Poster to be presented at BOSC 2013, ISMB. We have evolved Research Objects as a mechanism to preserve digital resources related to research, by providing mechanisms, formats and architecture for describing aggregated resources (hypothesis, workflow, datasets, scripts, services), their relations (is input for, explains, used by), provenance (graph was derived from dataset A, B and C) and attribution (who contributed what, and when?). The website myExperiment is already popular for collaborating on, publishing and sharing scientific workflows, however we have found that for understanding and preserving a workflow over time, its definition is not enough, specially faced with workflow decay, services and tools that change over time. We have therefore adapted the research object model as a foundation for the myExperiment packs, allowing uploading of workflow runs, inputs, outputs and other files relevant to the workflow, relating them with annotations and integrated the Wf4Ever architecture for performing decay analysis and tracking a research object’s evolution as it and its constituent resources change over time. Submitted abstract: https://docs.google.com/document/d/1jaAuPV-EnbsyI14L56HKHBQP7eDVfeXGLlK-LwohnWw/edit?usp=sharing See also PPTX version at http://www.slideshare.net/soilandreyes/2013-0718-myexperiment-research-objects-poster

1. myExperiment Research Objects: Beyond Workflows and Packs
Stian Soiland-Reyes1, Don Cruickshank2, Finn Bacall1, Jun Zhao2, Khalid Belhajjame1, David De Roure3, Carole A. Goble1
1 School of Computer Science, University of Manchester, UK
2 Department of Zoology, University of Oxford, UK
3 Oxford e-Research Centre, University of Oxford, UK
ABSTRACT
We have evolved Research Objects as a mechanism to preserve digital resources
related to research, by providing mechanisms, formats and architecture for
describing aggregated resources (hypothesis, workflow, datasets, scripts, services),
their relations (is input for, explains, used by), provenance (graph was derived from
dataset A, B and C) and attribution (who contributed what, and when?).
The website myExperiment is already popular for collaborating on, publishing and
sharing scientific workflows, however we have found that for understanding and
preserving a workflow over time, its definition is not enough, specially faced with
workflow decay, services and tools that change over time. We have therefore
adapted the research object model as a foundation for the myExperiment packs,
allowing uploading of workflow runs, inputs, outputs and other files relevant to the
workflow, relating them with annotations and integrated the Wf4Ever architecture
for performing decay analysis and tracking a research object’s evolution as it and its
constituent resources change over time.
MAKING RESEARCH OBJECTS
myExperiment is a website for collaboration and sharing of experiments, in
particular scientific workflows. We are enhancing myExperiment’s packs to be based
on the Research Object model, allowing users to form collections of workflows,
example input data, results, presentation slides, hypothesis, workflow runs and
documentation, effectively building a Research Object (RO). These uploaded
resources can then be further related, typed, described and given their own
attribution provenance record. ROs are versioned and shareable.
WF4EVER ARCHITECTURE
The architecture for Research Objects is realized as a Linked Data platform of
RESTful web services that support preservation aspects such as decay monitoring
and evolution tracking, presented to the user through a regular web interface on
myExperiment.
RESEARCH OBJECT MODEL
A research object (RO) is described in an RDF manifest which lists the aggregated
resources and their annotations as separate RDF graphs containing user
annotations (title, description, example value), typing information (hypothesis,
workflow, input data, etc) and automatically extracted metadata (provenance,
workflow structure).
The ontologies for the RO Model is based on standards for aggregations (OAI-ORE)
and annotations (Annotation Ontology, W3C Open Annotation Core OAC).
RESEARCH OBJECTS AS FILES
A RO Bundle is a JSON-LD-based serialization of a research object as a ZIP file
(Adobe UCF, ePub), allowing a hybrid of embedded resources and external
references (URIs). This allows a self-contained RO to be downloaded, transferred,
modified and inspected without requiring a dedicated web server, well suited for
desktop environments such as scientific workflow systems.
Taverna uses RO Bundle to make a workflow run bundle, a single file that contains
the input and output values, the workflow definition, complete with provenance
of the run and intermediate values. This allows sharing of a workflow run, e.g.
uploading to myExperiment, and later reloaded in a different Taverna installation.
This work was enabled by the Wf4Ever project funded by the European Commission’s 7th FWP
(FP7-ICT-2007-6 270192), and the myGrid platform grant by the EPSRC (EP/G026238/1)
Project sites http://www.myexperiment.org/ http://www.wf4ever-project.org/
Source code http://myexperiment.rubyforge.org/svn/ https://github.com/wf4ever/
License BSD 3-Clause License MIT license
http://www.researchobject.org/
Research
Object
Resource
Resource
Resource
Annotation
Annotation
Annotation
oa:hasTarget
oa:hasBody
ore:aggregates
Manifest
Annotation graph
http://purl.org/wf4ever/model
outputA.txt
outputC.jpg
outputB/
intermediates/
1.txt
2.txt
3.txt
de/def2e58b-50e2-4949-9980-fd310166621a.txt
inputA.txt
workflow
URI
references
attribution
execution
environment
Aggregating in Research Object
ZIP folder structure (RO Bundle)
mimetype
application/vnd.wf4ever.robundle+zip
workflowrun.prov.ttl
(provenance)
.ro/manifest.json
http://alpha.myexperiment.org/packs/387
http://sandbox.wf4ever-project.org/portal/
The Research Object is stored and manipulated in a Research Object Digital Library
using REST APIs, allowing any tools to view and modify the RO, like the RO portal:
https://w3id.org/bundle
REST API
RDF triple store
(RO structure,
Annotations)
RO index
Uploaded files
RO Portal
Checklist
service
...