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Research Objects,
SEEK4Science and
FAIRDOM
ProfessorCarole Goble CBE FREng FBCS
The University of Manchester, UK
The Softw...
Metadata objects – not necessarily encapsulated!
Platform Independent framework to Bundle, Port and Link
(scattered) resou...
Manifest Metadata
Manifest Construction
• Identification – id, title, creator, status….
• Aggregates – list of ids/links t...
Manifest Construction
Unique identifiers as
names for things.
doi, epic, orcid, purl, RII,
Identifiers.org
Mechanism of
ag...
FAIR Manifest Descriptions: RO types
Content Annotation Profiles
Checklist
Provenance
Versioning
Dependencies
NISO-JATS
Du...
FAIRDOMHub Sys Bio Commons
https://doi.org/10.15490/seek.1.investigation.56
Aggregating Commons
Links into public resources
Integration with public
resources
Integration with
modelling tools
FAIRDOM...
RO Unzip
• Reproducibility
• Versioning
• Systematic and
extensible meta-
data collection
• Cross platform
exchange
• Publ...
SEEK Demo
Video
Other Implementations
• COMBINE Archive +RO
• Workflows RO Bundle
• STELARAsthma eLabs
• Data Publishing
• ATLAS LHC Exper...
Links
• Researchobject.org
• Fair-dom.org
• Seek4science.org
Research Objects, SEEK and FAIRDOM
Research Objects, SEEK and FAIRDOM
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Research Objects, SEEK and FAIRDOM Slide 1 Research Objects, SEEK and FAIRDOM Slide 2 Research Objects, SEEK and FAIRDOM Slide 3 Research Objects, SEEK and FAIRDOM Slide 4 Research Objects, SEEK and FAIRDOM Slide 5 Research Objects, SEEK and FAIRDOM Slide 6 Research Objects, SEEK and FAIRDOM Slide 7 Research Objects, SEEK and FAIRDOM Slide 8 Research Objects, SEEK and FAIRDOM Slide 9 Research Objects, SEEK and FAIRDOM Slide 10 Research Objects, SEEK and FAIRDOM Slide 11 Research Objects, SEEK and FAIRDOM Slide 12 Research Objects, SEEK and FAIRDOM Slide 13
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Short talk on Research Object and their use for reproducibility and publishing in the Systems Biology Commons Platform FAIRDOMHub, and the underlying software SEEK.

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Research Objects, SEEK and FAIRDOM

  1. 1. Research Objects, SEEK4Science and FAIRDOM ProfessorCarole Goble CBE FREng FBCS The University of Manchester, UK The Software Sustainability Institute, UK carole.goble@manchester.ac.uk researchobject.org Schloss Dagstuhl Seminar 16041 Reproducibility of Data-Oriented Experiments in e-Science, 25-29 January 2016
  2. 2. Metadata objects – not necessarily encapsulated! Platform Independent framework to Bundle, Port and Link (scattered) resources, related experiments, and hold context Container Packaging: Zip files, Docker images, BagIt, … Catalogues & Commons Platforms: FAIRDOM SEEK, STELAR eLab Manifest Metadata Describes the aggregated resources, their annotations and their provenance Manifest
  3. 3. Manifest Metadata 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
  4. 4. Manifest Construction Unique identifiers as names for things. doi, epic, orcid, purl, RII, Identifiers.org Mechanism of aggregation to group things together. OAI-ORE Metadata about those things & how they relate to each other. W3C OADM http://w3id.org/ro/
  5. 5. FAIR Manifest Descriptions: RO types Content Annotation Profiles Checklist Provenance Versioning Dependencies NISO-JATS Dublin Core EFO ISA SBML JERM Gamble, Goble, Klyne, Zhao MIM:A Minimum Information Model vocabulary and framework for Scientific Linked Data, IEEE 8th Intl Conf on eScience , 2012 SED-ML SBOL MIAPE
  6. 6. FAIRDOMHub Sys Bio Commons https://doi.org/10.15490/seek.1.investigation.56
  7. 7. Aggregating Commons Links into public resources Integration with public resources Integration with modelling tools FAIRDOM Repositories SOPs models data Launch local executables Integration with lab tools Integration with lab management systems and local file stores Direct Upload BiVes
  8. 8. RO Unzip • Reproducibility • Versioning • Systematic and extensible meta- data collection • Cross platform exchange • Publishing Living Snapshot https://doi.org/10.15490/seek.1.investigation.56 https://dx.doi.org/10.1111/febs.13237
  9. 9. SEEK Demo Video
  10. 10. Other Implementations • COMBINE Archive +RO • Workflows RO Bundle • STELARAsthma eLabs • Data Publishing • ATLAS LHC Experiments using CDE, Docker, improved manifests for people
  11. 11. Links • Researchobject.org • Fair-dom.org • Seek4science.org
  • RebeccaWhite558694

    Nov. 26, 2021

Short talk on Research Object and their use for reproducibility and publishing in the Systems Biology Commons Platform FAIRDOMHub, and the underlying software SEEK.

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