and reusability of scientific data (FAIR principles, datafairport.org), and in particular to promote the use of (de facto) standards within and beyond the twelve biomedical sciences research infrastructures involved in BioMedBridges.

Please contact Morris Swertz to provide feedback on the registry and suggestions to expand its contents.

Workshop: Data strategies for research infrastructures

19 February 2015, Munich, Germany


Preserving complex data and/or making it available, accessible and discoverable for users requires robust plans to store, organise, integrate and, where applicable, distribute it. This knowledge exchange workshop is aimed at project managers and coordinators of research infrastructures, with the goal of helping participants to understand (1) the data challenges of their infrastructure, and (2) the data-related support needed by infrastructure users.

More information on the workshop is available here.

Biomarker discovery from biological and medical imaging

Expert workshop to remove obstacles to image data interoperability, 2-3 February 2015, EMBL, Heidelberg


Interoperability of large-scale image data sets is required for reuse and analysis of data sets that were generated at different Biological scales (e.g. cells and organs) and in different biomedical models. The BioMedBridges imaging experts aim to facilitate interoperability of different image data sets (cellular, mouse and human tissue) and to create the tools that facilitate the comparison of cellular phenotypes specific to individual genes with morphological imaging data from diseased tissue specimens (both human and mouse tissue). Correlative analysis of interoperable cell and tissue image datasets can link their associated annotations and metadata, ultimately leading to a powerful predictor of biomarkers as well as drug targets for cancer treatment. The link between cellular and tissue images and their genetic information can show the functional consequences of somatic mutations identified in cancer genome sequencing projects and could allow for prioritization of biomarkers for validation in clinical research.

One of the main obstacles to interoperability of biological and medical imaging data is the big diversity of standards and formats used during image acquisition and processing. To address this, BioMedBridges is organising a workshop on “Metadata Standards and Data Formats in high-throughput imaging” in collaboration with the Systems Microscopy project, which works on the standardization of imaging methods that are used to systematically analyze biological processes like cell division and migration. The workshop aims to stimulate high-level exchange between partners from both projects as well as with external experts who are working on imaging metadata standards and data formats. More information on WP6 Imaging is available here.


For more information on the workshop, contact Tanja Ninkovic or Gabriella Rustici.

Symposium: Open bridges for life science data

Save the date: 17-18 November 2015, Hinxton

The BioMedBridges open 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. The program (available here) includes focused workshops on various topics, including Sharing data from clinical and medical research, Image data interoperability and APIs and workflows. Confirmed speakers include Phil Bourne from the National Institutes of Health "Big Data to Knowledge" initiative, Kate Bushby (Newcastle University) and Jim Davies (Genomics England/100,000 Genomes project).

Room for additional workshops, seminars or exhibitions is still available (for more information contact Joy Friesner). Register here to receive event updates.

BioMedBridges "tool in the spotlight"

Manage data for targets, constructs and experiments with PiMS 


Over the last five years, there has been a significant convergence in methods used for protein production. Laboratory information, however, is still recorded in a variety of formats, including lab notebooks, spreadsheets, text documents, and local databases. In addition, scientists look up gene sequences, protein sequences, and standard protocols online. As a result data management is now one of the bottlenecks for increasingly busy protein expression laboratories.
PiMS was developed to address this. PiMS is a Laboratory Information Management System (LIMS) to support the unpredictable workflows of molecular biology and protein production labs. It supports scientists in keeping track of construct design, cloning, expression, protein purification, and crystallogenesis. It provides a web interface to do this, with a database behind the scenes. PiMS supports researchers in keeping track of, for example, recombinant protein expression, which is especially important for high throughput labs, long-term projects, and scattered collaborations including service provision.
 
As part of the BioMedBridges project, PiMS has been extended with an RDF interface. Its schema is compatible with the UniProt schema as well as the core RDF standards Dublin Terms and PROV-O. The extension to PROV-O will enable a future vision of tools which track the provenance of published biomedical results to the datasets and samples involved in the research project.
 
Find out more about PiMS here and how to get your (academic) license.

BioMedBridges workshops: reports available

Upcoming events

  • The workshop “Metadata Standards and Data Formats in high-throughput imaging”, jointly organized by the BioMedBridges and Systems Microscopy projects, will be held on 2-3 February 2015 at EMBL in Heidelberg. If you are interested in participating, please contact Tanja Ninkovic and Gabriella Rustici.
  • BioMedBridges: 3rd Annual General Meeting 2015, 17-18 February 2015, Munich, Germany (project partners only)
  • Workshop: Data sharing for research infrastructures, 19 February 2015 at ESO in Munich. The workshop is aimed at RI project managers and coordinators; registration is on a first come, first served basis.
  • BioMedBridges: Symposium; Open bridges for life science data, 17-19 November 2015, Hixton, UK

Announcements and news from the biomedical science research infrastructures

Until then, we wish you a very merry Christmas and a successful 2015!

More information:
info@biomedbridges.eu
www.biomedbridges.eu