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. 2020 Sep 21:6:e281.
doi: 10.7717/peerj-cs.281. eCollection 2020.

Towards FAIR protocols and workflows: the OpenPREDICT use case

Remzi Celebi #  1 , Joao Rebelo Moreira #  2 , Ahmed A Hassan  3 , Sandeep Ayyar  4 , Lars Ridder  5 , Tobias Kuhn  2 , Michel Dumontier  1
Affiliations

Towards FAIR protocols and workflows: the OpenPREDICT use case

Remzi Celebi et al. PeerJ Comput Sci. .

Abstract

It is essential for the advancement of science that researchers share, reuse and reproduce each other's workflows and protocols. The FAIR principles are a set of guidelines that aim to maximize the value and usefulness of research data, and emphasize the importance of making digital objects findable and reusable by others. The question of how to apply these principles not just to data but also to the workflows and protocols that consume and produce them is still under debate and poses a number of challenges. In this paper we describe a two-fold approach of simultaneously applying the FAIR principles to scientific workflows as well as the involved data. We apply and evaluate our approach on the case of the PREDICT workflow, a highly cited drug repurposing workflow. This includes FAIRification of the involved datasets, as well as applying semantic technologies to represent and store data about the detailed versions of the general protocol, of the concrete workflow instructions, and of their execution traces. We propose a semantic model to address these specific requirements and was evaluated by answering competency questions. This semantic model consists of classes and relations from a number of existing ontologies, including Workflow4ever, PROV, EDAM, and BPMN. This allowed us then to formulate and answer new kinds of competency questions. Our evaluation shows the high degree to which our FAIRified OpenPREDICT workflow now adheres to the FAIR principles and the practicality and usefulness of being able to answer our new competency questions.

Keywords: Drug repurposing; FAIR data principles; FAIR workflows; Ontology-driven healthcare; Reproducibility; Research Object; Scientific workflows and protocols; Semantic web.

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Conflict of interest statement

The authors declare there are no competing interests.

Figures

Figure 1
Figure 1. Unified semantic model for workflows.
Figure 2
Figure 2. OpenPREDICT Workflow (version 0.1) with manual and computational steps.
See this image and copyright information in PMC

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