ELIXIR UK Node presentation to the ELIXIR Board
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The document provides information about ELIXIR-UK, which is the UK node of ELIXIR, a European infrastructure for biological information. ELIXIR-UK is a network of 18 UK organizations and has established training programs, services, and communities. It coordinates UK participation in ELIXIR and related EU projects. ELIXIR-UK also works to establish interoperability across biological data resources and help make these resources FAIR (Findable, Accessible, Interoperable, Reusable). It is working to establish BioFAIR, a proposed new institute that would coordinate UK life science data infrastructure.
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ELIXIR UK Node presentation to the ELIXIR Board
- 1. European Life Sciences Infrastructure for Biological Information www.elixir-europe.org ELIXIR-UK Carole Goble and Neil Hall Heads of Node
- 2. ELIXIR-UK Node: a Network of 18 Organisations Legal signatory Node Coordination Office Head of Node Head of Node Cardiff University, Earlham Institute, Edinburgh Genomics, Heriot Watt University, Imperial College London, Newcastle University, Rothamsted Research, The University of Birmingham, The University of Liverpool, The University of Manchester, The University of Nottingham, University of Bradford, University College London, University of Cambridge, University of Dundee, University of Edinburgh, University of Leicester, University of Oxford Nœud ELIXIR-UK: un réseau de 18 organisations
- 3. ELIXIR UK Node Established in 2013 with starter grant (2014- 2017) focused on networking and training • Training Coordinators • TeSS Training Portal • The Carpentries Expansion in 2016 to full range of Node activities • Reflecting the services, activities, platforms and communities engaged in Coordination office funded (2017-2020) • Node Coordinator • Communications and Networking funds Neil Hall Head of Node Earlham Institute Carole Goble Head of Node Manchester Nicola Soranzo TechCoordinator Earlham Institute Gabriella Rustici TrainingCoordinator Cambridge Catherine Hunter Node Coordinator, Earlham Institute
- 4. ELIXIR UK Node Neil Hall Head of Node Earlham Institute Carole Goble Head of Node Manchester Nicola Soranzo TechCoordinator Earlham Institute Gabriella Rustici TrainingCoordinator Cambridge Catherine Hunter Node Coordinator, Earlham Institute Node Funding ELIXIR funds Impl studies, platform funding, staff exchange EU ELIXIR Awards Competitively won Investigator won services and activities Node-Node collaborations In kind The UK doesn’t currently run dedicated ESFRI e-Infrastructure call
- 5. UK funding landscape • Coordination office funding £750k (2 posts) • Communications • Workshops • Meetings and Travel • Administration of Elixir funds • 15 node –services receiving ~ £6,000,000 from UKRI, EU Wellcome Trust and NIH. • No funding direct from node £ £ Node Services Meetings Comms Workshops
- 6. UK funding landscape • Coordination office funding £750k (2 posts) • Communications • Workshops • Meetings and Travel • Administration of Elixir funds • 15 node –services receiving ~ £6,000,000 from UKRI, EU Wellcome Trust and NIH. • No funding direct from node
- 7. ELIXIR RELATED EU Projects PROJECT INSTITUTIONS EOSC-Pilot University of Manchester University of Oxford Heriot Watt University EOSC-Life University of Manchester University of Oxford University of Cambridge University of Dundee ELIXIR-Excelerate University of Manchester University of Oxford University of Cambridge University of Edinburgh Heriot Watt University Earlham institute ELIXIR-Converge University of Manchester University of Cambridge CORBEL University of Manchester IMI FAIRplus University of Manchester University of Oxford Heriot Watt University EJP-RD University of Manchester University of Cambridge EOSC-Enhance University of Manchester
- 8. ELIXIR and the UK Landscape The vatican £8.7 Bn Funding £1 Bn £0.6 Bn 24 research intensive universities
- 9. Policy Wrangling Revisions to the OECD Recommendation of the Council concerning Access to Research Data from Public Funding
- 10. UK e-Infrastructure for Life Science Landscape Biological sciences, health and food themes “Significant expansion of the UK node of ELIXIR to support BioFAIR, a data sustainability institute supporting the coordination and development of UK life science data”
- 11. ELIXIR-UK Serves Membership ELIXIR UK BioFAIR a data sustainability institute supporting the coordination and development of UK life science data BioFAIR Digital Object Commons for UK Life Science. Mobilising and coordinating UK life science data infrastructure community Accessing funding and engagement opportunities by UK members Developing ELIXIR Communities Executing the Strategic Plan Services SDPs Platforms Communities Portals Activities EU Projects Node-Node cooperations
- 12. A Network • Helping our members run and participate in meetings • Sponsoring meetings • 2020 UK Bioinformatics Conference to coincide with UK All Hands ELIXIRAll Hands 2018, Berlin Biohackathon, November 2018, near Paris ELIXIR UK All Hands, 2018, Birmingham Dagstuhl Seminar FAIR e- Infrastructures Nov 2018
- 13. 4 Platforms 15 Services with SDPs 2/3 ELIXIR Portals 7Communities 2 ExCo 3 EIP RIRs 1/6 CDRs not EBI/SIB 2 Leader ship 18 organisations 16+1 Implementation Studies 8 ELIXIR EU project awards 7 WP leaderships In numbers 9 In review 2 Platform funding 2 WGs
- 14. Focus A lot of Node co-operations EBI are of course strong partners • Communities • Services • Interoperability • FAIRification • Markup • Workflows
- 15. Focus Training Interoperability Data Management Structural Bioinformatics Model Organisms Systems Biology Animal Health Microbial Biotechnology Metabolomics Plant Sciences Tools
- 16. Communities
- 17. Highlight: 3DBioinfo To develop the infrastructure for FAIR structural and functional annotations To create open resources for sharing, integrating and benchmarking software tools for modelling the proteome in 3D To develop tools to Describe, Analyse, Annotate, and Predict Nucleic Acid Structures To help develop models for protein-ligand interactions 3DBioInfo Launch, Basel, 2018Christine Orengo, UCL Increasing Interoperability between ELIXIR Protein Structure and Sequence Resources and Expanding these Resources with 3D-Models of CATH Domains, built by SWISS-MODEL CATH protein structure classification Core Data Resource, Jalview multiple sequence alignment editing, visualisation and analysis tool PHYRE2 protein structure prediction Co-led Commissioned Service:
- 18. The ELIXIR Node Services UK developed Service Best Practice. 9 new services in review. https://f1000research.com/articles/5-2894/v2 Dundee Resource for SequenceAnalysis and Structure Prediction CDR RIR Portal
- 19. PHI-base http://www.phi-base.org/ Expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions.
- 20. Highlight: The TeSS Training Portal https://tess.elixir-europe.org ELIXIR training portal to aggregate events and training materials 77% increase in users 2018-2019 75 content providers 284 Upcoming events 10657 past 1328 materials 1K users / month 50:50 manual/auto Born native of ELIXIR
- 21. The TeSS Training Portal in a Nutshell automatically aggregate training resources link to registries content embedded with widgets in 3rd party sites curation tools
- 22. Organising and Navigating Content Concept Maps and Learning Paths Experiments Funded by Commissioned services Concept maps Learning outcome templates Generate learning paths Relate to Service Bundles
- 23. Community Contributions for Content and Code, and Wider uptake -> from start-up to maturity Open Development Framework Metadata processors Scraper development Curation Contributions Embedded widgets Scale Contribution Modularise, Packaging, Governance Other communities. Around topics, communities, organisations, geographical. CZI, EJP-RD, HDR-UK, ARDC, EOSC. TeSS needs to be packaged, marketed, and supported properly Content User UX Added value
- 24. TeSS, the UK Node and the ELIXIR Platform a native ELIXIR infrastructure service Changes in UK leadership • Manchester -> Cambridge Resources challenge • 1.5 FTE dedicated development in one organisation (4 people needed) • Over dependence on Niall • Lack resources to build UK base National funding challenges • Seen as an ELIXIR not UK service • Incorporation into BioFAIR proposal Resources for content curation • Affects quality of service UK Node ELIXIR Platform Excelerate Impl Studies 2014 2016 2019 2021 A native ELIXIR Infrastructure Service to be collective managed by all ELIXIR Nodes
- 25. Highlight: Interoperability …. Data, Tools platform, impl studies and EU grants FAIRification of data infrastructure FAIRmetrics, capability models, processes FAIR Cookbook Bioschemas With NL, DE, EBI, LU … Data FAIRification Workflows & Software Workflow Registry Containerisation, Galaxy CommonWorkflow Language, GA4GH Research Objects FAIR Software Practices Registries, portability, interoperability With ES, BE, DE, FR, EBI, NL … FAIRmetrics
- 26. Highlight: Interoperability …. Data, Tools platform, impl studies and EU grants FAIRification of data infrastructure FAIRmetrics, capability models, processes FAIR Cookbook Bioschemas With NL, DE, EBI, LU … Data FAIRification Workflows & Software Workflow Registry Containerisation, Galaxy CommonWorkflow Language, GA4GH Research Objects FAIR Software Practices Registries, portability, interoperability With ES, BE, DE, FR, EBI, NL …
- 27. MG-RAST / EBI Mgnify [Rob Finn] Nature, 02 September 2019
- 28. Highlight: Bioschemas Exploiting schema.org for FAIRer Life Sciences resources ELIXIR-UK direct the initiative & promote ResearchSchemas Community initiative Schema.org specs Support software Foster adoption and use Find, register, index, search resources Resource mark up for tools Metadata movement between resources Registry auto curation Leveraging a de facto widely adopted standard Alasdair Gray, HWU
- 30. Bioschemas Strategy mostly funded by ELIXIR Impl Studies, EIP Platform funding, Excelerate and in kind from EU Phase 1: Inception & Community Building (2015) Phase 2: Specs & Provider Markup (2017) Phase 3: Adoption and Community Users (2019) ELIXIR Strategic Implementation Study ELIXIR UK, HU, BE, FR, NL, LU, PT, IT, DE, Hub Impact EOSC Pilot, EOSC Enhance RDA ResearchSchemas GO-FAIR Discovery OpenAIRE ResearchGraph Community Not for Profit, Governance Rare Diseases Plant Sciences Toxicology Intrinsically Disordered Proteins
- 31. Highlight: Data Management Capabilities Common Data Management Toolkits, Node-Node joint enterprises
- 32. Community Plant Sciences Genotype-Phenotype Data Management and Validation Toolkit FAIR data Analysis Search engine Metadata Access
- 33. Serving the UK: BioFAIR bringing together all our expertise for the UK differentiated from EMBL-EBI Federated Digital Object Commons partnered with national infrastructure Integrated data services and toolkits and training Data sustainability institute supporting the coordination and development of UK life science data Data Management services and capability -> ELIXIR CONVERGE
- 34. Serving the UK: BioFAIR bringing together all our expertise for the UK differentiated from EMBL-EBI Recognition now that this is needed BBSRC Review of Data Driven Bioscience BBSRC Bioscience Big Ideas Pipeline UKRI “infrastructure roadmap” Brexit - every crisis is an opportunity …
- 35. ELIXIR-UK Navigating a fragmented national landscape Outstanding people and track record Doing a lot on borrowed resources Significant contributions to ELIXIR And EOSC Node-Node co-operations BioFAIR a data sustainability institute supporting the coordination and development of UK life science data BioFAIR Digital Object Commons for UK Life Science.
Editor's Notes
- EMBL-EBI is the features case study
- UK’s Genome3D group a pillar of the community
- What is the benefit to the members?
- Workflows, software
- Workflows, software