On the reproducibility of science: Unique identification of research resources in the biomedical literature

Nicole A. Vasilevsky, Matthew H. Brush, Holly Paddock, Laura Ponting, Shreejoy J. Tripathy, Gregory M. LaRocca, Melissa Haendel

Research output: Contribution to journalArticle

123 Scopus citations

Abstract

Scientific reproducibility has been at the forefront of many news stories and there exist numerous initiatives to help address this problem.We posit that a contributor is simply a lack of specificity that is required to enable adequate research reproducibility. In particular, the inability to uniquely identify research resources, such as antibodies and model organisms, makes it difficult or impossible to reproduce experiments even where the science is otherwise sound. In order to better understand the magnitude of this problem, we designed an experiment to ascertain the "identifiability" of research resources in the biomedical literature. We evaluated recent journal articles in the fields of Neuroscience, Developmental Biology, Immunology, Cell and Molecular Biology and General Biology, selected randomly based on a diversity of impact factors for the journals, publishers, and experimental method reporting guidelines.We attempted to uniquely identify model organisms (mouse, rat, zebrafish, worm, fly and yeast), antibodies, knockdown reagents (morpholinos or RNAi), constructs, and cell lines. Specific criteria were developed to determine if a resource was uniquely identifiable, and included examining relevant repositories (such as model organism databases, and the Antibody Registry), as well as vendor sites. The results of this experiment show that 54% of resources are not uniquely identifiable in publications, regardless of domain, journal impact factor, or reporting requirements. For example, in many cases the organism strain in which the experiment was performed or antibody that was used could not be identified. Our results show that identifiability is a serious problem for reproducibility.Based on these results, we provide recommendations to authors, reviewers, journal editors, vendors, and publishers. Scientific efficiency and reproducibility depend upon a research-wide improvement of this substantial problemin science today.

Original languageEnglish (US)
Article numbere148
JournalPeerJ
Volume2013
Issue number1
DOIs
Publication statusPublished - 2013

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Keywords

  • Antibodies
  • Cell lines
  • Constructs
  • Knockdown reagents
  • Materials and methods
  • Model organisms
  • Scientific reproducibility

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)
  • Neuroscience(all)

Cite this

Vasilevsky, N. A., Brush, M. H., Paddock, H., Ponting, L., Tripathy, S. J., LaRocca, G. M., & Haendel, M. (2013). On the reproducibility of science: Unique identification of research resources in the biomedical literature. PeerJ, 2013(1), [e148]. https://doi.org/10.7717/peerj.148