Future of the Project. BioMedBridges 3rd Annual General Meeting 18 February 2015, Munich Janet Thornton

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1 Future of the Project BioMedBridges 3rd Annual General Meeting 18 February 2015, Munich Janet Thornton

2 What were goals of BioMedBridges? GOAL 1: To provide computational data and service bridges between the BMS RIs, linking basic biological research and data to clinical research and associated data

26 tools and services produced or extended within BioMedBridges WebMicroscope Ontology Tree Viewer MetalPDB AMPS-NMR Bigr XNAT, XNAT MetalS2 MaxOcc Clinical Trials Information Mediator Online

3 26 tools and services produced or extended within BioMedBridges WebMicroscope Ontology Tree Viewer MetalPDB AMPS-NMR Bigr XNAT, XNAT MetalS2 MaxOcc Clinical Trials Information Mediator Online Dictionary of common molecular identifiers myequivalents Shape Matching Tool GenoBridge BBMRI-EU catalog BBMRI-Portal MousePhenotype Legal and ethics tool Tools and Services Registry MOLGENIS, MOLGENIS compute Metadata Model and Mapping Registry PIMS, PiMS LIMS FindGeo BBMRI-NL catalog

4 Collaborative tools: Links for the future Common tools and services for data integration Lines indicate tools that are either co-developed or link pairs of RIs Thicker lines = larger number of common tools third generation RIs are now well integrated!

5 What were goals of BioMedBridges? To provide secure, robust and ethical access to data for a wide range of users: Legal Assessment Tool - LAT Security Framework Ethics framework

6 What were goals of BioMedBridges? To allow interoperability between data and services in the biological, medical, translational and clinical domains Examples Biomedical data tools to allow integration of biomedical image XNAT data into TransMart (infrastructure currently used for omics data patient-to-bench ) Improving access to biobanks and their data, plus integration with public data Diabetes ontology (mouse & human) UniChem links chemical biology resources

7 CHALLENGES Communication between RIs (technical and social) Involvement of relevant community (eg to adopt an ontology); clinicians Engagement with other members of ESFRI infrastructures Coverage space is vast and sometimes overwhelming; BMB can only contribute drops in the ocean but these can be the acorns from which big trees grow.

8 What were goals of BioMedBridges? To bring together the ESFRI BMS RIs with the European computer hardware e-infrastructures: GÉANT, DANTE, EGI, PRACE & CERN:- Developed links to EGI & EUDAT Links to CERN Usage of Geant Better contacts with e-infrastructures

9 STILL to COME! Within BMB Completion of major components of BMB Open Bridges Symposium Future Initiatives (ESFRIs et al) Basis for the future Quantitative Clinical Medicine Multiscale analysis from molecules to organisms Tracking biodiversity Mining of Big Data Translational Research

10 Sustainability Many WPs have a preliminary plan for sustainability, but details need to be worked out Mainly through relevant ESFRI, but also through other established routes e.g. CCP-EM Funding not always available Sustainability is easier if there is a large, involved user and developer community

Sustainability and Reuse Visualising and leveraging ontologies in queries Sharing and integrating medical imaging data Reuse CTTV, Euro- BioImaging CTMM-TRAIT Source code Hosting Bug fixes New

11 Sustainability and Reuse Visualising and leveraging ontologies in queries Sharing and integrating medical imaging data Reuse CTTV, Euro- BioImaging CTMM-TRAIT Source code Hosting Bug fixes New features Expertise Funding Knowledge/ docume ntation Licenses Integrating mouse phenotype data for studying diabetes and obesity CTTV Sharing protein engineering knowledge Federating biobank queries for translational research CTTV Biosample information integration and discovery CTTV Leveraging the utility of compound screening functional assays CTTV Connectivity-Based searching in UniChem CTTV Connect clinical and lab workflows using TranSMART, Galaxy CTMM-TRAIT Linking clinical trials to the drugs, genes, and results they reference?

12 IMPACT Built bridges between the BMS RIs Established collaborations between RIs on the technical level Raised visibility of BMS RIs as a community Increased collaborations with the e-infrastructures Raised awareness, understanding and expertise of the strategic importance of data and related issues, within RIs Sown the seeds for future better integration between biological Highlighted the data challenges and identified priority areas in need of urgent attention

13 Lessons Learned One size does not fit all The use cases are really valuable at the beginning to influence the development of tools Integration with global efforts is essential Legal issues are difficult and changing Not always a single solution - Solutions evolve Dissemination and user engagement remains a challenge

BioMedBridges Open Symposium 17-18 November 2015, Genome Campus, Hinxton Open meeting hosted by ELIXIR, up to 300

14 BioMedBridges Open Symposium November 2015, Genome Campus, Hinxton Open meeting hosted by ELIXIR, up to 300 delegates Room for workshops: BioMedBridges and BMS RIs Still lots of room available! Sponsor exhibition/ poster session/ dinner?

research Ruth March, Astra Zeneca: How the big data explosion is transforming pharma ESFRI Representation BOTTLE OF

15 External speakers Confirmed speakers include: Phil Bourne, NIH: Open data in a global ecosystem Helen Firth, University of Cambridge: Deciphering Developmental Disorders Peter Luijten, University of Utrecht: The role of imaging in translational research Ruth March, Astra Zeneca: How the big data explosion is transforming pharma ESFRI Representation BOTTLE OF CHAMPAGNE FOR BEST REPRESENTED ESFRI (Excluding ELIXIR) Parallel workshops BMS RIs and relevant external initiatives and organisations

Computational Challenges in Life Sciences Research Infrastructures

Computational Challenges in Life Sciences Research Infrastructures Alvis Brazma European Bioinformatics Institute European Molecular Biology Laboratory European Bioinformatics Institute (EBI) EBI is in