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Research Objects, SEEK and FAIRDOM


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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 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, Mechanism of aggregation to group things together. OAI-ORE Metadata about those things & how they relate to each other. W3C OADM
  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
  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
  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 • • •