Testing the reproducibility and robustness of the cancer biology literature by robot
Journal article, 2022

Scientific results should not just be 'repeatable' (replicable in the same laboratory under identical conditions), but also 'reproducible' (replicable in other laboratories under similar conditions). Results should also, if possible, be 'robust' (replicable under a wide range of conditions). The reproducibility and robustness of only a small fraction of published biomedical results has been tested; furthermore, when reproducibility is tested, it is often not found. This situation is termed 'the reproducibility crisis', and it is one the most important issues facing biomedicine. This crisis would be solved if it were possible to automate reproducibility testing. Here, we describe the semi-automated testing for reproducibility and robustness of simple statements (propositions) about cancer cell biology automatically extracted from the literature. From 12 260 papers, we automatically extracted statements predicted to describe experimental results regarding a change of gene expression in response to drug treatment in breast cancer, from these we selected 74 statements of high biomedical interest. To test the reproducibility of these statements, two different teams used the laboratory automation system Eve and two breast cancer cell lines (MCF7 and MDA-MB-231). Statistically significant evidence for repeatability was found for 43 statements, and significant evidence for reproducibility/robustness in 22 statements. In two cases, the automation made serendipitous discoveries. The reproduced/robust knowledge provides significant insight into cancer. We conclude that semi-automated reproducibility testing is currently achievable, that it could be scaled up to generate a substantive source of reliable knowledge and that automation has the potential to mitigate the reproducibility crisis.

literature

reproducibility

biology

cancer

robustnesses

testings

Author

Katherine Roper

University of Manchester

A. Abdel-Rehim

Department of Chemical Engineering and Biotechnology

Sonya Hubbard

University of Manchester

Martin Carpenter

University of Manchester

Andrey Rzhetsky

University of Chicago

Larisa N. Soldatova

Goldsmiths, University of London

Ross King

Alan Turing Institute

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

University of Cambridge

Chalmers, Computer Science and Engineering (Chalmers)

Journal of the Royal Society Interface

1742-5689 (ISSN) 1742-5662 (eISSN)

Vol. 19 189 20210821

Subject Categories

Computer and Information Science

Cancer and Oncology

DOI

10.1098/rsif.2021.0821

PubMed

35382578

More information

Latest update

4/21/2022