Reassessing data management in increasingly complex phenotypic datasets

2025/10/01 by Cyril Pommier, Isabelle Alic, Llorenç Cabrera‐Bosquet +6 · 1 voice
Computer Science · Decision Sciences · Biochemistry, Genetics and Molecular Biology · #Research Data Management Practices #Scientific Computing and Data Management #Gene expression and cancer classification

paper · doi:10.1016/j.tplants.2025.09.001

openalex publication_date 2025/10/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/01

Abstract

Phenotypic datasets are increasingly rich and heterogeneous, with images, time courses, manual measurements, processed variables, and metadata. The management of such datasets navigates between partly incompatible objectives: (i) facilitate data analysis by extracting, organizing, and storing relevant variables; and (ii) allow reuse of raw, synthesized, and computed data (FAIR principles). For the first objective, 'dedicated datasets' can be extracted from raw information and tailored for the user's data analysis, but they result in a massive loss of information. We advocate that, for the second objective, 'sensu stricto phenomic datasets', upstream of dedicated datasets, should organize data without loss of information with data-science tools, in a 'theory-agnostic' way. They allow different users to build their own 'dedicated datasets' according to planned data analysis.

Citations

• Enabling reusability of plant phenomic datasets with MIAPPE 1.1
• Many researchers were not compliant with their published data sharing statement: a mixed-methods study
• Soybean photosynthesis and crop yield are improved by accelerating recovery from photoprotection
• Eleven quick tips for properly handling tabular data
• Genomic prediction of maize yield across European environmental conditions
• Toward interoperable bioscience data

Discussions

• Trends in Plant Science’s 30th anniversary special issue highlights the article "Reassessing data management in increasingly complex phenotypic datasets" (Pommier et al. 2025) doi.org/10.1016/j.tp... [bsky, 0 points, 0 comments]