research objects @ harmony 2014
DESCRIPTION
A short presentation given during the COMBINE archive session at HARMONY 2014: http://co.mbine.org/events/HARMONY_2014TRANSCRIPT
Sean Bechhofer, Stian Soiland-Reyes, Matthew Gamble
University of Manchester
[email protected]@seanbechhofer
Harmony 2014, Manchester
Research Objects
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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
3Goble: SSI Collaborations Workshop 2014
Why? Preservation
4Wf4Ever Final Review Presentations
ROs as a Currency
5
CreatorContributorCollaborator
CuratorReader FinderTrainer
ComparatorRe-User
EvaluatorReviewerTraineeTrainerReader
Publisher
Curator
Librarian
RepositoryManager
• 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
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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
8Graceful 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
9Graceful 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
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RO Core
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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
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Christine Borgman, UCLAMichel Dumontier, StanfordScott Edmunds, GigaSciencePaul Groth, VU AmsterdamBrian Hole, Ubiquity PressPaolo Manghi, ISTI of CNRBrian Matthews, STFC
Paolo Missier, Newcastle UniversitySusanna Sansone, Oxford University/Nature PublishingHerbert Van de Sompel, LANLKaitlin Thaney, Mozilla ScienceMark Wilkinson, UPMKaty Wolstencroft, Leiden University