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How are we Faring with FAIR? (and what FAIR is not)

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Keynote presented at the workshop FAIRe Data Infrastructures, 15 October 2020
https://www.gmds.de/aktivitaeten/medizinische-informatik/projektgruppenseiten/faire-dateninfrastrukturen-fuer-die-biomedizinische-informatik/workshop-2020/

Remarkably it was only in 2016 that the ‘FAIR Guiding Principles for scientific data management and stewardship’ appeared in Scientific Data. The paper was intended to launch a dialogue within the research and policy communities: to start a journey to wider accessibility and reusability of data and prepare for automation-readiness by supporting findability, accessibility, interoperability and reusability for machines. Many of the authors (including myself) came from biomedical and associated communities.  The paper succeeded in its aim, at least at the policy, enterprise and professional data infrastructure level. Whether FAIR has impacted the researcher at the bench or bedside is open to doubt. It certainly inspired a great deal of activity, many projects, a lot of positioning of interests and raised awareness. COVID has injected impetus and urgency to the FAIR cause (good) and also highlighted its politicisation (not so good).
In this talk I’ll make some personal reflections on how we are faring with FAIR: as one of the original principles authors; as a participant in many current FAIR initiatives (particularly in the biomedical sector and for research objects other than data) and as a veteran of FAIR before we had the principles.

Keynote presented at the workshop FAIRe Data Infrastructures, 15 October 2020
https://www.gmds.de/aktivitaeten/medizinische-informatik/projektgruppenseiten/faire-dateninfrastrukturen-fuer-die-biomedizinische-informatik/workshop-2020/

Remarkably it was only in 2016 that the ‘FAIR Guiding Principles for scientific data management and stewardship’ appeared in Scientific Data. The paper was intended to launch a dialogue within the research and policy communities: to start a journey to wider accessibility and reusability of data and prepare for automation-readiness by supporting findability, accessibility, interoperability and reusability for machines. Many of the authors (including myself) came from biomedical and associated communities.  The paper succeeded in its aim, at least at the policy, enterprise and professional data infrastructure level. Whether FAIR has impacted the researcher at the bench or bedside is open to doubt. It certainly inspired a great deal of activity, many projects, a lot of positioning of interests and raised awareness. COVID has injected impetus and urgency to the FAIR cause (good) and also highlighted its politicisation (not so good).
In this talk I’ll make some personal reflections on how we are faring with FAIR: as one of the original principles authors; as a participant in many current FAIR initiatives (particularly in the biomedical sector and for research objects other than data) and as a veteran of FAIR before we had the principles.

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How are we Faring with FAIR? (and what FAIR is not)

  1. 1. How are we Faring with FAIR (and what FAIR is not) Carole Goble The University of Manchester FAIRDOM ELIXIR, EOSC-Life, IBISBA, BioExcel CoE, FAIRplus carole.goble@manchester.ac.uk The views expressed in this talk are my own Workshop: FAIRe Data Infrastructures, 15 October 2020
  2. 2. Data discovery and reuse at scale through good data management 2016 A set of PRINCIPLES to enhance the value of all digital resources and their reuse by PEOPLE and by MACHINES Scientific Data 3, 160018 (2016) doi:10.1038/sdata.2016.18 [Credit: Susanna Sansone]
  3. 3. Branding a trend, stimulating a movement … 2014 2016 2015 Open Science Data Sharing Recognition & Credit Reproducibility Data-driven Science Automation, AI
  4. 4. The compulsory COVID-19 reference “COVID is a good example .. there must be loads of legacy data. We’re desperately trying to go back and look at what we knew from SARS 10 years ago” – Pharma manager, FAIRplus project https://www.covid19dataportal.org/ https://www.nature.com/articles/s41431-020-0635-7 https://www.rd-alliance.org/group/rda-covid19-rda-covid19-omics-rda-covid19-epidemiology-rda-covid19- clinical-rda-covid19-1 https://doi.org/10.15497/rda00052
  5. 5. The compulsory COVID-19 reference +ve • Data sharing boost – • Impossible becomes normal • Data infrastructure investments • Mobilising rapid response -ve • Political, technical and territorial issues • Licensing, access to datasets, quality … • Short-term vs long term sustainability • Collection and governance bottlenecks https://covid19.galaxyproject.org/
  6. 6. The compulsory what are the FAIR principles slide … in a break out box, without explanation or justification. Aspirational, not a standard. Relaunch a dialogue within the research and policy communities. Reboot a journey to wider accessibility and reusability of data. Prepare the community for automation-readiness by supporting FAIR for machines. In the paper… 15 overlapping and ambiguous …. Jacobsen et al FAIR Principles: Interpretations and Implementation Considerations, J Data Intelligence (2020) Mons et al Cloudy, increasingly FAIR; Revisiting the FAIR Data guiding principles for the European Open Science Cloud. Information Services & Use. 37. 1-8. 10.3233/ISU-170824 (2017)
  7. 7. FAIR Principles in spirit identifiers, metadata, availability, standards [adapted from Susanna Sansone] Findable Accessible Interoperable Reusable Globally unique, resolvable, and persistent identifiers ▪ To retrieve and connect data Community defined descriptive metadata that is catalogued / searchable ▪ To enhance discoverability and reusability Common terminologies and standards ▪ To use the same terms and they mean the same thing Detailed provenance ▪ To contextualize the data and facilitate reproducibility Terms of access ▪ Open as possible, closed as necessary Terms of use ▪ Clear licences, ideally to enable innovation and reuse Automation
  8. 8. FAIR Services in practice identifiers, metadata, availability, standards Findable Accessible Interoperable Reusable Persistent Identifiers Metadata Services Access Control Repositories & registries Data applications “the internet of data and services”
  9. 9. Not one size fits all FAIR is a set of guiding principles that provide for a contract of expectation between data providers and users. A continuum of features, attributes and behaviours, via many different implementations for different use cases. Communities will need to develop their own FAIR profile: • for their portfolios of data, processes, governance, policies, assessment A limited pan-discipline profile.
  10. 10. Funders Public Health Educators WHY?WHO? Data integration Reannotation
  11. 11. Credit to: A global movement rather quickly…a FAIR frenzy! Many of these projects will speak today. Researcher, clinician confusion. Community coordination cacophony
  12. 12. Movement Start up Phase: Picking apart the Principles, Inventing Indicators, Assessment and Maturity Frameworks 1. (Re)define the principles and what they mean 2. Measure the “FAIRness level” of data The target, before & after levels of data FAIRness in various “FAIRification” processes 3. Measure an organisation’s capability & performance for FAIR data generation & management Support strategic investment decisions, cost/benefit analysis, processes & monitoring, capacity building, change management for FAIR by Design DOI: 10.15497/RDA0050 Dataset maturity model Data Management Infrastructure maturity model
  13. 13. What were the principles about? Contract Compliance Certification? Judgement Endorsement Regulation Trusted Repositories Commitment of a community of providers Federation of FAIR data, registries and services Comparison, Monitoring, Review,Quality Assessment Expectation setting of a data provider Self-evaluation Awareness, Reporting Community respectful Context aware Health data - Regulation
  14. 14. What were the principles about? Contract Compliance Certification? EOSC Strategic Research & Innovation Agenda consultation 2020: metrics & certification least popular action area FAIRware The Tyranny of Metrics
  15. 15. FAIR is a Spectrum Not all data are equal, not all will be worth it Spectrum of FAIR indicators Different levels of maturity and importance to different stakeholders and communities Communities define levels, depths, coverage [Barend Mons] FAIRify • just in case • just in time • just enough Dataset portfolio
  16. 16. FAIR is not Not Fuzzy “enhancing the ability of machines to automatically find and use data or any digital object, and support its reuse by individuals” INCF Statement Not Free Not Fast Not Simple Needs experts, stewards, infrastructure, processes, maintenance … “FAIR is non-trivial, and domain specific at anything other than the most superficial level” - MarkWilkinson From high effort high gain to low effort light gain All require consensus, process change and maintenance. • Mons et al Cloudy, increasingly FAIR; Revisiting the FAIR Data guiding principles for the European Open Science Cloud. Information Services & Use. 37. 1-8. 10.3233/ISU-170824. • Dunning et alAre the FAIR Data Principles fair? IDCC17 Not One Approach Not about turning everything into RDF
  17. 17. Coverage and Implementation ChoicesVary Findable Accessible Interoperable Reusable Shallow wide, low cost, loose federation restricted value Deep narrow, tight federation harmonisation high cost, high value https://fairplus.github.io/cookbook-dev/intro https://bioschemas.org/ https://www.go-fair.org/2020/07/08/a- three-point-framework-for-fairification/
  18. 18. FAIR by Design At the start of a collection, built in throughout the life cycle change management, capacity building FAIRifying Retrospectively Legacy datasets, build a cohort, cost benefit and FAIR readiness over a collection of datasets
  19. 19. Other FAIRVariants FA(I)R Interoperability is the hardest and most costly to define, implement & maintain Interoperability is usually for a purpose not “just in case” FAIR is not about harmonising all metadata to one schema FAIR+R Reproducibility is not the same as Reusability FAIR for all digital objects – software, workflows, SOPs, models, containers, training materials … Depends on availability and metadata Containers FAIR++ Business and change analysis. Cost Benefit Analysis. Scientific / BusinessValue Quality control Impact Process maturity Sustainability FAIR for all digital objects – software, workflows, SOPs, models, containers, training materials … EC Report: Turning FAIR into Reality, 2018 https://www.natureindex.com/news-blog/what- scientists-need-to-know-about-fair-data, 2019 47% respondents needed greater clarification
  20. 20. Step back… Why do we need FAIR? KnowledgeTurning, Information Flow Josh Sommer, Chordoma Foundation, 2011 Promote information flow • groups and disciplines • organisational boundaries at all levels • technical infrastructure • enable federation Biomedical flow • needs to control the information flow – Ethical & governance frameworks,GDPR, consent • federation feasibility varies Fragmented and independent resources, infrastructures, governance Community enclaves. Churn which leads to knowledge loss. Scattered Fragmentation and knowledge churn
  21. 21. FAIR is not synonymous with Open respect authority and governance frameworks
  22. 22. Federated System of Catalogues and Repos federation means common agreements and compliance respecting accountability and responsibility • Connected by PIDs • Moving metadata around • Common vocabularies • Common cataloguing data elements • Term cross-walks and mappings • Shared API standards.
  23. 23. FAIR Profile for Biomedical Community Findable Accessible Interoperable Reusable Awareness of data Thin metadata sparingly shared Data visiting Not open but access controlled Limited exchange under strict governance Authentication and authorisation protocols Data visiting Ethics, consent, privacy preservation Compliance , Governance Standards and Regulation are different things Federated analysis Combining clinical, research and public health data. Different scales, collected for different purposes Standards for Usage Access • Beacon API for genomic variants • Data Use Ontology – usage restrictions • GA4GH Passports – access policies Community standards Trusted Research Environments Community implementation profiles GO-FAIR implementation networks federated
  24. 24. FAIR Data Management for Projects FAIR by Design because not everything can be fixed at the end Platform to build Project Product Hubs Projects to collaborate and get their results organised and retained • Metadata cataloguing: collection & organisation • PIDs, ontologies, metadata for machines • Controlled sharing and access • Plug into ecosystem of other registries and repositories • Data submission brokering to community repositories • Credit to contributors FAIR itself • FAIR Services are not necessarily FAIR themselves (e.g. COVID Data Portal) http://fair-dom.org
  25. 25. Commons, Separated Groups
  26. 26. Investigation Study Analysis Data Model SOPAssay https://fairdomhub.org/investigations/56 Metadata Provenance Standards Federated Catalogue, IntegratedView PIDs fairdomhub.org
  27. 27. https://www.nature.com/articles/s41597-020-0477-8 https://covid.pages.uni.lu/ Curating FAIR models
  28. 28. Mixture of shared and private objects organised by metadata https://www.health-atlas.de/
  29. 29. e.g. (Pillar III) in-house data in-house data All LiSyM Patient-related clinical data Aggregated data API External Tools API LiSyM: German Liver Systems Medicine Network FAIR but never Open [Wolfgang Mueller, HITS] Share table structure Share common code Share summaries
  30. 30. Embed into Practices National Data Infrastructure Authorised Access Secure data Spreadsheets
  31. 31. FAIR along the Pipeline Understanding the pipeline, moving metadata across resources FAIR stewardship effort and pipeline design ELIXIR RDMToolkit
  32. 32. The FAIR data infrastructure needed …. tools, services, registries & catalogues, repositories… Federation of fair repositories & registries with mixed authority models FAIR services – metadata services, ontology servers, search engines, PID services, validators, integrators, annotators, assessors, brokers … Interfaces - shared APIs, common terms, cross-walks. FAIR digital objects. FAIRsFAIR confusagram, FAIR Ecosystem Components:Vision, V2.0 10.5281/zenodo.3734273 (missing the processing of data…)https://www.eoscsecretariat.eu/working-groups/fair-working-group
  33. 33. More than indicators, metrics and tech Infrastructure “digital technologies (hardware, software), resources (data, services, digital libraries, standards), comms (protocols, access rights, networks), people and organisational structures” Data stewardship Software Engs Professionalisation POSSIBLE Processes Organisational & Cultural change NORMATIVE Incentives Cost Benefit REWARDING Governance Regulatory Frameworks ACCEPTABLE Policy REQUIRED Education Training UNDERSTOOD Sustainability -TRUSTED
  34. 34. How is FAIR faring? Maturing… • Shifted the conversation • Concept & mobilisation frenzy • Rush to measure & certify • Community specific • FAIR not FOIR It’s now the phase to embed, sustain and yield benefits for users A marathon journey not a sprint It is not simple, but it is no longer optional
  35. 35. Acknowledgements Special thanks to • Susanna Sansone (University of Oxford, OERC) • Frederik Coppens (VIB) • Barend Mons (GO-FAIR) • Oya Deniz Beyan (Fraunhofer) • Ibrahim Emam (Imperial College) • FAIRDOM, GO-FAIR, FAIRplus and ELIXIR colleagues FAIRDOM is sponsored by

Editor's Notes

  • https://www.gmds.de/aktivitaeten/medizinische-informatik/projektgruppenseiten/faire-dateninfrastrukturen-fuer-die-biomedizinische-informatik/workshop-2020/
    perform in a specified way in a particular situation or over a particular period.
    Personal reflections

    with a keynote presentation about the FAIR guiding principles for scientific data management and stewardship and their implementation in the life sciences,

    Remarkably it was only in 2016 that the ‘FAIR Guiding Principles for scientific data management and stewardship’ appeared in Scientific Data. The paper was intended to launch a dialogue within the research and policy communities: to start a journey to wider accessibility and reusability of data and prepare for automation-readiness by supporting findability, accessibility, interoperability and reusability for machines. Many of the authors (including myself) came from biomedical and associated communities.  The paper succeeded in its aim, at least at the policy, enterprise and professional data infrastructure level. Whether FAIR has impacted the researcher at the bench or bedside is open to doubt. It certainly inspired a great deal of activity, many projects, a lot of positioning of interests and raised awareness. COVID has injected impetus and urgency to the FAIR cause (good) and also highlighted its politicisation (not so good).
    In this talk I’ll make some personal reflections on how we are faring with FAIR: as one of the original principles authors; as a participant in many current FAIR initiatives (particularly in the biomedical sector and for research objects other than data) and as a veteran of FAIR before we had the principles.


  • 3000 google scholar citations
  • The paper was intended to launch a dialogue within the research and policy communities: to start a journey to wider accessibility and reusability of data and prepare for automation-readiness by supporting findability, accessibility, interoperability and reusability for machines.
  • Hidden slide
  • Linking and moving metadata around
    Common metadata and ids, shared APIs and cross-walks
  • HIDDEN SLIDE
  • Like a goldrush
  • HIDDEN SLIDE
  • Not everything that can be counted counts. Not everything that counts can be counted – Einstein & William Bruce Cameron

    FAIRsFAIR will partner with the Research on Research Institute (RoRI) in FAIRware, a new initiative to build open source software tools and systems with the potential to transform uptake of the FAIR principles by researchers.  

    https://www.eoscsecretariat.eu/open-consultation-eosc-strategic-research-and-innovation-agenda

    https://www.fairsfair.eu/fairsfair-data-object-assessment-metrics-request-comments
  • There will be a "mixed economy" of FAIR data in a community. Something may be FAIR but not useful or high quality. Something may be essential but not fully FAIR.
  • Simple word but is not simple to do.
    And be incremental

    Not one approach - RDF
  • https://www.nature.com/articles/s41431-020-0635-7

    https://www.go-fair.org/implementation-networks/overview/vodan/

    ‘recipes’ for making different types of data FAIR
  • Different stages where the FAIR goes
    The steps towards FAIR
  • FAIR is not about a resource’s
    Quality or
    Impact or
    Scientific value or Business value

  • across and within groups and disciplines
    across and within organisational boundaries at all levels: the lab, the project, the organisation, the community, the country
    across all technical infrastructure platforms, repositories, registries, tools
    enable federation



    Fit for purpose scholarly comms
    Fit for purpose publishing
    while collaborating to compete in churning
  • Secure data sharing

  • Different levels
    FAIR Accountability and Responsibility
    Links in interfaces, common vocabularies, common minimum cataloguing terms and cross-walks, shared API standards.
    Generic approaches (e.g. using schema.org), Generic infrastructure (e.g. Ontology Lookup Service), Generic catalogues (e.g. WorkflowHub)


    Federated System of Systems ecosystem of catalogues, repositories, of different types. Degree to which you can get compliance

    National and regional level…
    Tiered levels….

    Registries federated or not
    Degree you can get everyone working together


    Neylon, Knowledge Exchange Report: http://www.knowledge-exchange.info/event/ke-approach-open-scholarship


    Zoo of catalogues and registries. LOTS of catalogies
    Some flock around 1
    Some rely on federated metadata

    Moving between stages, moving things through boundaries.

    NIH meeting for institutional repositories https://www.scgcorp.com/repositories2020/regclosed.



    in the
    Commons goods

    Micro, meso and macro players.

    OpenAIRE repository – helps find, access and reuse. Not meant to be interoperable.
  • What is special about biomedical
    EOSCLife recommendations
    Heterogeneous, fragmented
  • But its content may vary in its FAIRness!

  • Curating retrospectively….
  • HIDDEN SLIDE
  • LiSyM Data ManagementShare table structure
    Create & share common code
    Make it easy-to-install
    Create and share summaries

  • HIDDEN SLIDE Basic research data management solution, simplifying daily study
    management tasks
    • GUI effective in engaging users in the platform
    • Main structure modeled after biological research
    • Next steps
    – Testing large data files
    – Adapting labels to be more suitable for our enviroment
    – Establish more automation facilitating the RESTful service
    – Looking into advanced features of SEEK

  • FAIRDOM SEEK + NeLS
    First mile - FAIR data management for projects at the “first mile”
    Last mile - Organise data / models to deposit / link to (ELIXIR) datasets

    FAIR across the pipeline, across infrastructures, across platforms
    The FAIR chain of custody
    Provenance metadata propagation
    Synch registered SOPs and data transformations in NeLS
    Permissions and AAI through NeLS Portal and FAIRDOM SEEK

    FAIR stewardship effort and pipeline design
    Manual and automated
    Ramps and skills (see Filip Pattyn, TuesdayLots about “my silo is fair”

    SEEK register data and make it available in samples, so they can look at the samples when they are made public with no problem.
    There is an issue if they want to access the original data as only Norwegian researchers can log in to the NeLS portal

    Technically SOPs recorded in SEEK can/should carry information about data transformations that happened in NeLS

    However, that relies on rese

    Provenance of data analysis is provided by our Galaxy instances, and we would like to capture some of that into NeLS and SBI (for possibly later reopening in Galaxy or elsewhere), but that is not implemented yet.

    If you think of more generic data provenance over time, what is added to a dataset when etc, NeLS does not support that.archers adding it, which means it practice it won't exist

    es, we register data and make it avaialble in samples, so they can look at the samples when they are made public with no problem. There is an issue if they want to access the original data as only Norwegian researchers can log in to the NeLS portal

    so we can track provenance from the registration point in SEEK

    Given NeLS is run by ELIXIR Norway I would expect them at the very least to have a plan, f not some things implemented, but we will see
  • Moving DOs across
    FAIR digital objects – moving around
    Links in interfaces, common vocabularies, common minimum cataloguing terms and cross-walks, shared API standards.
    Generic approaches (e.g. using schema.org), Generic infrastructure (e.g. Ontology Lookup Service), Generic catalogues (e.g. WorkflowHub)


    Globally unique, resolvable, and persistent identifiers
    Community defined descriptive metadata that is catalogued / searchable
    Common terminologies and standards
    Detailed provenance
    Terms of access Terms of use
  • HIDDEN SLIDE

    Was 7 recommendations, now 6
    Mentions certification but does not argue for it.
  • PEOPLE MATTER! Its about community building and consensus
  • BTW: Majority of researchers have never heard of FAIR
    https://www.natureindex.com/news-blog/what-scientists-need-to-know-about-fair-data

  • HIDDE SLIDE
  • ×