Overview of project progress

BioMedBridges 3rd Annual General Meeting 17 February 2015, Munich

Janet Thornton

Ten biomedical sciences research

infrastructures: stronger through

common links

BioMedBridges project partners 1   EMBL   ELIXIR   European Molecular Biology Laboratory   Germany  2   UOXF   INSTRUCT   University of Oxford   UK  3   KI   BBMRI   Karolinska Institutet   Sweden  4   STFC   INSTRUCT   Science and Technology Facilities Council   UK  5   UDUS   ECRIN   Heinrich Heine University Düsseldorf   Germany  6   FVB   EU-Openscreen   Forschungsverbund Berlin e.V./Leibniz-Institut für Molekulare Medizin   Germany  7   TUM-MED   BBMRI   Technische Universität München   Germany  8   SZN   EMBRC   Stazione Zoologica Anton Dohrn   Italy  9   ErasmusMC   EuroBioImaging   Erasmus University Medical Center Rotterdam   Netherlands  10   TMF   EU-Openscreen   Technologie- und Methodenplattform für die vernetzte medizinische Forschung e.V.   Germany  11   HMGU   Infrafrontier   Helmholtz Zentrum München   Germany  12   MUG   BBMRI   Medizinische Universität Graz   Austria  22   VU-VUMC   EATRIS   Vrije Universitaeit Amsterdam Medical Centre   Netherlands  14   Inserm   ECRIN/ERINHA   Institut National de la Santé et de la Recherche Médicale   France  15   UCPH   ELIXIR   University of Copenhagen   Denmark  16   UH   EATRIS   University of Helsinki, Institute for Molecular Medicine Finland   Finland  17   EGI   e-Infrastructure   European Grid Infrastructure   Netherlands  18   CSC   e-Infrastructure   Centre for Scientific Computing Finland   Finland  19   UMCG   BBMRI   University Medical Centre Groningen   Netherlands  20   CIRMMP   INSTRUCT   Consorzio Interuniversitario di Risonanze Magnetiche di Metalloproteine   Italy  21   DANTE   e-Infrastructure   Delivery of Advanced Network Technology to Europe   UK  

Welcome to BBMRI-ERIC and INFRAFRONTIER GmbH as full project

partners!

BMB Scientific Advisory Board ¡ Professor Eero Vuorio, University of Turku, Finland

(Chair) ¡ Dr. Lee Harland, UK* ¡ Professor Larry Hunter, University of Colorado, USA ¡ Dr Anne-Marie Tasse, McGill University, Canada (for

Professor Bartha Maria Knoppers) ¡ Professor Babis Savakis, University of Crete,

Greece

*(not able to attend)

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BMB E-Advisory Task Force ¡  Neil Geddes (Chair), STFC, UK (resigned)

¡  representing e-Science ¡  John Chevers (replacing Dai Davies), DANTE

¡  representing DANTE & networking ¡  Bob Jones, CERN

¡  representing a large institute with a huge computational infrastructure

¡  Kimmo Koski (represented by Per Oster), CSC, Finland

¡  representing EUDAT & HPC ¡  Steven Newhouse, EGI, NL

¡  Representing the Grid community

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Day 1: Tuesday, 17 February 12:00 to 20:30 Location: Auditorium 12:00 Registration and lunch 12:30 Overview of project progress Janet Thornton/Stephanie Suhr 13:00 Work package presentations:

Update on status, progress, outlook and plans for sustainability of project output (20 min each) Work package leaders

15:00 Wrap-up and focus areas from work package presentations Janet Thornton 15:10 Flash presentations (5 min each) - urgent or important topics - Open to all

15.30 Coffee 16:30 to 19:00 Work package meetings (WP5, 6 & 7)

Organised by work package leaders – any others? 19:00 Poster/networking session and working dinner (HERE) Bavarian specialty buffet

Agenda

Components of this meeting

¡ Updates on progress from WPs ¡  Meetings of the WPs

¡  Priorities for final year of project

¡  Updates from BMS RIs – including sustainability

¡  Committee and advisory board meetings (closed) ¡  Executive Steering Committee ¡  Scientific Advisory Board ¡  E-Advisory Task Force ¡  Feedback session: Exec Steering Comm + SAB + E-advisory Task Force

What were goals of BioMedBridges? ¡  To provide computational ‘data and service’ bridges

between the BMS RIs, linking basic biological research and data to clinical research and associated data

¡  To provide secure, robust and ethical access to data for a wide range of users

¡  To allow interoperability between data and services in the biological, medical, translational and clinical domains

¡  To bring together the ESFRI BMS RIs with the European computer ‘hardware’ e-Infrastructures: GÉANT, DANTE, EGI, PRACE & CERN

Standards description & harmonisation

Technical integration

Secure access

Trai

ning

Tech

nolo

gy w

atch

Interoperability of large scale image data sets

Improving the link between mouse models and human data

Personalized Medicine

Integrating structural data

Integrating disease-related data and terminology

Three construction work packages to build the technical bridges

•  “Secure Access” and “Standards” will facilitate the effective sharing of data

•  “Technical integration” will construct the e-infrastructure

Five inter-related use cases

• To test the technical and data developments of the construction work packages

• Each use case focusses on a particular ESFRI Research Infrastructure

• Training participants to ensure common understanding

• Training the user community on the standards and tools developed

• Capturing the expertise from e-infrastructure providers

• Ensuring BioMedBridges adopts the state of the art

Goals of 2015 AGM ¡ To review third year of project ¡ To plan further for the 4th & final year – making

detailed plans for last deliverables ¡ To discuss sustainability ¡ To explore enhancement of user engagement and

impact ¡ To strengthen collaborations going forward

Mid-term review passed! ¡ Results (finally) received in December 2014 ¡ Overall very positive comments, including

¡  Good progress ¡  Excellent collaboration within the project

¡ Areas for possible improvement/overall recommendations: ¡  Solve issue of sustainability before the end of the project

(see below) Make outcomes of use cases available as widely as possible

¡  Further include ERINHA and other less active RIs in the project

¡  Increase dissemination activities

Highlights 2014 ¡ Metadata Model and Mapping registry ¡ Service registry (BMB -> ELIXIR): example for

sustainability ¡ CMPO (Cellular Microscopy Phenotype Ontology) ¡ Diabetes and Obesity Ontology ¡ Shape matching software – unlocking data

resources

Planned Interactions in WPs

●  Network analysis of BMS RIs showing collaboration within different work packages

●  Thicker lines (edges) = larger number of work packages each pair of RIs collaborates in

●  Proximity = higher degree of overlap between RIs on deliverables (larger number of shared deliverables)

Legal and ethics tool Tools and Services Registry MOLGENIS, MOLGENIS compute Metadata Model and Mapping Registry

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

PIMS, PiMS LIMS FindGeo BBMRI-NL catalog

26 tools and services produced with BioMedBridges

Collaborative tools ●  Common tools and services

contributing to data integration

●  Lines between any two BMS RIs indicate tools that are either co-developed or tools that will be useful to link up pairs of RIs sometime in the future

●  Thicker lines = larger number of common tools

→ All RIs are connected at least through generic tools → third generation BMS RI are well “tied in”!

Project status: deliverables

Project status: deliverables

Adjustments to the project plan

○  Second amendment to the Grant Agreement ○ Waiting for approval by the end of February.. ○  Includes major changes: ○  Last WP10 deliverable changed to biobank

information federation via MIABIS ○  Several other adjustments below inclusion

threshold, e.g. transfer of funds from FIMM to UMCG (WP8, WP10)

Collaboration: workshops

¡ BMS RI and e-infrastructures ¡  15-16 May 2014, Hinxton ¡  Recommended by e-infrastructure advisory board ¡  REPORT: http://dx.doi.org/10.5281/zenodo.13942

¡ Supporting researchers using sensitive data ¡  30 June, TMF, Berlin ¡  Participants incl. experts from BBMRI, EATRIS ¡  REPORT: http://dx.doi.org/10.5281/zenodo.12246

¡ Standards (WP3): ¡  24 June 2014, Schiphol airport ¡  Standards experts from all BMS RIs and wider community invited,

including CDISC, identifiers.org ¡  Resource integration workshop ¡  1 October, EMBL-EBI, Hinxton ¡  Common goals and integration of

BioMedBridges Standards Registry, Biosharing.org, identifiers.org, EDAM, Tools and Data Services Registry

¡ A common vocabulary to classify resources in the life sciences ¡  Brussels, 15 October ¡  Topics to be able to integrate resources: training courses, jobs,

resources, etc. ¡  REPORT: http://dx.doi.org/10.5281/zenodo.13231

Collaboration: workshops

Upcoming workshops ¡ “Metadata Standards and Data Formats in high-

throughput imaging” ○  jointly organized by BioMedBridges WP6 and Systems

Microscopy ○ will be held on 2-3 February 2015 at EMBL, Heidelberg ○ contact Tanja Ninkovic (ninkovic@embl.de) and Gabriella

Rustici(gabry@ebi.ac.uk)

Upcoming workshops ¡ Data strategies for research infrastructures

¡  19 February, Munich (ESO headquarters) ¡  For project managers, coordinators ¡  Info needed for a project manager to do their job, for example:

○ What to look out for ○ Budget implications ○ Short, medium and long-term plans ○ RI-wide data strategy

○ Open beyond BioMedBridges ○ ca. 25 workshop participants, including

from new Ris, EUDAT etc.

BioMedBridges Open Symposium ○ 17-18 November 2015, Genome Campus, Hinxton ○ Open meeting hosted by ELIXIR, up to 300 delegates ○ Room for workshops: BioMedBridges and BMS RIs ○ Still room available!

○  Exhibition/ poster session/ dinner

External speakers ○ Confirmed:

○  Phil Bourne, NIH: “Open data in a global ecosystem” ○  Mathias Uhlén, SciLifeLab: “The future of proteomics – integrating proteomic and

genomic data” ○  Helen Firth, University of Cambridge: “Deciphering Developmental Disorders” ○  Willem Ouwehand, University of Cambridge: “Using Genomics Data in the clinic and

for clinical research” ○  Jan Ellenberg, EMBL and Euro-BioImaging ○  Peter Luijten, University of Utrecht: “The role of imaging in translational research” ○  Soren Brunak, ELIXIR-DK

○ Maybe (tbc) ○  Ruth March, Astra Zeneca: “How the big data explosion is transforming pharma”

○ Confirmed podium discussion “Omics and translational data” ○  Chair: Ewan Birney, EMBL-EBI ○  Jim Davies, University of Oxford, Genomics England/100,000 Genomes Project ○  Kate Bushby, Newcastle University, RD Connect

Dissemination: website

○ Website update ○  Showcase project outputs during the final year and running up to

the Open Symposium ○  User personae:

○ Working bioinformatician: expert user looking for direct access to tools

○ Biomedical or clinical researcher: possible first time or infrequent user who benefits from information on the context of tools and resources, and “what they do”

○ Funders and the general public: looking for general information about the project, including aims, contexts, and benefits

Dissemination: tools pages

Dissemination: project output on Zenodo ○  All deliverable reports, position papers

and workshop reports or summaries ○  part of OpenAIRE, also provides “long-

tail data storage” for H2020 open data pilot

○  doi provides better way to cite and reference project output

○  Publications tagged with specific EC-funded projects are automatically displayed on CORDIS information pages

→ Publications more visible as they are made available to entire scientific community

→ Publications stored in a stable, long-term repository (as opposed to project-specific website that will become redundant after the project terminates).

5 most popular tools: 1. UniChem widesearch... 2. xx 3. GenoBridge…………... 4. xx 5. xx

Building data bridges in biology and medicine

●  Tools ●  Training ●  News ●  Meetings ●  About

BioMedBridges builds bridges between biological, medical, translational and clinical data resources, bringing together scientists with a wide variety of scientific backgrounds to share knowledge and data, and opening up and integrating available resources. Read more about the research infrastructures and our objectives.

Imaging resources Clinical trials support Diabetes and obesity research Drug discovery Working with sensitive data Data integration and standards Personalised medicine tools

Ethical Governance

○  Audit conducted by Independent External Ethics Advisor (supported by project manager) ¡  Fix any issues before report to Commission ¡  September-November 2014 ¡  Report and formal deliverable submitted in December

○  Next step: report of compliance at project completion

Priorities for the final project year

○  Sustainability ○  Impact (user feedback, metrics) ○  Lessons learned

Lessons learned

○ Important project output!

○  What worked, what didn’t work – what is feasible? ○  Where should future initiatives pick up ○  Best practices, guidelines

Meeting: today

¡ Flash presentations - end of day 1 ¡  Present urgent or important things you want to alert

your colleagues to and/or get feedback on ¡  up to ten presentations ¡  slots available!

¡ Poster session and buffet dinner Presentation topic Name 1 EGI-Engage: competence centres Gergely Sipos 2 Imaging data activities Rafael Jimenez 3 Online training modules Tom Hancocks 4 Licensing issues: software and data Chris Morris

Meeting: Day 2

○ Summary of first day: focus areas ○ Presentations by BMS RI Directors/Coordinators

or representatives: RI status ○ priorities and next steps