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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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

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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

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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