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Towards FAIR protocols and workflows: the OpenPREDICT use case.

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.

SUBMITTER: Celebi R

PROVIDER: S-EPMC7924452 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundIn Europe, progress in the development of health policies that address the needs of migrants and ethnic minorities has been slow. This is partly due to the absence of a strategic commitment by the health authorities. The Ministry of Public Health commissioned the ETHEALTH (EThnicity &HEALTH) group to formulate relevant recommendations to the public authorities with a view to reducing health inequalities among ethnic minorities. This paper describes the political process and the outcomes of the ETHEALTH expert group.ResultsAfter ten meetings, the ETHEALTH group came up with 46 recommendations, which were presented at a national press conference in December 2011. Target groups concerned by these recommendations covered both irregular migrants and migrants entitled to the national insurance coverage. Recommendations were supported by the need of combining universal approaches to health care with more specific approaches. The scope of the recommendations concerned health care as well as prevention, health promotion and access to health care. When analysing the content of the recommendations, some ETHEALTH recommendations were not fully measurable, and time-related; they were, however, quite specific and realistic within the Belgian context. The weak political commitment of an executive agency was identified as a major obstacle to the implementation of the recommendations.ConclusionsThe ETHEALTH group was an example of scientific advice on a global health issue. It also demonstrated the feasibility of coming up with a comprehensive strategy to decrease ethnic health inequalities, even in a political context where migration issues are sensitive. Two final lessons may be highlighted at the end of the first phase of the ETHEALTH project: firstly, the combination of scientific knowledge and practical expertise makes recommendations SMART; and, secondly, the low level of commitment on the part of policymakers might jeopardise the effective implementation of the recommendations.

Project description:INTRODUCTION:Despite progress in scaling up antiretroviral treatment, HIV prevention strategies have not been successful in significantly curbing HIV incidence in Latin America. HIV prevention interventions need to be expanded to target the most affected key populations with a combination approach, including new high impact technologies. Oral pre-exposure prophylaxis (PrEP) is recommended as additional prevention choice for individuals at higher risk of infection and could become a cost-effective prevention tool. We discuss the barriers and solutions for a fair consideration of PrEP as part of combination HIV prevention strategies in Latin America. DISCUSSION:Although demonstration projects are ongoing or being planned in a number of countries, to date no Latin American country has implemented a public PrEP programme. The knowledge of policymakers about PrEP implementation needs to be strengthened, and programmatic guidance and cost estimate tools need to be developed to support adequate planning. Despite high levels of awareness among health providers, especially if engaged in HIV or key population care, willingness to prescribe PrEP is still low due to the lack of national policies and guidelines. Key populations, especially men who have sex with men, transgender women and sex workers, have been engaged in demonstration projects, and qualitative research shows high awareness and willingness to use PrEP, especially if accessible in the public sector for free or at affordable price. Concerns of safety, adherence, effectiveness and risk compensation need to be addressed through targeted social communication strategies to improve PrEP knowledge and stimulate demand. Alliance among policymakers, civil society and representatives from key populations, healthcare providers and researchers will be critical for the design and successful implementation of PrEP demonstration projects of locally adapted delivery models. The use of mechanisms of joint negotiation and procurement of antiretrovirals could reduce costs and significantly increase the cost-effectiveness of PrEP. CONCLUSIONS:PrEP is an additional prevention tool and should be implemented in combination and synergy with other prevention interventions. PrEP programmes should target high-risk individuals from key populations for higher cost-effectiveness. Demonstration projects may generate strategic information for and lead to the implementation of full-scale PrEP programmes.

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Towards FAIR protocols and workflows: the OpenPREDICT use case.

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