The document discusses the importance of reproducible research in scientific publication, emphasizing argumentation and the verification of results through explicit method representation. It details the concept of research objects, which aggregate essential experimental resources including data, methods, and contributors, and outlines standards for annotation and resource aggregation. The evolving focus is on various use cases and vocabularies to enhance the utility of research objects in scientific communities.

1. Sean Bechhofer, Stian Soiland-Reyes, Matthew Gamble
University of Manchester
sean.bechhofer@manchester.ac.uk
@seanbechhofer
Harmony 2014, Manchester
Research Objects
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2. 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

3. Why? Reproducible Science
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Goble: SSI Collaborations Workshop 2014

4. Why? Preservation
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Wf4Ever Final Review Presentations

5. ROs as a Currency
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Creator
Contributor
Collaborator
Curator
Reader
Finder
Trainer
Comparator
Re-User
Evaluator
Reviewer
Trainee
Trainer
Reader
Publisher
Curator
Librarian
Repository
Manager

6. • 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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7. Identity
• Mechanisms for referring to the resources that are aggregated
within a Research Object
• URIs
– Web Resources
• DOIs
– Documents/papers/datasets
• ORCID IDs
– Researchers
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8. 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
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Graceful Degradation

9. 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
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Graceful Degradation

10. 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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11. RO Core
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12. 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, 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