ECRs, publish your datasets and methods as mini-papers

KamounLab
4 min readFeb 7, 2022

Do you have useful datasets and methods? Consider publishing them as “mini-papers” prior to formal publication in a journal.

Cite as: Kamoun, S. (2022). ECRs, publish your datasets and methods as mini-papers. Zenodo https://doi.org/10.5281/zenodo.5997932

“Mini-papers” are the underrated scholarly outputs of academia. For many Early Career Researchers (ECRs), publishing a full fledged research article is a daunting task. So, why not break down this task into smaller, less intimidating units and publish them as datasets or method papers?

We had a real case example with Thorsten Langner et al. paper on mini-chromosomes of the blast fungus (Magnaporthe oryzae) that was ultimately published in early 2021 in PLOS Genetics.

The paper builds on three different pre-publications that served as milestones in this scientific publishing journey.

First, the nanopore sequencing of genomic DNA from M. oryzae isolates was posted on Zenodo in February 2019. Zenodo is an open-access repository developed under the European OpenAIRE initiative. This Win et al. Technical Note provides the metadata and genome sequencing details of Thorsten’s paper. It is cited as reference 57 in the PLOS Genetics paper.

Win et al. 2019. https://doi.org/10.5281/zenodo.2564950

Second, the method and protocol for mini-chromosome isolation and sequencing described in Langner et al. was first published in November 2019 in another platform protocols.io, which promotes sharing and discussion of reproducible methods. This protocols.io article was also cited in the PLOS Genetics paper as reference 75

Langner, T. et al. 2019 https://dx.doi.org/10.17504/protocols.io.9t7h6rn

Finally, an earlier version of the paper itself was published as a preprint in the bioRxiv server in January 2020, more than a year before the PLOS Genetics paper went online.

Langner et al. 2020. https://doi.org/10.1101/2020.01.10.901983

Thorsten happily tweeted a paper thread about the paper in January 2020, again over one year before the journal article was posted.

Paper threads are the latest academic publishing genre and you can find here my tips about writing them. They can definitely expand the reach of your science beyond your immediate academic network. Thorsten’s preprint and tweet were widely shared on social media and helped promote his work months before journal publication. No wonder the preprint movement is known as ASAPbio.

One common and important factor in the three pre-publications mentioned above is that they all include a doi — a digital object identifier. This is important as it makes your scholarly product permanent and unambiguous in the internet, therefore the work can be cited with confidence. A blog post like this one for example, can be modified even years after publishing. Assigning your work to a DOI doesn’t allow you to do that, and this is critical for scientific discourse. Note, however, that you can still post additional versions or revisions of your DOI article.

The DOI System

I often get the question of whether posting these mini-papers and preprints will prevent from publishing later on in a journal. The answer is obviously no given the example above. Pretty much all academic publishers these days accept preprints. Check all the green “unrestricted” on this wikipedia list of academic publishers preprint policy. It wasn’t always like this, but the scientific publishing world has been adjusting to the digital age, and the popular preprint movement is irresistible.

It goes without saying that posting mini-papers and preprints will help beef up an ECR’s CV. It gives your potential employers and fellowship reviewers some concrete outputs to evaluate you months before your work makes it into journals. In addition, your peers will get to know you and benefit from your resources. Hey, you may become popular as that nice person who shared early on their invaluable datasets and knowledge.

Check for instance this amazing 18 new aphid genome assemblies that were made available to the community through a Zenodo paper. In just one go, Tom Mathers and colleagues at the John Innes Centre more than doubled the number of available genomes of this fascinating insect pest. I’m sure this can only help advance Tom’s career and gain him further exposure among his peers. The last I checked the Zenodo article had ~500 page views just a couple of days after posting.

So, consider doing your bit to help transition academic publishing into the open science era. Share your datasets and methods as doi in Zenodo or other platforms in a way that gives you full credit and will not prevent you from formally publishing in journals. Scholarly outputs aren’t just journal articles, engaging with the wider community can make a big difference for early career scientists. It’s all part of the perspective that you will be eventually judged as a scientist for your varied and original outputs, rather than some silly metrics. Check Yasin Dagdas’ inspiring thread on academic job interviews, and consider how mini-papers would fit in your career narrative.

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KamounLab

Biologist; passionate about science, plant pathogens, genomics, and evolution; open science advocate; loves travel, food, and sports; nomad and hunter-gatherer.