Research Shared: researchobject.org
Project Website: http://www.researchobject.org/ researchobjects.org is a community project that has developed an approach to describe and package up all resources used as part of an investigation as Research Objects (RO’s). RO’s - provide two main features; a manifest - a consistent way to provide a well-typed, structured description of the resources used in an investigation; and a ‘bundle’ - a mechanism for packaging up manifests with resources as a single, publishable unit. RO’s therefore carry the research context of an experiment - data, software, standard operating procedures (SOPs), models etc - and gather together the components of an experiment so that they are findable, accessible, interoperable and reproducible (FAIR). RO’s combine software and data into an aggregative data structure consisting of well described reconstructable parts. RO’s have the potential to address a number of challenges pertinent to open research including: a) supporting interoperability between infrastructures by using ROs as a primary mechanism for exchange and publication b) supporting the evolution of research objects as a living collection, enabling provenance tracking c) providing the ability to pivot research object components (data, software, models) that are not restricted to the traditional publication. Here we present work towards the development and adoption of ROs: (i) A series of specifications and conventions, using community standards, for the RO manifest and RO bundles. (ii) Implementations of Java, Python and Ruby APIs and tooling against those specifications; (iii) Examples of representations of the RO models in various languages (e.g. JSON-LD, RDF, HTML).
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Research Shared: researchobject.org
- 1. Research Shared BOSC July 11th 2015, Dublin Norman Morrison, The University of Manchester researchobject.org
- 2. Framework A framework to bundle, exchange and link (scattered) resources about experiments.
- 3. Framework desiderata Technology Independent. The least possible The simplest feasible Graceful degradation Standard tooling
- 4. How? The Container Packaging: Zip files, Docker images, BagIt, Web, … Catalogues & Commons: FAIRDOM SEEK, Farr Commons CKAN, myExperiment, Zenodo, Figshare, … Manifest Describes the aggregated resources, their annotations and provenance Manifest
- 5. Manifest Manifest Construction • Identification – id, title, creator, status…. • Aggregates – list of ids/links to resources • Annotations – list of annotations about resources Manifest Manifest Description • Checklists – what should be there • Provenance – where it came from • Versioning – its evolution • Dependencies – what else is needed Manifest
- 6. Manifest id: doi:10.000/zenodo.123 createdOn: 2015-‐07-‐10T16:46:00Z createdBy: http://orcid.org/0000-‐0001-‐9842-‐9718 aggregates: -‐ id: /sequence/specimen5.bam conformsTo: http://gemrb.org/iesdp/file_formats/ie_formats/bam_v1.htm -‐ id: http://example.com/blog/about-‐specimen5 authoredBy: http://orcid.org/0000-‐0001-‐7066-‐3350 -‐ id: http://www.myexperiment.org/workflows/3355 history: provenance/workflow-‐evolution.ttl annotations: -‐ about: /sequence/specimen5.bam content: annotations/specimen5-‐properties.jsonld createdBy: http://orcid.org/0000-‐0001-‐7066-‐3350 -‐ about: /sequence/specimen5.bam content: http://example.com/blog/about-‐specimen5 oa:motivatedBy oa:questioning
- 7. RO Principles Use unique identifiers as names for things. Use some mechanism of aggregation to group things together. Provide metadata about those things & how they relate to each other.
- 8. Get tooled up https://github.com/ResearchObject
- 9. Real world examples • Reviewed to Reproduced • Workflow run (CWL) • Farr Commons • Capturing and describing Docker images for CERN Atlas analyses • FAIR-DOM http://fair-dom.org/ – SEEK http://seek4science.org/ • FAIR Publishing - RO to Figshare
- 10. Reviewed to Reproduced
- 11. Reviewed to Reproduced From González-Beltrán et al. doi: 10.1371/journal.pone.0127612 Reproducibility Same data Same code Systematic and extensible meta-data collection ✔ ✔
- 12. Workflow Run workflowrun.prov.ttl (RDF) outputA.txt outputC.jpg outputB/ intermediates/ 1.txt 2.txt 3.txt de/def2e58b-50e2-4949-9980-fd310166621a.txt inputA.txt workflow attribution execution environment Aggregating in Research Object ZIP folder structure (RO Bundle) mimetype application/vnd.wf4ever.robundle +zip .ro/ manifest.json URI reference s Exchange Reproducibility Same data Same code Systematic and extensible meta- data collection Uses RO Model WF Extension - basis of CWL ✔ ✔ ✔ ✔
- 13. RO’s and Sensitive data
- 14. Farr Commons Exchange Systematic and extensible meta-data collection ✔ ✔
- 15. Use case: ATLAS Collider Data Analytics Portable, lightweight application runtime and packaging tool. Image ATLAS and CMS detector data Charles Vardeman, Da Huo All data and files of the execution + Instructions convert bundle manifest Relate files and layers Add provenance and annotations Link in other content run Exchange Reproducibility Same data Same code Same run time environment Systematic and extensible meta- data collection ✔ ✔ ✔
- 16. FAIRDOM SEEK
- 17. FAIRDOM
- 18. Export as RO Model, Data, SOP, Parameters
- 19. RO Unzip Reproducibility Versioning Systematic and extensible meta-data collection ✔ ✔ ✔
- 20. FAIR Publishing
- 21. Research Objects • Reproducibility – Same data, same code, same run time environment • Versioning • Exchange • Systematic and extensible meta-data collection
- 22. Research Objects Publish a digital record of your entire scientific enterprise You can give it to someone else You can get credit for it People think you are a good person You get a promotion • Why does this matter to Biologists?
- 23. Okay, but what does it cost?
- 24. Conclusion • Simple solution, addressing needs towards transparent FAIR principles – Findable, Accessible, Interoperable, Reproducible • Adoption – Training • Online tutorials • Face to face – Need more tools that take advantage of the RO Framework and lower the cost (technological debt) of reproducibility • Work together
- 25. Acknowledgements Carole Goble Stian Soiland-‐Reyes Matt Gamble Rob Haines Sean Bechhofer Phil Crouch Finn Bacall Stuart Owen Carole Goble Khalid Belhajjame Graham Klyne Jun Zhao Daniel Garijo, Oscar Corcho Esteban García Cuesta University of Manchester University of Oxford Lancaster University UPM http://researchobject.org http://fair-‐dom.org http://www.seek4science.org http://www.farrinstitute.org http://www.wf4ever-‐project.org http://myexperiment.org Raul Palma iSOCO PSNC Paris 6