Open Science meets Food Modelling: Introducing the Food Modelling Journal (FMJ)

Filter, Matthias; Candela, Leonardo; Guillier, Laurent; Nauta, Maarten; Georgiev, Teodor; Stoev, Pavel; Penev, Lyubomir

doi:10.3897/fmj.1.46561

Cited by 6 publications

(6 citation statements)

References 23 publications

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“…This approach makes it possible to easily create executable papers linking to VRE resources. 23 Finally, to collaboratively manage foodborne outbreaks data, the data catalog service was exploited, leading to implementing a reference catalog for the specific community. 24…”

Section: The Agri-food Communitymentioning

confidence: 99%

Virtual research environments co‐creation: The D4Science experience

Assante

Candela

Castelli

et al. 2022

Concurrency and Computation

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Virtual research environments are systems called to serve the needs of their designated communities of practice. Every community of practice is a group of people dynamically aggregated by the willingness to collaborate to address a given research question. The virtual research environment provides its users with seamless access to the resources of interest (namely, data and services) no matter what and where they are. Developing a virtual research environment thus to guarantee its uptake from the community of practice is a challenging task. In this article, we advocate how the co‐creation driven approach promoted by D4Science has proven to be effective. In particular, we present the co‐creation options supported, discuss how diverse communities of practice have exploited these options, and give some usage indicators on the created VREs.

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Section: The Agri-food Communitymentioning

confidence: 99%

Virtual research environments co‐creation: The D4Science experience

Assante

Candela

Castelli

et al. 2022

Concurrency and Computation

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“…A specific example of the above approach has been implemented by the Food Modeling Journal (FMJ) 5 . 37 This new open access journal has been designed and launched to support the needs of the risk assessment and food modeling community (see Section 3.2). It promotes the publishing of scientific research outcomes in novel article formats like the "Executable Model Paper" based on the information exchange standard Food Safety Knowledge Metadata Language (FSK-ML).…”

Section: Realising Executable Papers and Supporting The Food Modeling Journalmentioning

confidence: 99%

“…A specific example of the above approach has been implemented by the Food Modeling Journal (FMJ) 37 . This new open access journal has been designed and launched to support the needs of the risk assessment and food modeling community (see Section 3.2).…”

Section: Exploitation Scenariosmentioning

confidence: 99%

Realizing virtual research environments for the agri‐food community: The AGINFRA PLUS experience

Assante

Boizet

Candela

et al. 2020

Concurrency and Computation

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The enhancements in IT solutions and the open science movement are injecting changes in the practices dealing with data collection, collation, processing, analytics, and publishing in all the domains, including agri-food. However, in implementing these changes one of the major issues faced by the agri-food researchers is the fragmentation of the "assets" to be exploited when performing research tasks, for example, data of interest are heterogeneous and scattered across several repositories, the tools modelers rely on are diverse and often make use of limited computing capacity, the publishing practices are various and rarely aim at making available the "whole story" including datasets, processes, and results. This paper presents the AGINFRA PLUS endeavor to overcome these limitations by providing researchers in three designated communities with Virtual Research Environments facilitating the use of the "assets" of interest and promote collaboration. K E Y W O R D Sagroclimatic modeling, food safety risks assessment, food security, virtual research environment INTRODUCTIONThe developments in information and communication technologies, including big data availability and management, web and cloud technologies,as well as open science-related practices are not yet fully embraced by the Agriculture and Food Science research domain. 1,2 The fragmentation of "resources" needed to exploit these new opportunities across several and heterogeneous "places" is certainly one of the major factors hindering this uptake process, for example, data are heterogeneous and scattered across several repositories, modeling tools and supporting systems are diverse, the amount of available computing capacity varies a lot across teams and laboratories.The AGINFRA PLUS project has been set up to develop an innovative approach in Agri-food digital science practices aiming at overcoming the limitations stemming from the above settings by leveraging on existing e-Infrastructures and services. In particular, AGINFRA PLUS promotes the exploitation of Virtual Research Environments (VREs) 3 to provide designated communities with seamless access to the data, services, and

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“…Prior to peer-review of submitted omics data paper manuscripts, all underlying datasets go through mandatory data auditing, cleaning and quality checks to assure that they meet the journal standards for publication [56]. This is done by a data auditor, whose role is to technically evaluate the submitted datasets for compliance to a data quality checklist [57] and to provide authors with a detailed report, including recommendations for improving the dataset.…”

Section: Omics Data Papers and Underlying Datasets Undergo Peer-reviementioning

confidence: 99%

A Streamlined Workflow for Conversion, Peer-Review and Publication of Omics Metadata as Omics Data Papers

Dimitrova¹,

Meyer²,

Buttigieg³

et al. 2020

Preprint

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Data papers have emerged as a powerful instrument for open data publishing, obtaining credit, and establishing priority for datasets generated in scientific experiments. Academic publishing improves data and metadata quality through peer-review and increases the impact of datasets by enhancing their visibility, accessibility, and re-usability. We aimed to establish a new type of article structure and template for omics studies: the omics data paper. To improve data interoperability and further incentivise researchers to publish high-quality data sets, we created a workflow for streamlined import of omics metadata directly into a data paper manuscript. An omics data paper template was designed by defining key article sections which encourage the description of omics datasets and methodologies. The workflow was based on REpresentational State Transfer services and Xpath to extract information from the European Nucleotide Archive, ArrayExpress and BioSamples databases, which follow community-agreed standards. The workflow for automatic import of standard-compliant metadata into an omics data paper manuscript facilitates the authoring process. It demonstrates the importance and potential of creating machine-readable and standard-compliant metadata. The omics data paper structure and workflow to import omics metadata improves the data publishing landscape by providing a novel mechanism for creating high-quality, enhanced metadata records, peer reviewing and publishing of these. It constitutes a powerful addition for distribution, visibility, reproducibility and re-usability of scientific data. We hope that streamlined metadata re-use for scholarly publishing encourages authors to improve the quality of their metadata to achieve a truly FAIR data world.

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Open Science meets Food Modelling: Introducing the Food Modelling Journal (FMJ)

Cited by 6 publications

References 23 publications

Virtual research environments co‐creation: The D4Science experience

Virtual research environments co‐creation: The D4Science experience

Realizing virtual research environments for the agri‐food community: The AGINFRA PLUS experience

A Streamlined Workflow for Conversion, Peer-Review and Publication of Omics Metadata as Omics Data Papers

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