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Using a Suite of Ontologies for Preserving Workflow-Centric Research Objects

33 Pages Posted: 11 Jul 2018 First Look: Accepted

See all articles by Khalid Belhajjame

Khalid Belhajjame

Université Paris Dauphine - PSL Research University

Jun Zhao

Lancaster University - School of Computing and Communications

Daniel Garijo

Universidad Politécnica de Madrid - Ontology Engineering Group

Matthew Gamble

University of Manchester - School of Computer Science

Kristina Hettne

Leiden University - Medical Center (LUMC)

Raul Palma

Universidad Politécnica de Madrid - Ontology Engineering Group; Poznan Supercomputing and Networking Center

Eleni Mina

Leiden University - Medical Center (LUMC)

Oscar Corcho

Universidad Politécnica de Madrid - Ontology Engineering Group; University of Manchester - School of Computer Science

Jose Manuel Gomez-Perez

iSOCO - Madrid

Sean Bechhofer

University of Manchester - School of Computer Science

Graham Klyne

University of Oxford - Department of Zoology

Carole Goble

University of Manchester - School of Computer Science

Abstract

Scientific workflows are a popular mechanism for specifying and automating data-driven in silico experiments. A significant aspect of their value lies in their potential to be reused. Once shared, workflows become useful building blocks that can be combined or modified for developing new experiments. However, previous studies have shown that storing workflow specifications alone is not sufficient to ensure that they can be successfully reused, without being able to understand what the workflows aim to achieve or to re-enact them. To gain an understanding of the workflow, and how it may be used and re-purposed for their needs, scientists require access to additional resources such as annotations describing the workflow, datasets used and produced by the workflow, and provenance traces recording workflow executions.

In this article, we present a novel approach to the preservation of scientific workflows through the application of research objects—aggregations of data and metadata that enrich the workflow specifications. Our approach is realised as a suite of ontologies that support the creation of workflow-centric research objects. Their design was guided by requirements elicited from previous empirical analyses of workflow decay and repair. The ontologies developed make use of and extend existing well known ontologies, namely the Object Reuse and Exchange (ORE) vocabulary, the Annotation Ontology (AO) and the W3C PROV ontology (PROVO). We illustrate the application of the ontologies for building Workflow Research Objects with a case-study that investigates Huntington’s disease, performed in collaboration with a team from the Leiden University Medial Centre (HG-LUMC). Finally we present a number of tools developed for creating and managing workflow-centric research objects.

Keywords: Research Object, Scientific Workflow, Preservation, Annotation, Ontologies, Provenance

Suggested Citation

Belhajjame, Khalid and Zhao, Jun and Garijo, Daniel and Gamble, Matthew and Hettne, Kristina and Palma, Raul and Mina, Eleni and Corcho, Oscar and Gomez-Perez, Jose Manuel and Bechhofer, Sean and Klyne, Graham and Goble, Carole, Using a Suite of Ontologies for Preserving Workflow-Centric Research Objects (May 2015). Journal of Web Semantics First Look. Available at SSRN: https://ssrn.com/abstract=3199184 or http://dx.doi.org/10.2139/ssrn.3199184

Khalid Belhajjame (Contact Author)

Université Paris Dauphine - PSL Research University ( email )

Place du Maréchal de Lattre de Tassigny
Paris cedex 16, 75775
France

Jun Zhao

Lancaster University - School of Computing and Communications ( email )

InfoLab21, South Drive
Lancaster University
Lancaster, LA1 4WA
United Kingdom

Daniel Garijo

Universidad Politécnica de Madrid - Ontology Engineering Group ( email )

Madrid
Spain

Matthew Gamble

University of Manchester - School of Computer Science ( email )

Kilburn Building, Oxford Road
Manchester M13 9GH, M13 9PL
United Kingdom

Kristina Hettne

Leiden University - Medical Center (LUMC) ( email )

Albinusdreef 2
Leiden, 2333 ZA
Netherlands

Raul Palma

Universidad Politécnica de Madrid - Ontology Engineering Group ( email )

Madrid
Spain

Poznan Supercomputing and Networking Center ( email )

Poznan
Poland

Eleni Mina

Leiden University - Medical Center (LUMC)

Albinusdreef 2
Leiden, 2333 ZA
Netherlands

Oscar Corcho

Universidad Politécnica de Madrid - Ontology Engineering Group ( email )

Madrid
Spain

University of Manchester - School of Computer Science

Kilburn Building, Oxford Road
Manchester M13 9GH, M13 9PL
United Kingdom

Jose Manuel Gomez-Perez

iSOCO - Madrid ( email )

Av. del Partenón, 10, Planta 1
Campo de las Naciones, Oficina 1 - 3 A
Madrid, 28042
Spain

Sean Bechhofer

University of Manchester - School of Computer Science ( email )

Kilburn Building, Oxford Road
Manchester M13 9GH, M13 9PL
United Kingdom

Graham Klyne

University of Oxford - Department of Zoology ( email )

New Radcliffe House
Radcliffe Observatory Quarter
Oxford, OX13 5QL
United Kingdom

Carole Goble

University of Manchester - School of Computer Science ( email )

Kilburn Building, Oxford Road
Manchester M13 9GH, M13 9PL
United Kingdom

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