Structuring research methods and data with the research object model: genomics workflows as a case study

Kristina Hettne; Harish Dharuri; Jun Zhao; Katherine Wolstencroft; Khalid Belhajjame; Stian Soiland-Reyes; Eleni Mina; Mark Thompson; Don Cruickshank; Lourdes Verdes-Montenegro; Julian Garrido; David de Roure; Oscar Corcho; Graham Klyne; Reinout van Schouwen; Peter A C 't Hoen; Sean Bechhofer; Carole Goble; Marco Roos

doi:10.1186/2041-1480-5-41

Structuring research methods and data with the research object model: genomics workflows as a case study

Kristina Hettne, Harish Dharuri, Jun Zhao, Katherine Wolstencroft, Khalid Belhajjame, Stian Soiland-Reyes, Eleni Mina, Mark Thompson, Don Cruickshank, Lourdes Verdes-Montenegro, Julian Garrido, David de Roure, Oscar Corcho, Graham Klyne, Reinout van Schouwen, Peter A C 't Hoen, Sean Bechhofer, Carole Goble, Marco Roos

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Abstract

BACKGROUND:One of the main challenges for biomedical research lies in the computer-assisted integrative study of large and increasingly complex combinations of data in order to understand molecular mechanisms. The preservation of the materials and methods of such computational experiments with clear annotations is essential for understanding an experiment, and this is increasingly recognized in the bioinformatics community. Our assumption is that offering means of digital, structured aggregation and annotation of the objects of an experiment will provide necessary meta-data for a scientist to understand and recreate the results of an experiment. To support this we explored a model for the semantic description of a workflow-centric Research Object (RO), where an RO is defined as a resource that aggregates other resources, e.g., datasets, software, spreadsheets, text, etc. We applied this model to a case study where we analysed human metabolite variation by workflows.RESULTS:We present the application of the workflow-centric RO model for our bioinformatics case study. Three workflows were produced following recently defined Best Practices for workflow design. By modelling the experiment as an RO, we were able to automatically query the experiment and answer questions such as "which particular data was input to a particular workflow to test a particular hypothesis?", and "which particular conclusions were drawn from a particular workflow?".CONCLUSIONS:Applying a workflow-centric RO model to aggregate and annotate the resources used in a bioinformatics experiment, allowed us to retrieve the conclusions of the experiment in the context of the driving hypothesis, the executed workflows and their input data. The RO model is an extendable reference model that can be used by other systems as well.AVAILABILITY:The Research Object is available at http://www.myexperiment.org/packs/428The Wf4Ever Research Object Model is available at http://wf4ever.github.io/ro

Original language	English
Number of pages	41
Journal	Journal of Biomedical Semantics
Volume	5
Issue number	1
DOIs	https://doi.org/10.1186/2041-1480-5-41
Publication status	Published - 2014

Keywords

research object
genomics
workflow
Semantic Web models
Scientific workflows
Digital Libraries
Genome wi de association study

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POST-PEER-REVIEW-NON-PUBLISHERS.PDFAccepted author manuscript, 3.68 MBLicence: CC BY
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http://www.jbiomedsem.com/content/5/1/41Licence: CC BY
http://www.researchobject.org/Licence: CC BY
http://www.wf4ever-project.org/Licence: CC BY
http://www.myexperiment.org/packs/428Licence: CC BY
http://wf4ever.github.io/roLicence: CC BY

Cite this

Hettne, K., Dharuri, H., Zhao, J., Wolstencroft, K., Belhajjame, K., Soiland-Reyes, S., Mina, E., Thompson, M., Cruickshank, D., Verdes-Montenegro, L., Garrido, J., de Roure, D., Corcho, O., Klyne, G., van Schouwen, R., 't Hoen, P. A. C., Bechhofer, S., Goble, C., & Roos, M. (2014). Structuring research methods and data with the research object model: genomics workflows as a case study. Journal of Biomedical Semantics, 5(1). https://doi.org/10.1186/2041-1480-5-41

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title = "Structuring research methods and data with the research object model: genomics workflows as a case study",

abstract = "BACKGROUND:One of the main challenges for biomedical research lies in the computer-assisted integrative study of large and increasingly complex combinations of data in order to understand molecular mechanisms. The preservation of the materials and methods of such computational experiments with clear annotations is essential for understanding an experiment, and this is increasingly recognized in the bioinformatics community. Our assumption is that offering means of digital, structured aggregation and annotation of the objects of an experiment will provide necessary meta-data for a scientist to understand and recreate the results of an experiment. To support this we explored a model for the semantic description of a workflow-centric Research Object (RO), where an RO is defined as a resource that aggregates other resources, e.g., datasets, software, spreadsheets, text, etc. We applied this model to a case study where we analysed human metabolite variation by workflows.RESULTS:We present the application of the workflow-centric RO model for our bioinformatics case study. Three workflows were produced following recently defined Best Practices for workflow design. By modelling the experiment as an RO, we were able to automatically query the experiment and answer questions such as {"}which particular data was input to a particular workflow to test a particular hypothesis?{"}, and {"}which particular conclusions were drawn from a particular workflow?{"}.CONCLUSIONS:Applying a workflow-centric RO model to aggregate and annotate the resources used in a bioinformatics experiment, allowed us to retrieve the conclusions of the experiment in the context of the driving hypothesis, the executed workflows and their input data. The RO model is an extendable reference model that can be used by other systems as well.AVAILABILITY:The Research Object is available at http://www.myexperiment.org/packs/428The Wf4Ever Research Object Model is available at http://wf4ever.github.io/ro",

keywords = "research object, genomics, workflow, Semantic Web models, Scientific workflows, Digital Libraries, Genome wi de association study",

author = "Kristina Hettne and Harish Dharuri and Jun Zhao and Katherine Wolstencroft and Khalid Belhajjame and Stian Soiland-Reyes and Eleni Mina and Mark Thompson and Don Cruickshank and Lourdes Verdes-Montenegro and Julian Garrido and {de Roure}, David and Oscar Corcho and Graham Klyne and {van Schouwen}, Reinout and {'t Hoen}, {Peter A C} and Sean Bechhofer and Carole Goble and Marco Roos",

year = "2014",

doi = "10.1186/2041-1480-5-41",

language = "English",

volume = "5",

journal = "Journal of Biomedical Semantics",

issn = "2041-1480",

publisher = "Springer Nature",

number = "1",

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Hettne, K, Dharuri, H, Zhao, J, Wolstencroft, K, Belhajjame, K, Soiland-Reyes, S, Mina, E, Thompson, M, Cruickshank, D, Verdes-Montenegro, L, Garrido, J, de Roure, D, Corcho, O, Klyne, G, van Schouwen, R, 't Hoen, PAC, Bechhofer, S , Goble, C & Roos, M 2014, 'Structuring research methods and data with the research object model: genomics workflows as a case study', Journal of Biomedical Semantics, vol. 5, no. 1. https://doi.org/10.1186/2041-1480-5-41

TY - JOUR

T1 - Structuring research methods and data with the research object model: genomics workflows as a case study

AU - Hettne, Kristina

AU - Dharuri, Harish

AU - Zhao, Jun

AU - Wolstencroft, Katherine

AU - Belhajjame, Khalid

AU - Soiland-Reyes, Stian

AU - Mina, Eleni

AU - Thompson, Mark

AU - Cruickshank, Don

AU - Verdes-Montenegro, Lourdes

AU - Garrido, Julian

AU - de Roure, David

AU - Corcho, Oscar

AU - Klyne, Graham

AU - van Schouwen, Reinout

AU - 't Hoen, Peter A C

AU - Bechhofer, Sean

AU - Goble, Carole

AU - Roos, Marco

PY - 2014

Y1 - 2014

N2 - BACKGROUND:One of the main challenges for biomedical research lies in the computer-assisted integrative study of large and increasingly complex combinations of data in order to understand molecular mechanisms. The preservation of the materials and methods of such computational experiments with clear annotations is essential for understanding an experiment, and this is increasingly recognized in the bioinformatics community. Our assumption is that offering means of digital, structured aggregation and annotation of the objects of an experiment will provide necessary meta-data for a scientist to understand and recreate the results of an experiment. To support this we explored a model for the semantic description of a workflow-centric Research Object (RO), where an RO is defined as a resource that aggregates other resources, e.g., datasets, software, spreadsheets, text, etc. We applied this model to a case study where we analysed human metabolite variation by workflows.RESULTS:We present the application of the workflow-centric RO model for our bioinformatics case study. Three workflows were produced following recently defined Best Practices for workflow design. By modelling the experiment as an RO, we were able to automatically query the experiment and answer questions such as "which particular data was input to a particular workflow to test a particular hypothesis?", and "which particular conclusions were drawn from a particular workflow?".CONCLUSIONS:Applying a workflow-centric RO model to aggregate and annotate the resources used in a bioinformatics experiment, allowed us to retrieve the conclusions of the experiment in the context of the driving hypothesis, the executed workflows and their input data. The RO model is an extendable reference model that can be used by other systems as well.AVAILABILITY:The Research Object is available at http://www.myexperiment.org/packs/428The Wf4Ever Research Object Model is available at http://wf4ever.github.io/ro

AB - BACKGROUND:One of the main challenges for biomedical research lies in the computer-assisted integrative study of large and increasingly complex combinations of data in order to understand molecular mechanisms. The preservation of the materials and methods of such computational experiments with clear annotations is essential for understanding an experiment, and this is increasingly recognized in the bioinformatics community. Our assumption is that offering means of digital, structured aggregation and annotation of the objects of an experiment will provide necessary meta-data for a scientist to understand and recreate the results of an experiment. To support this we explored a model for the semantic description of a workflow-centric Research Object (RO), where an RO is defined as a resource that aggregates other resources, e.g., datasets, software, spreadsheets, text, etc. We applied this model to a case study where we analysed human metabolite variation by workflows.RESULTS:We present the application of the workflow-centric RO model for our bioinformatics case study. Three workflows were produced following recently defined Best Practices for workflow design. By modelling the experiment as an RO, we were able to automatically query the experiment and answer questions such as "which particular data was input to a particular workflow to test a particular hypothesis?", and "which particular conclusions were drawn from a particular workflow?".CONCLUSIONS:Applying a workflow-centric RO model to aggregate and annotate the resources used in a bioinformatics experiment, allowed us to retrieve the conclusions of the experiment in the context of the driving hypothesis, the executed workflows and their input data. The RO model is an extendable reference model that can be used by other systems as well.AVAILABILITY:The Research Object is available at http://www.myexperiment.org/packs/428The Wf4Ever Research Object Model is available at http://wf4ever.github.io/ro

KW - research object

KW - genomics

KW - workflow

KW - Semantic Web models

KW - Scientific workflows

KW - Digital Libraries

KW - Genome wi de association study

U2 - 10.1186/2041-1480-5-41

DO - 10.1186/2041-1480-5-41

M3 - Article

SN - 2041-1480

VL - 5

JO - Journal of Biomedical Semantics

JF - Journal of Biomedical Semantics

IS - 1

ER -

Structuring research methods and data with the research object model: genomics workflows as a case study

Abstract

Keywords

Access to Document

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WF4EVER: Wf4Ever - Advanced Workflow Preservation Technologies for Enhanced Science

Enabling precision medicine via standard communication of HTS provenance, analysis, and results

CWL+Research Object == Complete Provenance

CWL Viewer: The Common Workflow Language Viewer

Workshop on Research Objects

THOR Ambassador Newsletter 2017-06

Cite this

Structuring research methods and data with the research object model: genomics workflows as a case study

Abstract

Keywords

Access to Document

Other files and links

Fingerprint

Projects

WF4EVER: Wf4Ever - Advanced Workflow Preservation Technologies for Enhanced Science

Research output

Enabling precision medicine via standard communication of HTS provenance, analysis, and results

CWL+Research Object == Complete Provenance

CWL Viewer: The Common Workflow Language Viewer

Activities

Workshop on Research Objects

Press/Media

THOR Ambassador Newsletter 2017-06

Cite this