Introduction to Research Objects - http://www.researchobject.org. Presented at the Software Sustainability Institute's Collaborations Workshop 2015, University of Oxford, March 2015

1. An Introduction to
Research Objects
Collaborations Workshop
March 16th 2015, Oxford
Matthew Gamble, University of Manchester
researchobject.org

2. Why Research Objects?
Support the publication of more than just PDFs,
making data, code, and other resources first class
citizens of scholarship
researchobject.org
Going Beyond the PDF.

3. What are Research Objects?
researchobject.org
A common mechanism for publishing research
artefacts in a consistent and useful way on the Web.
world wide web
Both conceptual model and technical implementations.

4. Research Artefacts
As part of a research investigation you might for example have:
Slides hosted on slideshare,
Code in a github repository,
Data in figshare or community db,
Preprint on arxiv.org
etc.
researchobject.org

5. Collections
researchobject.org
Recognition that there is often a need to publish
collections of these resources together as one
shareable, cite-able resource.

6. Research Objects
researchobject.org

7. Research Objects
researchobject.org

8. Research Objects
researchobject.org
?

9. Research Objects
researchobject.org
Enrich these resources and collections with any and all
additional information and metadata required to
make research reusable, and reproducible!

10. 3 Principles
researchobject.org
Use unique identifiers as names for things.
Use some mechanism of aggregation to
group things together.
Provide metadata about those things
& how they relate to each other.

11. 3 Principles
researchobject.org
Use unique identifiers as names for things.
Use some mechanism of aggregation to
group things together.
Provide metadata about those things
& how they relate to each other.
Point of Extendability

12. In Reality
researchobject.org
Research Object Manifest
What about resources that aren’t already on the web?
aggregates - List of ids/links to resources
annotations - List of annotations about
resources
RO Metadata - id, title, creator, status etc.
Structured document that contains:

13. Manifest
researchobject.org
title: my research object
id : www.example.org/myresearchobject
createdOn : 2013-03-05 17:29:03
createdBy : “A. Turing”
aggregates: http://researchobject.org/blog/1
www.myexperiment.org/workflow
annotations: “www.myexperiment.org/workflow shows that P!=NP”

14. Manifest
researchobject.org
title: my research object
id : www.example.org/myresearchobject
createdOn : 2013-03-05 17:29:03
createdBy : “A. Turing”
aggregates: http://researchobject.org/blog/1
www.myexperiment.org/workflow
annotations: “www.myexperiment.org/workflow shows that P!=NP”
That’s it! A shareable resource that describes our investigation.

15. Manifest
researchobject.org
{
"@context": [
"https://w3id.org/bundle/context"
],
"id": "/",
"createdOn": "2013-03-05T17:29:03Z",
"createdBy": {
"uri": "http://example.com/foaf#alice",
"orcid": "http://orcid.org/0000-0002-1825-0097",
"name": “A. Turing"
},
"aggregates": [{
"uri": “ http://researchobject.org/blog/1”
}, {
"uri": “http://www.myexperiment.org/workflow“
}],
"annotations": [{
"uri": "urn:uuid:d67466b4-3aeb-4855-8203-90febe71abdf",
"about": “http://www.myexperiment.org/workflow”,
"content": “http://www.example.org/workflow-properties.ttl”
}]
}
actually … That’s it!

16. Specifications
researchobject.org
ro ontology - defines core
concepts of research objects,
identity, aggregation, and
annotation, used in the manifest.
https://w3id.org/ro/

17. Files on my machine
Manifest - Web and Local
researchobject.org
title: my research object
id : www.example.org/myresearchobject
createdOn : 2013-03-05 17:29:03
createdBy : http://orcid.org/0000-0002-1825-0097
aggregates: /data/mydata.dat
http://researchobject.org/blog/1
www.myexperiment.org/myworkflow
annotations: /annotations/description-of-mydata.dat.txt
/annotations/workflow-provenance.rdf
/annotations/domain-specific-metadata.json

18. researchobject.org
ro-bundle – A zip-based serialisation research objects.
zipfile + manifest
Specifications
https://w3id.org/bundle/
“Backwards compatible” - Appears as just a Zip file!

19. RO Bundle
Just the files, no metadata
title, description, license,
comments, citations, tags,
authors, categories, views,
shares etc.

20. Tooling
researchobject.org
ro bundle API – A Java library that can be used to generate the zip-
based ro bundle archives. Taverna
ruby-ro-bundle – A Ruby library for working with Research Object
bundles.
ro-manager – A command line tool for creating research objects.
ro-python – A python library for building Research Objects Manifests
and Research Object bundles. (in progress)
rohub.org – A prototype web application for managing research
objects.
Libraries
User tools

21. Tooling
researchobject.org
ro-manager – A git-like command line tool
>ro init “my research object”
>ro add mydata.dat
>ro add “www.myexperiment.org/myworkflow“
>
>ro annotate domain-specific-metadata.json
>
>ro export #create the zip
Build research objects on the
command line

22. Tooling
researchobject.org
ro-manager – A git-like command line tool
Build research objects on the
command line
v1 - https://github.com/wf4ever/ro-manager
(prototype)
v2 - https://github.com/gambl/ro-python
To bring inline with spec (in-progress)

25. Tooling - CKAN plugin
researchobject.org
Coming Soon!
Plugin for open source
CKAN data repository to:
- build
- import
- export
research objects.
CKAN data model a very good fit.

26. Links
researchobject.org
https://github.com/apache/incubator-taverna-language/tree/master/taverna-robundle
RO bundle API
ruby-ro-bundle
ro-manager - ro command-line v1
ro-python & ro command
https://github.com/myGrid/ruby-ro-bundle
https://github.com/gambl/ro-python/
https://github.com/wf4ever/ro-manager

27. Discussion
researchobject.org
What type of resources would you want to include in your research objects?
Would you use research objects primarily for publication, archiving, exchange, or some other purpose?
Can you envision any barriers the adoption of research objects - by yourself?, by your community?
by publishers?
What additional information is required to make research data reusable? e.g. versioning,
provenance, standards used etc. Is it domain specific or general?
Have you ever struggled to replicate someone else’s investigation or experiment? If so
why?