It’s all about reproducibility

27 May 2015
By Natasha Karp

The Animal Research: Reporting of in Vivo Experiments (ARRIVE) guidelines lay out the reporting requirements to ensure all the information is available to allow reproducible research

The Animal Research: Reporting of in Vivo Experiments (ARRIVE) guidelines lay out the reporting requirements to ensure all the information is available to allow reproducible research

Research has shown that experiments involving animals are frequently not reported with sufficient detail to allow results to be reproduced [1]. We have an ethical responsibility to maximise the value returned from a study involving animals and ensure that the data are collected and presented in a way that maximises reproducibility.

This reproducibility issue identified with published papers lead to the Animal Research: Reporting of in Vivo Experiments (ARRIVE) guidelines [2], which lay out the reporting requirements to ensure all the information is available to allow reproducible research.

The International Mouse Phenotyping Consortium is a world-wide project to understand how genes function in the body by systematically recording the characteristics (phenotypes) of mice in which an individual gene has been switched off. These are known as knockout mice. The ultimate goal is to relate gene function to human disease.

It is a large scale project, with all mathematical and image data published in a public database [3]. The dataset grows daily, and currently includes data from 734,284 experiments. We have taken the ARRIVE guidelines and applied them to our large international database [4]. Applying these guidelines led to two sets of challenges.

The first problem centred on understanding each other and explaining exactly how experiments were implemented at each contributing institute. The fact that the project is international and multilingual wasn’t the only barrier to clear communication; a common issue in science is that we describe things in a multitude of ways and we use the same words to means different things. As an example, the phrase “control mouse” was thought to have no ambiguity but in fact there are four different interpretations.

The second set of challenges was specific to a database of this scale and arose from capturing the data, organising it and presenting it back to a user. This problem is on-going. As the database and tools implemented grow, we have to continue to test our interface and ensure the data are accessible.

Setting this target has been challenging, but worth the journey. We can already see benefits; the process has highlighted good practice across our phenotyping centres and has provided the transparency necessary for scientists around the world to fairly evaluate data that will assist in genetic research.

Natasha Karp is a senior biostatistician who supports the International Mouse Phenotyping Consortium.

References

  1. Kilkenny C, Parsons N, Kadyszewski E, Festing MF, Cuthill IC, et al. (2009) Survey of the quality of experimental design, statistical analysis and reporting of research using animals. PLoS One 4: e7824. DOI: 10.1371/journal.pone.0007824
  2. Kilkenny C, Browne WJ, Cuthill IC, Emerson M, Altman DG (2010) Improving bioscience research reporting: the ARRIVE guidelines for reporting animal research. PLoS Biol 8: e1000412. DOI:10.4103/0976-500X.72351
  3. International Mouse Phenotyping Consortium website http://www.mousephenotype.org/
  4. Karp, N  et al (2015) Applying the ARRIVE guidelines to an in vivo database.  PLOS Biology 3: e1002151. DOI: 10.1371/journal.pbio.1002151

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