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Introduction to FAIRDOM

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Introduction to FAIRDOM

  1. 1. Introduction to FAIRDOM Prof Carole Goble The FAIRDOM Consortium carole.goble@manchester.ac.uk http://fair-dom.org, http://fairdomhub.org FAIRDOM User Meeting, Lyon, France, 27 Oct 2018
  2. 2. modellers experimentalists
  3. 3. 10Year Anniversary! 2008 2010 2014 2018 2012 2016 2020
  4. 4. Supporting Projects, Managing Results many types, many versions experimentalists modellers
  5. 5. Collaboration: teams, disciplines Context: organised across kinds of research outputs What methods are been used to determine enzyme activity? What SOP was used for this sample? Where is the validation data for this model? Is there any group generating kinetic data? Is this data available? Track versions of my model Whats the relationship between the data and model? Which data belong to which publications? SOPs workflows models data samples publications
  6. 6. FAIR for projects, at source
  7. 7. organising, sharing and reusing research reviewing, publishing and reproducing research organising, retaining, tracking and reusing research across many projects & pipelines at scale retaining, reusing and showcasing research; better research documentation best practice research results stewardship & management better experimental design and collaboration
  8. 8. FAIRDOM FAIR Asset for Projects Project Support Free Public ResourceCommunity Activities Open Source Software Platforms Stewardship Services Customised Installations Consultancy Training Community Development Training & Summer Schools Outreach, Guides,Website Policy work 50+ installations 118+ projects Supports standards integrate with other platforms FAIRDOM Association Governance & coordination of partners
  9. 9. Reach • Germany • Netherlands • Norway • UK • Spain • Switzerland (openBIS) • France • Slovenia • Russia • USA • South Africa • Belgium • EU projects
  10. 10. Project Egosystems • Multi-disciplinary teams • Multi-site collaborations • Self-depositing, self-curating • Variable stewardship skills • Different platforms
  11. 11. Create Capture Organise Manage Share Store Preserve Dissem- inate Access Reuse Process Analyse Science 2.0 Repositories: Time for a Change in Scholarly Communication Assante, Candela, Castelli, Manghi, Pagano, D-Lib 2015 Research Support
  12. 12. Create Capture Organise Manage Share Store Preserve Dissem- inate Access Reuse Process Analyse Science 2.0 Repositories: Time for a Change in Scholarly Communication Assante, Candela, Castelli, Manghi, Pagano, D-Lib 2015 Research Support
  13. 13. A Project Commons for Research products Organise > Share > Disseminate Self managed spaces Yellow pages Single entry point over external systems Project Commons Project Commons Platform Service hosted at HITS Institutional Guarantee to 2029
  14. 14. Project Investigation Programme Project Management
  15. 15. Investigation Study Analysis Data Model SOP(Assay) https://fairdomhub.org/investigations/56
  16. 16. Organise Manage Share Dissem- inate Investigation Studies Assay/Analysis Entry level Entry level Record level: subject thematic standards Metadata Standards based JERM v2 Sample model RDF – Linked Data Bioschemas.org, DCAT
  17. 17. Organise Manage Share Dissem- inate Selective Sharing Jurgen Hannstra Vrije Universiteit, Amsterdam Using FAIRDOM my own lab colleagues saw what I was doing and called to collaborate!
  18. 18. Snapshot Publishing Organise Manage Share Dissem- inate Licenses Snapshots for ISA DOI improvements
  19. 19. Samples: new features, auto templates, auto extraction
  20. 20. One place integrated view for catalogue Federates many fragmented resources Upload or register a reference
  21. 21. Jon OlavVik, Norwegian University of Life Science Structured & systematic organisation Retaining context, integrated view Investigation Study Assay
  22. 22. Jon OlavVik, Norwegian University of Life Science External resources, integrated view Structured & systematic organisation Investigation Study Assay
  23. 23. Integration with the Ecosystem read and write JSON API, metadata exchange along the pipeline ELNs
  24. 24. FAIRDOMTools Integrated in FAIRDOMHub Modelling SBML Simulations Model repository and on line simulator >600 curated models Model reproducibility Model simulation repository >200 SED-ML simulation experiments, one-click, life simulation of manuscript figures, including incorporation of experimental data from FAIRDOMHub. Linked to scientific journals, e.g. Molecular Systems Biology REST-API, search, simulate models in JWS as part of workflow Build, edit, annotate your own model (or SED-ML script) from scratch or starting from existing model, in your own user space. Model versioning & comparisons
  25. 25. FAIRDOMTools Integrated into SEEK Metadata Spreadsheet based tooling for metadata capture Metadata templates -> template library Automated extraction, sample type support, systematic collection, unique identifiers
  26. 26. FAIRDOM Integrated with SEEK Lab Mgt, Stores, Analysis National infrastructures On site tracking; data analytic pipelines; Extract,Transform and Load direct from the instruments; large data management; LIMS; auto-archiving; Cloud-hosted openBIS ELN-LIMS Browse data stored through SEEK. Select & register into SEEK, attach to an Assay. Extract registered data and metadata as Samples Data if relevant. Share and manage project data through national storage solutions; Execute pipelines using national compute solutions; National bioinformatics helpdesk Open source integrated Java platform for analysis of data generated by omics technologies
  27. 27. Link NeLS file and associated metadata to SEEK. Access to NeLS from SEEK. Days/Weeks Months Years Decades ola@uib.no ola@uib.no Publications Open registration https://f1000research.com/articles/7-968/v1
  28. 28. Stand up your own SEEK Centres, large and national projects Local skills for admin support Local retention In flight management Private sharing Customisation Skinned look and feel
  29. 29. FAIRDOM Project Stewardship Support
  30. 30. Independent researchers Facilities Centres Projects Programmes Infrastructures User bases and their workflows • Stewardship professionalism • In-flight project support as you go • Post-project publishing upload in one go • Data pipeline support • Customisations and Integrations with other systems • Hub or own SEEK installations or both
  31. 31. Facilities and Centres Environmental Molecular Sciences Laboratory External investigators collaborate with teams of EMSL scientists to apply multiple types of analytical approaches to solve complex problems in the biological, physical, chemical and environmental sciences. • Over 130 different instruments • Automation and scale • “Metadata transactions” – Pipeline support – At every step of the workflow, the necessary metadata is captured. – Completed data set (and all of the associated metadata) pushed to SEEK. • Data manager dashboards
  32. 32. European Research Infrastructures Special Installations of SEEK “First Mile” Data Management for National Projects and bridge to National and EU Research Infrastructures • Data Management Planning & Capacity Building • Integration with national data infrastructures • Integration with Galaxy & Notebooks • Deposition into ELIXIR Archives • General Omics & Bioinformatics Platform for computational workflows and SOPs • Integration with national infrastructures • Integration with Galaxy, KNIME , CWL , GitHub
  33. 33. Keynote: Frederik Coppens, Deputy Head of Node ELIXIR Belgium NETTAB 2018, 22-24 Oct 2018
  34. 34. https://www.ibisba.eu/ Providing a research infrastructure network to Europe’s Industrial Biotechnology Community
  35. 35. FAIRDOM Association e.V. German based legal entity for governance and coordination Development & Delivery Partners Development Partners
  36. 36. Standard Community-level activities FAIRDOMHub DIY local installations Free training & support Premium Direct support of projects In house installation support Full customer service Super-Premium Partner in projects Extensive tailoring Integrations with platforms Custom and dedicated services In house installation support On board stewards How you can support us and how we provide support… Erasmus MC Wageningen In kind contributions Infrastructure support Subsidised
  37. 37. THE TEAM THE FUNDERS
  38. 38. modellers experimentalists
  39. 39. Thanks to our sponsors, partners and collaborators

Editor's Notes

  • http://www.fair-dom.org http://www.fairdomhub.org http://www.seek4science.org
  • ERASysAPP:
    Preserve results beyond projects.
    Organise & link data, models, processes.
    Exchange & search initiative‘s assets.
    Share & disseminate results
    Improve standard curation practice.
    Pool capacities

    ISBE:
    Sys Bio data and model stewardship platform, services, policy.
    Capacity building, improve practice
    Knowledge Network/Hub focal point
    EU RIs, community initiatives, global standards bodies
  • Published 15 March 2016
  • Capitalising on investments
    Retaining results post-project
    Pooling, transfer, sharing results
    Public collections
    Skilling workforce
    Compliance audit/metrics
    New publishable assets
    Business models
    Reproducibility

    Doing science with collaborators
    Publishing & getting credit
    Productivity
    Access to resources, results, collections
    Retention of my results post student
    Repeatability - reviewer wants more 
    Competitiveness, protecting assets
    Managing costs
    Compliance
  • EU projects
    IBISBA1.0, Timet, EmPowerPutida, Mesi Strat, mycosynvax, NMTrypl….
    and others installations we don’t know
  • FAIR
    Organise & link assets
    Standardised, consistent
    reporting
    Reproducible
    publications
    Yellow pages

  • New asset type to support Documents
    General Documents that don’t fit to SOPs or Data – such as project reports or minutes
    Can be linked to Assays
    Future plans to categorise and be included in JERM ontology (directly or with mappings to a suitable existing ontology)
  • JERM version 2 ontology
    Dedicated website: https://jermontology.org
    Updated to remove SysMO specific terms and reflect new sample model
    Mappings added for Dublin Core and Prov/Pav
    RDF updated and extended, along with improvements to SPARQL store integration
    https://sparql.fairdomhub.org/sparql

  • Licenses: The “R” in “FAIR”
    Tied to opendefinition.org

    Finer grained snapshots for publication
    Snapshots are packages frozen in time, based on Research Objects, along with a DOI
    Now available for Assays and Studies, as well as Investigations

    Easier and more intuitive publishing with DOI generation
  • What I really like about the SEEK is how it clarifies what we're talking about. No more "can we discuss 'the gene expression data'? [airquotes].
    Instead I just copy the hyperlinked text [point] into an email.
    The ISA graph places every asset in context, saving us from lots of explanations and misunderstandings.
    Since the inception of Digital Life Norway, DigiSal has advocated a strategy for interoperability and knowledge management also vs the Research Council of Norway

    Some of the new Digital Life projects are planning to adopt FAIRDOM

    Programmatic access to datasets in SEEK e.g. from R
    How to handle big, non-public assets that reside e.g. on our own cluster (ongoing dialogue between FAIRDOM and Norwegian e-infrastructure for Life Sciences, NeLS)
    How to handle multifile assets, e.g. RNAseq data shoehorned into MIAME format

    Dialogue between FAIRDOM, Digital Life Norway, and the Research Council of Norway

    Integration with the Norwegian e-infrastructure for Life Sciences, NeLS

  • What I really like about the SEEK is how it clarifies what we're talking about. No more "can we discuss 'the gene expression data'? [airquotes].
    Instead I just copy the hyperlinked text [point] into an email.
    The ISA graph places every asset in context, saving us from lots of explanations and misunderstandings.
    Since the inception of Digital Life Norway, DigiSal has advocated a strategy for interoperability and knowledge management also vs the Research Council of Norway

    Some of the new Digital Life projects are planning to adopt FAIRDOM

    Programmatic access to datasets in SEEK e.g. from R
    How to handle big, non-public assets that reside e.g. on our own cluster (ongoing dialogue between FAIRDOM and Norwegian e-infrastructure for Life Sciences, NeLS)
    How to handle multifile assets, e.g. RNAseq data shoehorned into MIAME format

    Dialogue between FAIRDOM, Digital Life Norway, and the Research Council of Norway

    Integration with the Norwegian e-infrastructure for Life Sciences, NeLS

  • Better RightField support and automatic extraction
    New master template metadata sheet
    Automatically applied for Sample type templates
    Built on JERM 2 ontology
    New wizard for Data File upload
    Split into logical steps
    Easier to skip through, less daunting than a large form
    Can be populated based on content after upload
  • Support for Swiss projects EnhanceR, openRDM.swiss and ETHZ researchers.
    Open source software licensed under the Apache License v2.0
    Metadata linking, samples
    Assays and Studies imported from openBIS and linked to imported data sets, according to pre-defined fields and constraints
    More automation
    Contributed by SynthSys
    Currently being tested with Users – requires upgrade to latest openBIS which has only just been released

    Close integration with NeLS based around a specific set of use-cases
    Authenticate with NeLS securely and browse data sets available there
    Link reference to data set to an assay in SEEK
    From the data set - Sample metadata is automatically imported into SEEK and interlinked according to defined mappings
    Norwegian Elixir node
    Contracted paid bespoke development


  • The tools were linked at the point of long term storage in NeLS.

  • Docker containers – running as micro-services with Docker compose
    Easier deployment and upgrades
    Automatic builds
    Packaged optionally also with openBIS, and SPARQL RDF store
    Most new installations tend to be Docker based
    Used internally for testing, and also running instances for workshops and tutorials.




    Still working on SEEK to Hub upload

    Centres, large or national projects
    Local skills for admin support
    Local retention and “in flight” management
    Private sharing
    Customisation

    openBIS or SEEK
    openBIS (~60 known)
    SEEK (50, worldwide)
    Increase in SEEK installations
    openBIS and SEEK
    4 centres/projects
    We are funded to support all 4

    Greater emphasis needed on management dashboards
    Few openBIS + SEEK Installations – significant effort + support issues
    SEEK to SEEK (FAIRDOMHub) transfer/upload
    Customised installations route for sustainability (IBISBA, ELIXIR, EOSC)
    Turning into paying partners/customers
  • In-flight : Upload as you Go
    Organise: Working data, models, SOPs
    Communicate: Collaborate, share results
    Disseminate: publish snapshots with DOIs

    2. Dissemination: Upload in one Go
    Organise & Preserve: final results
    Publish: supp. Materials



  • Over 130 different instruments including:
    12 NMRs ranging from 100MHz to 850MHz
    10 different AFMs
    11 different ion microscopes
    7 optical-based microscopes
    8 classes of spectrometers
    42 different types of mass spectrometers including new 21T mass spectrometer
  • Bonus slide
  • Founders
    U Manchester, HITS, U Edinburgh, NFVL
    Reps from Leiden U, ETHZ
    Assisted by SBSM
    Runway: ELIXIR NO, ELIXIR BE, ELIXIR UK, ISBE SI

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