Findable and reusable workflow data products: A genomic workflow case study

Issue title: Semantic eScience: Methods, Tools and Applications

Guest editors: Daniel Garijo, Natalia Villanueva-Rosales and Tomi Kauppinen

Article type: Research Article

Authors: Gaignard, Alban^{a; *} | Skaf-Molli, Hala^b | Belhajjame, Khalid^c

Affiliations: [a] l’institut du thorax, INSERM, CNRS, University of Nantes, Nantes, France. E-mail: alban.gaignard@univ-nantes.fr | [b] LS2N, University of Nantes, Nantes, France. E-mail: hala.skaf@univ-nantes.fr | [c] PSL, Université Paris-Dauphine, LAMSADE, Paris, France. E-mail: kbelhajj@googlemail.com

Correspondence: [*] Corresponding author. E-mail: alban.gaignard@univ-nantes.fr.

Abstract: While workflow systems have improved the repeatability of scientific experiments, the value of the processed (intermediate) data have been overlooked so far. In this paper, we argue that the intermediate data products of workflow executions should be seen as first-class objects that need to be curated and published. Not only will this be exploited to save time and resources needed when re-executing workflows, but more importantly, it will improve the reuse of data products by the same or peer scientists in the context of new hypotheses and experiments. To assist curator in annotating (intermediate) workflow data, we exploit in this work multiple sources of information, namely: (i) the provenance information captured by the workflow system, and (ii) domain annotations that are provided by tools registries, such as Bio.Tools. Furthermore, we show, on a concrete bioinformatics scenario, how summarising techniques can be used to reduce the machine-generated provenance information of such data products into concise human- and machine-readable annotations.

Keywords: FAIR, Linked Data, scientific workflows, provenance, bioinformatics, data summaries

DOI: 10.3233/SW-200374

Journal: Semantic Web, vol. 11, no. 5, pp. 751-763, 2020