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2013 07-18 myExperiment research objects poster (PDF)

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Poster to be presented at BOSC 2013, ISMB. …

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

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  • 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 ...