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ARS Home » Pacific West Area » Corvallis, Oregon » Horticultural Crops Disease and Pest Management Research Unit » Research » Publications at this Location » Publication #388137
Research Project: Integrated Disease Management of Exotic and Emerging Plant Diseases of Horticultural Crops

Location: Horticultural Crops Disease and Pest Management Research Unit

Title: Openness and computational reproducibility in plant pathology: Where we stand and a way forward

Author
item SPARKS, ADAM - Department Of Primary Industries
item DEL PONTE, EMERSON - Universidade Federal De Vicosa
item ALVES, KAIQUE - Universidade Federal De Vicosa
item Foster, Zachary
item Grunwald, Niklaus - Nik

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/8/2023
Publication Date: 1/9/2023
Citation: Sparks, A.H., Del Ponte, E., Alves, K., Foster, Z.S., Grunwald, N.J. 2023. Openness and computational reproducibility in plant pathology: Where we stand and a way forward. Phytopathology. https://doi.org/10.1094/PHYTO-10-21-0430-PER.
DOI: https://doi.org/10.1094/PHYTO-10-21-0430-PER

Interpretive Summary: Open research practices promote transparency and reproducibility of scientific results and are required by many research funding agencies. Openly sharing protocols, data and computational code is central for current scholarly dissemination and communication, but in many fields, including plant health research, adoption of these practices has been slow. We randomly selected 300 articles published from 2012 to 2018 across 21 journals representative of the plant health research discipline and assigned evaluated them for openness and reproducibility. We found that most of the articles were not following suggested protocols for open science, and were failing to share data or code in a reproducible way. We provide ideas and tools to promote open, reproducible research practices among plant pathologists.

Technical Abstract: Open research practices have been highlighted extensively during the last ten years in many fields of scientific study as essential standards needed to promote transparency and reproducibility of scientific results. Scientific claims can only be evaluated based on how protocols, materials, equipment and methods were described; data were collected and prepared; and, analyses were conducted. Openly sharing protocols, data and computational code is central for current scholarly dissemination and communication, but in many fields, including plant pathology, adoption of these practices has been slow. We randomly selected 300 articles published from 2012 to 2018 across 21 journals representative of the plant pathology discipline and assigned them scores reflecting their openness and reproducibility. We found that most of the articles were not following protocols for open science, and were failing to share data or code in a reproducible way. We also propose that use of open-source tools facilitates reproducible work and analyses benefiting not just readers, but the authors as well. Finally, we also provide ideas and tools to promote open, reproducible research practices among plant pathologists.