Why Software and data papers are a bad solution to a real problem

6 minute read

I am unhappy and concerned with data/software papers: it’s is a bad answer to a real problem and we end up recapitulating the perverse incentives in academic publishing. The situation is neither helping those that value data and software, and open science in general, nor the dissemination of science in general.

The real issue

The problem we are facing is lack of credit for scientists, research software engineers and anyone who produces data and software; they do not get the academic credit for their contributions, despite the importance of data and scientific software, and end up without any clear career progression opportunities. The suggested solution is to publish data/software papers (or data/application notes, as they are often referred to). The intended fix is that this ties back in with the usual academic business, but ends up reinforcing the usual bean counting habit of relying on number papers rather than the actual inputs. As a result of relying on a broken system to fix the recognition of data/software, the papers that describe these inputs become a mere way to boost the number of publications and end up doing a terrible job at actually describing and promoting the outputs for what they really are.

Let me elaborate on this.

Bad software/data papers

I have come across terrible data papers, including some from reputable labs: full of typos, superficial data description, data provided as supplementary tables in pdf, … Similar situations for software, where the emphasis on the software and scientific software development and good enough practice is completely lost: minimal documentation, unreadable code (no spaces, miles-long lines, no indentation), completely inappropriate data structures, missing data, …

What we would really need is an in-depth/hands-on review of the data when submitted to the repository. The authors should provide evidence that their data is of good quality, describe the data with good (possibly interactive) visualisations, document the experimental design, show how they processed the data, make sure this can be reproduced, disseminate the raw and processed data in a way that enables others to easily re-use it, … I really don’t think these requests are extraordinary, but I hardly ever see data papers that match all these requirements.

This also applies to software. The review should focus on the software, like what happens for the Bioconductor project: meta-data, documentation, source code, unit testing, … rather then only (or mainly) the relevance of the software, or a systematic comparison with other software. I don’t mean to say this is not useful or important, but not relevant if the software is not up to standards anyway. And if the authors want to publish a comparison of different software, they shouldn’t try to grep an additional citation by drafting a quick and dirty application note.

Once these goals have been attained, the actual data/software in their original repositories is the important deliverable and one should be able to cite these, directly. As far as I am concerned, the additional paper is only a detail. Why not, if that’s what’s needed for the authors to get proper academic credit. But the data/software paper shouldn’t become a shortcut for credit at the expense of the actual deliverable. Let’s not forget that a paper is only an advertisement of the scholarship.

That was my first point, bad data and software papers.

Predatory publishing

Another perverse effect is the proliferation of data or software journals with very low standards but with a big appetite for poor data/software notes. Here, you’ll find your typical predatory publishers, such as Elsevier. Their business model is to publish the scientific paper and the data paper, which will cite each other so that they boost the citation statistics and their money income. I am not making this us; I did get my hands on an internal email that stated this quite explicitly.

Here’s the predatory business model:

At the research article revision stage, authors are offered the option to convert their supplementary data into a data article to be published in the open access Data in Brief journal. This comes, of course, at a minor cost; in this case £500. According the the editor, “the data is then easier to download and use, i.e. not behind a subscription paywall” (you can’t make that up, can you!). The Data in Brief and the research articles then automatically cite and link to each other. To add insult to injury, editors and reviewers are explicitly told that they are not required to review this Data in Brief article, but may need to look at it if the need to look into the supporting material.

The benefits, as outlined in the email are:

  • data that were once behind a subscription paywall is now open access, and
  • the link from the Data in Brief article drives more traffic to the research article and the research article gets an extra citation.

What it really means:

Let’s pretend we care about open access and data, increasing our self-citations and metrics, drive more traffic, earn more money. As the main paper will already be accepted, the data paper is just a formality and will hardly get reviewed. And we will explicitly tell the reviewers to ignore data in the main paper.

Unfortunately, the editors’ replies haven’t leaked to my inbox. But the mere fact that this something like that is considered is truly disgusting, but in line with Elsevier’s general policy.

Now, to be fair, there are also great examples out there. The Journal of Open Research Software (JORS), for example, covers how the software results can be trusted, concrete and useful suggestions for reuse of the software, addresses implementation and architecture, … The Journal of Open Source Software is a developer friendly journal for research software packages with a formal peer review process that is designed to improve the quality of the software submitted. (Note that I haven’t published in any of those so far.)

What can we do?

Ideally, the repositories would have the man power and expertise to do an in-depth review of every submission, and, if necessary, provide the support to get every submission to a good standard. Then, no journals would even consider publishing any output that didn’t pass this in-depth technical review and proceed with the interpretation of the data. But that’s not going to happen.

I just want to reiterate how Elsevier’s predatory model is the exact opposite: don’t care about the data, just use it as a pretend open access solution and make scientists pay more for the scam.

If you don’t care about all this, and just mind the final piece of advertisement of your research, just keep on how you are doing. Otherwise, make sure you put every effort in doing the very best job you can in documenting your data and developing your software. Publish them ahead of the actual paper, and make sure as many as possible get a chance to look at then and comment. If you ever review a paper with software or data, go through it with a fine-toothed comb, and don’t hesitate to highlight what’s wrong and what needs to be improved. Don’t hesitate to praise a good software or data article when you read one too, of course.

I plan to start a systematic and extensive guide describing how to document a data set in mass spectrometry-based proteomics.

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