Introduction to FAIRDOM
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FAIRDOM User Meeting, Lyon, France, 27 Oct 2018 Introduction to FAIRDOM Project and platforms
Carole GobleFollow
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Introduction to FAIRDOM
- 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. modellers experimentalists
- 3. 10Year Anniversary! 2008 2010 2014 2018 2012 2016 2020
- 4. Supporting Projects, Managing Results many types, many versions experimentalists modellers
- 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. FAIR for projects, at source
- 8. 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
- 9. 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
- 10. Reach • Germany • Netherlands • Norway • UK • Spain • Switzerland (openBIS) • France • Slovenia • Russia • USA • South Africa • Belgium • EU projects
- 11. Project Egosystems • Multi-disciplinary teams • Multi-site collaborations • Self-depositing, self-curating • Variable stewardship skills • Different platforms
- 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. 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
- 14. 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
- 15. Project Investigation Programme Project Management
- 16. Investigation Study Analysis Data Model SOP(Assay) https://fairdomhub.org/investigations/56
- 17. 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
- 18. 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!
- 19. Snapshot Publishing Organise Manage Share Dissem- inate Licenses Snapshots for ISA DOI improvements
- 21. Samples: new features, auto templates, auto extraction
- 22. One place integrated view for catalogue Federates many fragmented resources Upload or register a reference
- 23. Jon OlavVik, Norwegian University of Life Science Structured & systematic organisation Retaining context, integrated view Investigation Study Assay
- 24. Jon OlavVik, Norwegian University of Life Science External resources, integrated view Structured & systematic organisation Investigation Study Assay
- 25. Integration with the Ecosystem read and write JSON API, metadata exchange along the pipeline ELNs
- 26. 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
- 27. FAIRDOMTools Integrated into SEEK Metadata Spreadsheet based tooling for metadata capture Metadata templates -> template library Automated extraction, sample type support, systematic collection, unique identifiers
- 28. 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
- 29. 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
- 30. 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
- 31. FAIRDOM Project Stewardship Support
- 32. 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
- 33. 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
- 34. 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
- 35. Keynote: Frederik Coppens, Deputy Head of Node ELIXIR Belgium NETTAB 2018, 22-24 Oct 2018
- 36. https://www.ibisba.eu/ Providing a research infrastructure network to Europe’s Industrial Biotechnology Community
- 37. FAIRDOM Association e.V. German based legal entity for governance and coordination Development & Delivery Partners Development Partners
- 38. 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
- 39. THE TEAM THE FUNDERS
- 40. modellers experimentalists
- 41. 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