Pre- and Post-publication Verification for Reproducible Data Mining in Macromolecular Crystallography

Helliwell, John R.

doi:10.1007/978-1-0716-2095-3_10

Cited by 1 publication

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References 62 publications

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“…The challenge here is not with published studies and their data but with the release to the public of unpublished raw data. This is starting in earnest as synchrotron facilities such as Diamond, ESRF and Soleil have established data policies which envisage release three years after measurement (Helliwell, 2022). Effective data reuse of unpublished raw data depends on adequate metadata about the sample being made available.…”

Section: Introduction: the Nature Of The Challenge To Reproducibility...mentioning

confidence: 99%

Raw diffraction data are our ground truth from which all subsequent workflows develop

Helliwell¹

2022

Acta Crystallogr D Struct Biol

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Defining best practice in science is challenging. International consensus is facilitated by the International Science Council via its members such as the International Union of Crystallography (IUCr). The crystallographic community has many decades of tradition linking articles with the underpinning data, and is admired across all sciences accordingly. Crystallography has always been at the forefront of harnessing new technology in the service of consensus. Technology has provided new vast data-archiving opportunities, allowing the preservation of raw diffraction data, along with article and database depositions of a model's coordinates and associated structure factors. The raw diffraction data, which can now be preserved, are the ground truth from which all subsequent workflows develop. Journal editorial boards provide a practical forum for setting the criteria to decide if a study's files are truly the version of record. Within that, reality involves a variance of reasonable workflows. But what is a reasonable variance? Workflows must be detailed carefully by authors in explaining what they have done. There is a great, and increasing, diversity of macromolecular crystallography analyses, and yet an increased constraint on how much can be written in an article about the workflow used. Raw data provide the ultimate reproducibility evidence. A part of reproducibility and replicability is using an agreed vocabulary; the meaning of words such as precision and accuracy and, more recently, the confidence of a protein structure prediction should feature in approaching `truth'.

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Section: Introduction: the Nature Of The Challenge To Reproducibility...mentioning

confidence: 99%

Raw diffraction data are our ground truth from which all subsequent workflows develop

Helliwell¹

2022

Acta Crystallogr D Struct Biol

Self Cite

View full text Add to dashboard Cite

show abstract

Pre- and Post-publication Verification for Reproducible Data Mining in Macromolecular Crystallography

Cited by 1 publication

References 62 publications

Raw diffraction data are our ground truth from which all subsequent workflows develop

Raw diffraction data are our ground truth from which all subsequent workflows develop

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