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Research Objects in Scientific
Publications
Daniel Garijo
Ontology Engineering Group
Universidad Politécnica de Madrid
Madrid, Spain
dgarijo@fi.upm.es

OEG, October 17th 2013
Outline
•
•
•
•
•

What is a Research Object?
Why Research Objects?
Research Object model at 5000 ft.
An example from the Life Sciences.
Research Object Overview.
• ORE
• Annotations
• Extensions

•
•
•
•
•

Eating our own dog food
6 step example
Cost vs benefit
RO Portal
RO hub

Research Objects in Scientific Publications

2
What is a Research Object (RO)?

Aggregation of resources that bundles together the contents of a research work

Research Objects in Scientific Publications

3
Why Research Objects?

•

Process preservation: URIs/DOIs for referencing resources.

•

Reusability of any part of the RO

•

Repeatability /Reproducibility: redeployment of the method

•

Traceability and error detection.

•

Attribution: able to cite data and publications of the RO

•

Understandability: Links between data, results and annotations.

•

Curation: by explicitly exposing the methods of the experiment.

Research Objects in Scientific Publications

4
RO Model at 5000 ft

+ Open Annotation

Research Objects in Scientific Publications

5
Example (Life sciences)

Research Objects in Scientific Publications

6
Research Objects: An Overview

•Vocabulary for describing Research Objects
•Generic
•Extensible to multiple domains
•Modular
RO Core

AO/OA

Research Objects in Scientific Publications

ORE

7
The Research Object Model: ORE

•ORE: Object Reuse and Exchange
•Resources can be further specialized according to the domain

Research Objects in Scientific Publications

8
The Research Object Model: Annotations

Research Objects in Scientific Publications

9
The RO Model

•Additional modules can be described on top of the Core
•Evolution
•Workflows
•Publications
•Etc.
Workflow
Evolution

Wfprov

Other

Wfdesc
RO Core

AO/OA

Research Objects in Scientific Publications

ORE

10
Eating our own dog food

•

Reproducibility is not only an issue
in the Life Sciences.

•

In computer science we:
•

Run experimental evaluations.

•

Reuse previous algorithms
and tools.

•

Build pipelines for processing
the inputs and obtain our
results.

http://petfoodadvisor.net/wp-content/uploads/2013/02/Cheap-Dog-Food.jpg

•WHY DON’T WE USE RESEARCH OBJECTS?
Research Objects in Scientific Publications

11
How? Minimal step by step example
• When writing a paper about a tool/algorithm/evaluation/survey
1. Create a permanent URL (purl, DOI, etc) for the Research Object

2. Distinguish between the resources that have been used from those that have
been generated.
•

A result was generated using/testing an algorithm/tool/framework.

•

An ontology was created from the CQs and ORSD of the domain.

•

A survey was performed by looking at these papers in the bibliography.

3. Describe the relationships among the resources and their dependencies.
4. Describe the resources in the RO (AO/OA, DC, schema, FOAF)
5. Add all the descriptions to a file (manifest)

6. State that the manifest is describing the purl of the RO.

7. You are done.
Research Objects in Scientific Publications

12
Annotating RDF/RDF-a can be exhausting
• Cost vs benefit.
•

It takes time, BUT

•

All your resources become easily
referenceable:
•

You provide context to your research

•

You ease the task of reusing your
software/papers

•
•
http://i3.kym-cdn.com/entries/icons/original/000/006/725/desk%20flip.jpg

There are tools to ease the task.

You don’t need to annotate everything!
•

The more you annotate, the better
your results will be understood.

Research Objects in Scientific Publications

13
http://sandbox.wf4ever-project.org/portal/home

•Creation of ROs
•Annotation and visualization of ROs
Research Objects in Scientific Publications

14
rohub.linkeddata.es

•Many approaches exist for making your stuff persistent
•Figshare, Purl, Datacite, RO Portal, etc.
•Rohub.linkeddata.es is a page (under development) for
pointing at the resources created in ROs of the OEG.
•3 ROs at the moment.
•Content negotiation (TTL and more)
•Annotated in RDF-a

•ROs as web pages with purls!
•http://rohub.linkeddata.es/ro-svmworkflow/
(http://purl.org/net/svm-opt-research-object)

http://esp.habitants.org/campana_cero_desalojos/jornadas_mu
ndiales_cero_desalojos__por_el_derecho_al_habitat_2013/work_in_progress
Research Objects in Scientific Publications

15
RO-ify your work!
http://researchobject.org/
Join the discussion…
W3C Research Object for Scholarly Communication
Community Group
http://www.w3.org/community/rosc/

Acknowledgements: Wf4Ever project
Research Objects in Scientific
Publications
Daniel Garijo
Ontology Engineering Group
Universidad Politécnica de Madrid
Madrid, Spain
dgarijo@fi.upm.es

OEG, October 17th 2013

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Research Objects in Scientific Publications

  • 1. Research Objects in Scientific Publications Daniel Garijo Ontology Engineering Group Universidad Politécnica de Madrid Madrid, Spain dgarijo@fi.upm.es OEG, October 17th 2013
  • 2. Outline • • • • • What is a Research Object? Why Research Objects? Research Object model at 5000 ft. An example from the Life Sciences. Research Object Overview. • ORE • Annotations • Extensions • • • • • Eating our own dog food 6 step example Cost vs benefit RO Portal RO hub Research Objects in Scientific Publications 2
  • 3. What is a Research Object (RO)? Aggregation of resources that bundles together the contents of a research work Research Objects in Scientific Publications 3
  • 4. Why Research Objects? • Process preservation: URIs/DOIs for referencing resources. • Reusability of any part of the RO • Repeatability /Reproducibility: redeployment of the method • Traceability and error detection. • Attribution: able to cite data and publications of the RO • Understandability: Links between data, results and annotations. • Curation: by explicitly exposing the methods of the experiment. Research Objects in Scientific Publications 4
  • 5. RO Model at 5000 ft + Open Annotation Research Objects in Scientific Publications 5
  • 6. Example (Life sciences) Research Objects in Scientific Publications 6
  • 7. Research Objects: An Overview •Vocabulary for describing Research Objects •Generic •Extensible to multiple domains •Modular RO Core AO/OA Research Objects in Scientific Publications ORE 7
  • 8. The Research Object Model: ORE •ORE: Object Reuse and Exchange •Resources can be further specialized according to the domain Research Objects in Scientific Publications 8
  • 9. The Research Object Model: Annotations Research Objects in Scientific Publications 9
  • 10. The RO Model •Additional modules can be described on top of the Core •Evolution •Workflows •Publications •Etc. Workflow Evolution Wfprov Other Wfdesc RO Core AO/OA Research Objects in Scientific Publications ORE 10
  • 11. Eating our own dog food • Reproducibility is not only an issue in the Life Sciences. • In computer science we: • Run experimental evaluations. • Reuse previous algorithms and tools. • Build pipelines for processing the inputs and obtain our results. http://petfoodadvisor.net/wp-content/uploads/2013/02/Cheap-Dog-Food.jpg •WHY DON’T WE USE RESEARCH OBJECTS? Research Objects in Scientific Publications 11
  • 12. How? Minimal step by step example • When writing a paper about a tool/algorithm/evaluation/survey 1. Create a permanent URL (purl, DOI, etc) for the Research Object 2. Distinguish between the resources that have been used from those that have been generated. • A result was generated using/testing an algorithm/tool/framework. • An ontology was created from the CQs and ORSD of the domain. • A survey was performed by looking at these papers in the bibliography. 3. Describe the relationships among the resources and their dependencies. 4. Describe the resources in the RO (AO/OA, DC, schema, FOAF) 5. Add all the descriptions to a file (manifest) 6. State that the manifest is describing the purl of the RO. 7. You are done. Research Objects in Scientific Publications 12
  • 13. Annotating RDF/RDF-a can be exhausting • Cost vs benefit. • It takes time, BUT • All your resources become easily referenceable: • You provide context to your research • You ease the task of reusing your software/papers • • http://i3.kym-cdn.com/entries/icons/original/000/006/725/desk%20flip.jpg There are tools to ease the task. You don’t need to annotate everything! • The more you annotate, the better your results will be understood. Research Objects in Scientific Publications 13
  • 14. http://sandbox.wf4ever-project.org/portal/home •Creation of ROs •Annotation and visualization of ROs Research Objects in Scientific Publications 14
  • 15. rohub.linkeddata.es •Many approaches exist for making your stuff persistent •Figshare, Purl, Datacite, RO Portal, etc. •Rohub.linkeddata.es is a page (under development) for pointing at the resources created in ROs of the OEG. •3 ROs at the moment. •Content negotiation (TTL and more) •Annotated in RDF-a •ROs as web pages with purls! •http://rohub.linkeddata.es/ro-svmworkflow/ (http://purl.org/net/svm-opt-research-object) http://esp.habitants.org/campana_cero_desalojos/jornadas_mu ndiales_cero_desalojos__por_el_derecho_al_habitat_2013/work_in_progress Research Objects in Scientific Publications 15
  • 16. RO-ify your work! http://researchobject.org/ Join the discussion… W3C Research Object for Scholarly Communication Community Group http://www.w3.org/community/rosc/ Acknowledgements: Wf4Ever project
  • 17. Research Objects in Scientific Publications Daniel Garijo Ontology Engineering Group Universidad Politécnica de Madrid Madrid, Spain dgarijo@fi.upm.es OEG, October 17th 2013