Open Access and Reproducibility in Plant Pathology Research: Guidelines and Best Practices-Reference-Cited by-同舟云学术

Open Access and Reproducibility in Plant Pathology Research: Guidelines and Best Practices

Published:2024-05 Issue:5 Volume:114 Page:910-916
ISSN:0031-949X
Container-title:Phytopathology®
language:en
Short-container-title:Phytopathology®

Author:

Grünwald Niklaus J.¹^ORCID,Bock Clive H.²,Chang Jeff H.³,De Souza Alessandra Alves⁴^ORCID,Ponte Emerson M. Del⁵^ORCID,du Toit Lindsey J.⁶^ORCID,Dorrance Anne E.⁷^ORCID,Dung Jeremiah⁸^ORCID,Gent David⁹^ORCID,Goss Erica M.¹⁰^ORCID,Lowe-Power Tiffany M.¹¹,Madden Laurence V.⁷^ORCID,Martin Frank N.¹²,McDowell John¹³,Naegele Rachel P.¹⁴,Potnis Neha¹⁵^ORCID,Quesada-Ocampo Lina M.¹⁶^ORCID,Sundin George W.¹⁷^ORCID,Thiessen Lindsey¹⁸,Vinatzer Boris A.¹³^ORCID,Zeng Quan¹⁹^ORCID

Affiliation:

1. U.S. Department of Agriculture-Agricultural Research Service, Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR 97331, U.S.A.

2. U.S. Department of Agriculture-Agricultural Research Service, Southeastern Fruit and Tree Nut Research Station, Byron, GA 31008, U.S.A.

3. Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, U.S.A.

4. Citrus Research Center “Sylvio Moreira”/Agronomic Institute–IAC, Corderiropolis, Sao Paulo, Brazil

5. Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil

6. Department of Plant Pathology, Washington State University, Mount Vernon, WA 98273, U.S.A.

7. Department of Plant Pathology, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, U.S.A.

8. Department of Botany and Plant Pathology, Central Oregon Agricultural Research and Extension Center, Oregon State University, Madras, OR 97741, U.S.A.

9. U.S. Department of Agriculture-Agricultural Research Service, Forage Seed and Cereal Research Unit, Corvallis, OR 97331, U.S.A.

10. Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, U.S.A.

11. Department of Plant Pathology, University of California Davis, Davis, CA 95616, U.S.A.

12. U.S. Department of Agriculture-Agricultural Research Service, Crop Protection and Improvement Research Center, Salinas, CA 93905, U.S.A.

13. School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, U.S.A.

14. U.S. Department of Agriculture-Agricultural Research Service, Sugarbeet and Bean Research Unit, East Lansing, MI 48824, U.S.A.

15. Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, U.S.A.

16. Department of Entomology and Plant Pathology and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC 27606, U.S.A.

17. Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A.

18. Domestic and Emergency Scientific Support, U.S. Department of Agriculture-Animal & Plant Health Inspection Service-Plant Protection and Quarantine, Raleigh, NC 27606, U.S.A.

19. Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT 06511, U.S.A.

Abstract

The landscape of scientific publishing is experiencing a transformative shift toward open access, a paradigm that mandates the availability of research outputs such as data, code, materials, and publications. Open access provides increased reproducibility and allows for reuse of these resources. This article provides guidance for best publishing practices of scientific research, data, and associated resources, including code, in The American Phytopathological Society journals. Key areas such as diagnostic assays, experimental design, data sharing, and code deposition are explored in detail. This guidance aligns with that observed by other leading journals. We hope the information assembled in this paper will raise awareness of best practices and enable greater appraisal of the true effects of biological phenomena in plant pathology.

Funder

National Institute of Food and Agriculture

Agricultural Research Service

Publisher

Scientific Societies

Link

https://apsjournals.apsnet.org/doi/pdf/10.1094/PHYTO-12-23-0483-IA

Reference19 articles.

1. Open access to scientific articles: a review of benefits and challenges

2. The need for transparency and good practices in the qPCR literature

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4. Metadata harmonization–Standards are the key for a better usage of omics data for integrative microbiome analysis

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