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A Linked Data Approach to Sharing Workflows and Workflow Results

A Linked Data Approach to Sharing Workflows and Workflow Results
A Linked Data Approach to Sharing Workflows and Workflow Results
A bioinformatics analysis pipeline is often highly elaborate, due to the inherent complexity of biological systems and the variety and size of datasets. A digital equivalent of the ‘Materials and Methods’ section in wet laboratory publications would be highly beneficial to bioinformatics, for evaluating evidence and examining data across related experiments, while introducing the potential to find associated resources and integrate them as data and services. We present initial steps towards preserving bioinformatics ‘materials and methods’ by exploiting the workflow paradigm for capturing the design of a data analysis pipeline, and RDF to link the workflow, its component services, run-time provenance, and a personalized biological interpretation of the results. An example shows the reproduction of the unique graph of an analysis procedure, its results, provenance, and personal interpretation of a text mining experiment. It links data from Taverna, myExperiment.org, BioCatalogue.org, and ConceptWiki.org. The approach is relatively ‘light-weight’ and unobtrusive to bioinformatics users.
0302-9743
340-354
Roos, Marco
531dacd7-98e7-4df0-b9cc-498ed4c53b2e
Bechhofer, Sean
67752347-1cb9-417f-937b-57923052c122
Zhao, Jun
9198f85d-41a5-4280-bf89-fb5624a4c3c5
Missier, Paolo
784fec92-c5a0-466e-92be-1f9cc43b697f
Newman, David
eb21ecdd-5ad0-49ec-9dd0-5bf98dc0c6f9
De Roure, David
02879140-3508-4db9-a7f4-d114421375da
Marshall, M. Scott
7f9f3c70-4e03-4e85-9cb8-635a98a87bcc
Roos, Marco
531dacd7-98e7-4df0-b9cc-498ed4c53b2e
Bechhofer, Sean
67752347-1cb9-417f-937b-57923052c122
Zhao, Jun
9198f85d-41a5-4280-bf89-fb5624a4c3c5
Missier, Paolo
784fec92-c5a0-466e-92be-1f9cc43b697f
Newman, David
eb21ecdd-5ad0-49ec-9dd0-5bf98dc0c6f9
De Roure, David
02879140-3508-4db9-a7f4-d114421375da
Marshall, M. Scott
7f9f3c70-4e03-4e85-9cb8-635a98a87bcc

Roos, Marco, Bechhofer, Sean, Zhao, Jun, Missier, Paolo, Newman, David, De Roure, David and Marshall, M. Scott (2010) A Linked Data Approach to Sharing Workflows and Workflow Results Lecture Notes in Computer Science, 6415, pp. 340-354.

Record type: Article

Abstract

A bioinformatics analysis pipeline is often highly elaborate, due to the inherent complexity of biological systems and the variety and size of datasets. A digital equivalent of the ‘Materials and Methods’ section in wet laboratory publications would be highly beneficial to bioinformatics, for evaluating evidence and examining data across related experiments, while introducing the potential to find associated resources and integrate them as data and services. We present initial steps towards preserving bioinformatics ‘materials and methods’ by exploiting the workflow paradigm for capturing the design of a data analysis pipeline, and RDF to link the workflow, its component services, run-time provenance, and a personalized biological interpretation of the results. An example shows the reproduction of the unique graph of an analysis procedure, its results, provenance, and personal interpretation of a text mining experiment. It links data from Taverna, myExperiment.org, BioCatalogue.org, and ConceptWiki.org. The approach is relatively ‘light-weight’ and unobtrusive to bioinformatics users.

PDF DigitalMaterialsAndMethods_TavernaMyExpBioCatCW_AIDA_revised.pdf - Accepted Manuscript
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More information

Published date: October 2010
Additional Information: ISBN 978-3-642-16557-3
Organisations: Web & Internet Science

Identifiers

Local EPrints ID: 271749
URI: http://eprints.soton.ac.uk/id/eprint/271749
ISSN: 0302-9743
PURE UUID: c3b4f74c-d906-4b91-accc-9edad16f4abc
ORCID for David Newman: ORCID iD orcid.org/0000-0001-5153-5396
ORCID for David De Roure: ORCID iD orcid.org/0000-0001-9074-3016

Catalogue record

Date deposited: 03 Dec 2010 11:06
Last modified: 18 Jul 2017 06:39

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Contributors

Author: Marco Roos
Author: Sean Bechhofer
Author: Jun Zhao
Author: Paolo Missier
Author: David Newman ORCID iD
Author: David De Roure ORCID iD
Author: M. Scott Marshall

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