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Research Objects @ HARMONY 2014
 

Research Objects @ HARMONY 2014

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A short presentation given during the COMBINE archive session at HARMONY 2014:

A short presentation given during the COMBINE archive session at HARMONY 2014:

http://co.mbine.org/events/HARMONY_2014

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  • What’s the purpose of publication?Publications intended to present results/positions, along with arguments that reinforce those positions.Reproducability reinforces the validity of our positions.May require us to include much more information than can be included in a paper:in particular, data sets and methods.

Research Objects @ HARMONY 2014 Research Objects @ HARMONY 2014 Presentation Transcript

  • Sean Bechhofer, Stian Soiland-Reyes, Matthew Gamble University of Manchester sean.bechhofer@manchester.ac.uk @seanbechhofer Harmony 2014, Manchester Research Objects 1
  • Why? Publication • Publications are about argumentation: Convince the reader of the validity of a position [Mesirov] – Reproducible Results System: facilitates enactment and publication of reproducible research. • Results are reinforced by reproducability [De Roure] – Explicit representation of method. • Verifiability as a key factor in scientific discovery. J. Mesirov Accessible Reproducible Research Science 327(5964), p.415-416, 2010 http://dx.doi.org/10.1126/science.1179653 D. De Roure and C. Goble Anchors in Shifting Sand: the Primacy of Method in the Web of Data Web Science Conference 2010, Raleigh NC, 2010 http://eprints.ecs.soton.ac.uk/20817/ Stodden et. al. Reproducible Research: Addressing the Need for Data and Code Sharing in Computational Science Computing in Science and Engineering 12(5), p.8-13, 2010 http://dx.doi.org/10.1109/MCSE.2010.113
  • Why? Reproducible Science 3 Goble: SSI Collaborations Workshop 2014
  • Why? Preservation 4 Wf4Ever Final Review Presentations
  • ROs as a Currency 5 Creator Contributor Collaborator Curator Reader Finder Trainer Comparator Re-User Evaluator Reviewer Trainee Trainer Reader Publisher Curator Librarian Repository Manager
  • • An aggregation object that bundles together experimental resources that are essential to a computational scientific study or investigation. – An identity – A suite of annotations (which can be about this bundle itself and/or the resources of the bundle) – Aggregated Resources:  data used  results produced in an experiment study;  (computational) methods employed to produce and analyse that data;  people involved in the investigation. Research Objects 6
  • Identity • Mechanisms for referring to the resources that are aggregated within a Research Object • URIs – Web Resources • DOIs – Documents/papers/datasets • ORCID IDs – Researchers 7
  • Aggregation • Open Archives Initiation Object Reuse and Exchange (OAI ORE) is a standard for describing aggregations of web resources – http://www.openarchives.org/ore/ • Uses a Resource Map to describe the aggregated resources • Proxies allow for statements about the resources within the aggregation • Several concrete serialisations – RDF/XML, Atom, RDFa 8 Graceful Degradation
  • Annotation • Open Annotation specification is a community developed data model for annotation of web resources – http://www.openannotation.org/spec/core/ • Developed by the W3C Open Annotation Community Group • Allows for “stand-off” annotations • Developed to fit with Web Architecture • Usage in a number of domains 9 Graceful Degradation
  • Annotation Content • Essential to the understanding and interpretation of the scientific outcomes captured by a Research Object as well as the reuse of the resources within it. – Provenance information about the experiments, the study or any other experimental resources – Evolution information about the Research Object and its resources, – Descriptions of computational methods – Dependency information or settings about the experiment executions 10
  • RO Core 11
  • Vocabularies and Domains • Thinking to date has been focused on “workflow-centric” ROs (cf. Wf4Ever presentation to come) – Specific vocabularies covering, e.g. workflow abstractions and provenance information: wfdesc, wfprov, ro-evo • Now shifting focus to other use cases, domains and problems – RO Advisory Board 12 Christine Borgman, UCLA Michel Dumontier, Stanford Scott Edmunds, GigaScience Paul Groth, VU Amsterdam Brian Hole, Ubiquity Press Paolo Manghi, ISTI of CNR Brian Matthews, STFC Paolo Missier, Newcastle University Susanna Sansone, Oxford University/Nature Publishing Herbert Van de Sompel, LANL Kaitlin Thaney, Mozilla Science Mark Wilkinson, UPM Katy Wolstencroft, Leiden University