Taxacom: an idea on data reuse preprint for systematics

Sat May 24 02:11:29 CDT 2025

Hello Richard,

Thank you for your reply. I think that?s a great suggestion. I?m familiar with JOSS; however, for example, it would take a lot of effort for me to teach my supervisor or my parents how to use Git or GitHub. While the idea is simple in theory, it?s not practical or accessible for everyone. I also know about DOI assignment through Zenodo, as one of the journals I work with as an associate editor uses it.

The reason I prefer a preprint platform over a journal is something I mentioned in my recent email to the mailing list. Platforms like bioRxiv and EcoEvoRxiv are indeed good options? I?ve even used bioRxiv to host two papers publishing new datasets. However, bioRxiv clearly states that articles without new data or analysis are outside its scope. EcoEvoRxiv might be more flexible, but taxonomy is a more specialized field compared to many others.

If we truly want to make taxonomy a science, then data reuse and the ability to reproduce others' work are essential. For example, I?ve already seen paleontological studies where the data doesn?t match the claims made, and the work is not reproducible. Alarmingly,  other people's research might end up continuing these flawed datasets. Even worse, some journals reject commentary papers that point out these problems. So, what other options are there? I believe only a dedicated platform like this could offer a solution.

It?s not just about naming species, though that?s certainly important in taxonomy. The real issue is data repeatability, because that?s what determines whether taxonomy is truly a science.

I'm delighted to invite anyone to join if you have an interest.

Best regards
Guoyi

Guoyi Zhang (she/her), MRes, PhD candidate
Personal Web<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmalacology.net%2F&data=05%7C02%7Ctaxacom%40lists.ku.edu%7C1263bcaec06d4441b84008dd9a92378e%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638836674993127862%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=vHepjbK34QhzJ3D66%2FIuTTUrZ1ZCIhvgMyNDQw6jB7E%3D&reserved=0> | OCRID<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Forcid.org%2F0000-0002-3426-9273&data=05%7C02%7Ctaxacom%40lists.ku.edu%7C1263bcaec06d4441b84008dd9a92378e%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638836674993141847%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=i04vy1mCzR9LGcavnRz0hcODe4Mbhb%2BbcMSHv5u4BGA%3D&reserved=0>
School of Biological, Earth and Environmental Sciences
University of New South Wales
Australian Museum Research Institute
Australian Museum

________________________________
From: Taxacom <taxacom-bounces at lists.ku.edu> on behalf of Richard Littauer via Taxacom <taxacom at lists.ku.edu>
Sent: Saturday, 24 May 2025 7:55
To: Tony Rees <tonyrees49 at gmail.com>
Cc: taxacom at lists.ku.edu <taxacom at lists.ku.edu>
Subject: Re: Taxacom: an idea on data reuse preprint for systematics

I realized a similar thing to you, Kuoi.

Last December, I set up Codex Mutabilis at codexmutabilis.com. The journal
infrastructure is not complex - it is a Jekyll blog set up on GitHub. New
articles can be submitted to the GitHub repository at
https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FRichardLitt%2Fcodexmutabilis.com&data=05%7C02%7Ctaxacom%40lists.ku.edu%7C1263bcaec06d4441b84008dd9a92378e%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638836674993151144%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=txuiJAcB4Dd2tKL0lFvO2nQTH%2BYjekfvRl412JU%2BPkU%3D&reserved=0. Each article can be
peer-reviewed easily on GitHub using the pull request process that most
coders have been using there for years. Each act is also valid according to
the Code to the best of my current knowledge, as I got an ISSN for the
paper as a whole from the New Zealand National Library.

There are a couple of things to do to make it better - specifically, set up
a pipeline to turn each post into a PDF and submit it to Zenodo for a DOI.
That's trivial. I've already done that for one of the records,
https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fzenodo.org%2Frecords%2F14377608&data=05%7C02%7Ctaxacom%40lists.ku.edu%7C1263bcaec06d4441b84008dd9a92378e%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638836674993160124%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=5jFbH53kaS9EFrx7dARxFGkeUnivCGvtS%2BuPRmlCO0A%3D&reserved=0. Another thing to do is to make it much
clearer to newcomers how to submit papers.

The two posts that are currently published are *not* peer-reviewed, as I
was testing out the process and I didn't have another editor to look at
them. This doesn't stop them being valid publications according to the
Code. (Both of the current papers also reference medieval Latin and
substantivization ? hopefully, we can agree that this is controversial, and
not derail this thread by talking about how dangerous this is here. I've
learned more since December, and I wouldn't start with these two papers the
way they are written, if I were writing these posts today. An easy fix is
for everyone to ignore these two papers if they disagree with them).

The process for submitting and reviewing is a simplified version of the Journal
of Open Source Software <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fjoss.theoj.org%2F&data=05%7C02%7Ctaxacom%40lists.ku.edu%7C1263bcaec06d4441b84008dd9a92378e%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638836674993169041%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=iGI9NPDWBin0x5pizyB%2FzcNAC9YK8V6hobpNzgBzOoE%3D&reserved=0>, where I am also
currently an editor. If you haven't seen JOSS before, do check it out; it's
amazing.

I would love to have help making this process easier. The entire point of
Codex Mutabilis is to make a fast publishing venue for the type of small
corrections Daniel mentions above. Codex Mutabilis, as it currently is,
satisfies all of the conditions Daniel mentions, too.

Kuoi:

> I?m considering the creation of a small, community-driven preprint
platform focused specifically on taxonomy, systematics, and data reuse

You don't need to set up a preprint platform. ArXiv and
https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.biorxiv.org%2F&data=05%7C02%7Ctaxacom%40lists.ku.edu%7C1263bcaec06d4441b84008dd9a92378e%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638836674993179688%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=aFq8CSiHriHhsqliCzKx%2F6TXhV3%2Fy65lx5q0u3lm%2Fr8%3D&reserved=0 already works for this. I think what we need is a
better journal for these sorts of works, and an easier, more transparent
review process to allow multiple reviews.

I've been submitting a few of the small works Daniel mentioned above to
traditional venues - Bull. Zoo. Nom., Zootaxa, etc. - and it really does
take a lot of effort. Formatting and editorial turn-around often seems to
take more work than it is worth. This is what I was hoping to solve with
Codex Mutabilis.

I have a paper describing the journal in review for a conference right now,
and should hear back next week. I will share the paper when I can.

Best,
R

On Sat, May 24, 2025 at 7:28?AM Tony Rees via Taxacom <taxacom at lists.ku.edu>
wrote:

> The phycological world identified a somewhat similar gap and introduced the
> e-journal "Notulae Algarum" to fill it, see
> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.notulaealgarum.com%2F&data=05%7C02%7Ctaxacom%40lists.ku.edu%7C1263bcaec06d4441b84008dd9a92378e%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638836674993188509%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=1vs9a1dsLfYjeFlC%2FPJsMJBSapssOu7CAe5hM9V4dcg%3D&reserved=0.
> You could look at this as a model, however it would be easy to
> underestimate the degree of effort, level of experience (both technical and
> academic), and long term commitment from both key persons and supporting
> agencies required. Just my view, and not really wishing to be the
> harbinger of bad news; however (having operated what has largely been a
> "single person" initiative for the past nineteen years) it is not really
> something that most sane persons would do without good resourcing, an
> understanding family (!), and a pretty long term personal commitment (and
> also an eventual exit strategy) - plus planning and implementation to avoid
> "single point of failure" scenarios. Just my 2 cents' worth of course,
>
> Regards - Tony
>
> Tony Rees, New South Wales, Australia
> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fabout.me%2FTonyRees&data=05%7C02%7Ctaxacom%40lists.ku.edu%7C1263bcaec06d4441b84008dd9a92378e%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638836674993197253%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=ITrWNa3eDnRlFZNeiNcF0QPtppXwTzwv%2FqH8sVhYL5Y%3D&reserved=0
> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.irmng.org%2F&data=05%7C02%7Ctaxacom%40lists.ku.edu%7C1263bcaec06d4441b84008dd9a92378e%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638836674993205986%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=AK1p88wyGP0Xdp41F8bjutWVKeJkvpOsS%2FymgfMpUwg%3D&reserved=0
>
>
> On Sat, 24 May 2025 at 01:42, Douglas Yanega via Taxacom <
> taxacom at lists.ku.edu> wrote:
>
> > I'm not good at being brief, but I'll try:
> >
> > For very small contributions of acts that affect zoological
> > nomenclature, *in principle* the Bulletin of Zoological Nomenclature -
> > the ICZN's journal - is a venue that handles several of the sorts of
> > things you refer to. The reality is that the turnaround time for
> > submissions to BZN is not fast, though it pains me to say it, as I am
> > one of the assistant editors.
> >
> > Not too long ago, I asked the other Commissioners if we might want to
> > set up some sort of "fast track" method of getting minor nomenclatural
> > notes into circulation, like within a month of submission, and the
> > response was lukewarm.
> >
> > I honestly think that there are a lot of taxonomists, myself included,
> > who are sitting on one to many minor things, like corrections to
> > spellings, unreplaced homonyms, unrecognized synonymies, gender
> > agreement corrections, First Reviser actions, and other small but
> > important items that need to be published, but are not part of some
> > larger revisionary work. I'm not a snail taxonomist, for example, so
> > what do I do if I discover a snail name that is being demonstrably
> > misspelled in the literature? To my mind, these sorts of things are
> > unified in that they should not require *significant* review, if any at
> > all. In many cases, all it truly requires is one *qualified* reviewer.
> >
> > The idea of a venue to disseminate these sorts of acts is, in that
> > respect, potentially very valuable if it can be implemented in such a
> > way that three crucial things are part of the model:
> >
> > (1) there is an interface where *multiple* people can see any and all
> > works submitted for publication, and *everyone* can act as a reviewer -
> > the model of "only a tiny number of anonymous reviewers" is the most
> > harmful self-imposed constraint on science that exists. This is why
> > papers keep getting published that contain homonyms, synonyms,
> > misspellings, multiple variant spellings, and other errors - NOT ENOUGH
> > REVIEWERS. There is literally no reason why a paper can't have several
> > dozen people review it, and catch every error before it makes it into
> > print. The system is not hard to implement - everyone who subscribes
> > gets auto-notified about every submission, and is free to review any of
> > them. A submission could have a dozen reviews or more within 24 hours.
> >
> > (2) submissions are time-stamped, and assigned useful keywords. It is
> > not helpful, for instance, if someone submits a new replacement name for
> > a homonym, and then someone else sees this and submits their own
> > suggestion for a replacement of the same name. A time stamp will ensure
> > that it's "first come, first published", and mandatory keywords will
> > make it easier to spot overlapping submissions. We can't have people at
> > one another's proverbial throats, and there is already - absurdly enough
> > - a cutthroat competition to replace homonyms. That sort of
> > unprofessional behavior should be discouraged.
> >
> > (3) the new e-journal complies FULLY with the provisions in the Code for
> > digital-only publication, so nomenclatural acts published in it are
> > *available*, and not technically unpublished (a MAJOR problem with many
> > existing e-journals, whose editors do not know or enforce the Code's
> > strict regulations).
> >
> > If you can address those three issues, I'm fairly sure you'll find there
> > is a real demand for that sort of venue.
> >
> > I might note that features #1 and #2 are both fully implemented in
> > Wikipedia and Wikispecies, so they've been proven to work. What these
> > venues lack is Code-compliance, and well-defined administrative
> oversight.
> >
> > Peace,
> >
> > --
> > Doug Yanega      Dept. of Entomology       Entomology Research Museum
> > Univ. of California, Riverside, CA 92521-0314  voicemail:951-827-8704
> > FaceBook: Doug Yanega (disclaimer: opinions are mine, not UCR's)
> >               https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Ffaculty.ucr.edu%2F~heraty%2Fyanega.html&data=05%7C02%7Ctaxacom%40lists.ku.edu%7C1263bcaec06d4441b84008dd9a92378e%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638836674993214631%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=grPOgxx1xSE%2FkycTIxO2UDjjlkmpyWhve%2Fo9yuHPLhw%3D&reserved=0
> >    "There are some enterprises in which a careful disorderliness
> >          is the true method" - Herman Melville, Moby Dick, Chap. 82
> > _______________________________________________
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> >
> > Nurturing nuance while assailing ambiguity for 38 years, 1987-2025.
> >
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--
Richard Littauer | burntfen.com <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.burntfen.com%2F&data=05%7C02%7Ctaxacom%40lists.ku.edu%7C1263bcaec06d4441b84008dd9a92378e%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638836674993223571%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=O1c2XdPKAyfADpFSxHAp4fI8tpRe3Xmtn5BuiwG%2FiEk%3D&reserved=0> | socials:
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