[Taxacom] "Taxon Filter" (was Re: Electronic publication)

Scott Thomson scott.thomson321 at gmail.com
Thu Jan 12 05:05:32 CST 2017

Hi everyone,

I also like this more fleshed out idea and if Lyubomir wants to do a test
run of working this I am fine with using my manuscripts in this. I have a
couple in prep that do a number of different nomenclatural acts,
descriptions as well as others that I would be willing to put through this.

Cheers, Scott

On Thu, Jan 12, 2017 at 4:54 AM, Donat Agosti <agosti at amnh.org> wrote:

> I can only second Lyubo's comment below and add some reasons, why such a
> change in publishing is the only way forwards. This does not mean on single
> journal, but journals that publish semantically enhanced content for which
> not just the metadata is accessible but the entire content.
> The current system, to say it mildly, is a complete failure.
> 1. We have an estimate of 10% of our literature digital, mainly through
> efforts of by BHL. The many silos of PDFs accumulated by individual
> scientists don't count, since they are not part of the community, i.e.
> accessible for everybody.
> 2. We do not have a catalogue of life for all living species, nor are we
> able to build one without an additional huge effort that is not on the
> horizon.
> 3. We do not know, what has been published in 2016.
> 4. The traditional publications are made for human consumption which makes
> data extraction extremely cumbersome.
> 5. We do not fulfill the role of taxonomy as a service to the widest
> community to deliver the reference system to share data about species and
> thus endanger taxonomy to become even more obsolete - which is not really
> necessary to happen with the current tools at our fingertips.
> After having now worked for over 14 years in modeling and extracting
> taxonomic content from publications, I don't see any silver lining that we
> can deal with the huge backlog of literature, and a slight for ongoing
> publishing. With a great effort we now can automatically extract content
> from scientific publications, that results together with those easily
> imported from taxpub/XML published articles from Pensoft with an estimate
> of 25% of the new described species for 2016, including the metadata, the
> taxonomic treatments, the illustrations and in many case the types
> material, including the collection code and specimen code. Additionally to
> the articles, the treatments and illustrations all have a persistent
> identifiers and include them whenever one cites another, and respective
> metadata.
> This is mainly based on born digital articles - tackling at a same level
> scanned articles is a magnitude more complex, which makes it even less
> hopeful that it will be done somewhere in the near future.
> For 2016, at Plazi we extracted 4 n.fam, 376 n.gen, and 4.684 n.sp.,
> 42.207 taxonomic treatments  of 40.870 unique names from 60 different
> journals. The data is accessible at http://plazi.org and
> http://biolitrepo.org.
> Plazi data is automatically imported in GBIF where it is one of the major
> name contributors and one of the few providing treatments, allowing linking
> a name usage to the respective treatment and from there to the original
> article and illustrations - which for a nomenclatural point of view allows
> to check, besides the exact publishing date, all what is needed to
> understand whether a name is available. But it also allows to start to
> understand the scientific bases for new names, which is all too often very
> thin, i.e. one single specimen based descriptions (see eg
> http://dx.doi.org/10.3897/BDJ.3.e5063 or consult the new taxa feature (
> http://tb.plazi.org/GgServer/static/newToday.html )
> Our taxonomists chance is that we have one of the most advanced
> publication system for the entire scientific publishing world available. In
> fact it has been published for the taxonomic world thanks to a
> collaboration with Pensoft who implemented it, and a collaboration with
> Plazi and the us National Library of Medicine, which for this reason also
> started to include taxonomic articles into PubMed.
> This has another advantage, that all is open access and thus available for
> anybody anywhere in the world. In fact the implementation of the Open
> Biodiversity Knowledge Management System (OBKMS) will make all the data
> that is being published at Pensoft and extracted by Plazi available into
> the Linked Open Data Cloud. With other words, our really important data
> will become a first class citizen it needs to be.  But it needs a community
> effort to make it  happen, that is to provide not a fraction but all the
> data of our discoveries. Please join this effort!
> Donat
> -----Original Message-----
> From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of
> Lyubomir Penev
> Sent: Thursday, January 12, 2017 9:53 AM
> To: Doug Yanega <dyanega at ucr.edu>
> Cc: Taxa com <taxacom at mailman.nhm.ku.edu>
> Subject: Re: [Taxacom] "Taxon Filter" (was Re: Electronic publication)
> Doug,
> As we have discussed with you before, we do have such a system and
> technical infrastructure in place. Saying that, I am very far from
> pretending that any of our journals should become the "only" place for
> publication of new names. Please do not get me wrong in that respect!
> I would imagine that such a system would work in the following way:
>    1. Author submits a manuscript to a journal
>    2. Journal (perhaps after some technical checks) opens the manuscript
>    for open peer review and automatically notifies all users that have
>    registered themselves for that taxon. Depending on the group, the
>    registration of reviewers can work at any taxonomic rank, assuming that
>    family and order ranks will be most widely used. If there are no
> reviewers
>    registered at a certain taxonomic rank, then the notifications could go
> to
>    all who have registered for the higher taxon rank, etc.
>    3. The manuscript is open for review for a certain period, say, 4 weeks.
>    All reviews, comments and replies are publicly available open to all, or
>    perhaps only to reviewers registered for the particular taxon, or for
> all
>    registered users (just a matter of policy!).
>    4. The author revises the manuscript and re-submits it to the public.
>    5. The subject editor decides to accept or reject it, based on the
>    reviews and revisions. If there are NO reviews, the subject editor may
> have
>    the rights to either accept or reject it by him/herself. His/her letter
> of
>    acceptance/rejection willbe made open to the public as well.
>    6. Once accepted, the manuscript will be OFFICIALLY published at a
>    certain date, which means assigning DOI, REGISTRATION of the new names
> at
>    ZooBank, and ARCHIVING in trusted international repositories.
>    7. After the official publication, the author may decide to publish a
>    revised/corrected version of the same article (for example to correct a
>    name, or even to add some new taxa to a checklist, or to a monographic
>    revision). In our system, the author needs only to press a button to
> return
>    the article back into editing mode, correct and publish it again (with
> or
>    without peer-review - just a matter of policy!) under a new DOI linked
> to
>    the previous version(s) via CrossMark. Previous versions are not erased
>    from the website, they are considered as earlier official version(s) of
> the
>    article.
> I would love to test the workflow with a keen group of taxonomists in a
> real-time pilot.
> Very best,
> Lyubomir
> On Wed, Jan 11, 2017 at 8:55 PM, Doug Yanega <dyanega at ucr.edu> wrote:
> > For the record, the "Taxon Filter" concept is one that Hinrich largely
> > borrowed from a model I have been proposing for some time now, and he
> > and I had extensive discussions prior to his adopting that name. There
> > is a very important aspect of the process which does not seem to have
> > been clearly explained, and I think it is highly relevant to several
> > of the issues raised in this present thread. Allow me to give a
> > hypothetical example to
> > illustrate:
> >
> > Suppose author X wants to describe a new species of bumblebee (the
> > genus Bombus, family Apidae, order Hymenoptera, class Insecta). They
> > have three female specimens, from two localities in Mexico.
> >
> > Under the status quo, they submit a manuscript to journal Y and it is
> > seen by three anonymous referees plus a subject editor before being
> > accepted, with minor revision, and published. Under the status quo, it
> > is ALSO possible that one of the referees (let's call them Z) might
> > realize "Oh, I have some specimens of this new species myself!" and
> > they could quickly publish their OWN description, and "scoop" author
> > X, usurping their discovery. Author X is furious, but cannot prove
> > that Z was one of the referees, because they are shielded by anonymity.
> >
> > Under the model that I and Hinrich have been advocating (at least my
> > version of which is NOT a "minimal requirements" model), this would be
> > quite different.
> >
> > Author X would submit their manuscript (in my model, the *whole*
> > thing) to THE single official venue - most likely ZooBank - that acts
> > as a registration portal for all new nomenclatural acts. The instant
> > it is submitted there, an automated message goes out to every
> > taxonomist who is a registered user of that venue AND who has
> > self-selected any of the following key words: Bombus, Apidae,
> > Hymenoptera, Insecta, Mexico, "new species" (among others). Instead of
> > just 3 anonymous referees, the manuscript is thereby opened to review
> > online by *hundreds* of people, including the majority of the world's
> > experts on bumblebees. If a person like Z is among the reviewers, they
> > CANNOT do anything to usurp the taxon as their own, because now there
> > is ONLY ONE VENUE. They would have to submit their manuscript for
> > registration to the *same* place, and have it seen by the *same*
> > reviewers, as author X - and *including* author X! It would be
> > immediately obvious that the two works referred to the same taxon, and
> > since author X had submitted first, their registration could still be
> > approved, but Z's would definitely be rejected. The BEST scenario that
> > Z could hope for here is that X would agree to add them as a
> > co-author. In fact, that could turn what might otherwise have been a
> > bitter rivalry into a cooperative, win-win venture. Especially if
> > author Z had specimens from different localities, or male specimens to
> > help better characterize the new species. For that matter, ANY of the
> > hundreds of reviewers might have additional specimens or data that
> > they could contribute (with or without co-authorship), and the
> > resulting species description could be *vastly* improved over the one
> > produced under the traditional publishing model. Open review makes a
> > level of collaboration possible that is NOT part of the present
> > competitive publishing model. So, we'd see not only a BETTER end
> > product, but one that is immune to being usurped, and - once
> > registered - can be submitted for publication wherever the author
> > wishes, and it won't make a difference how long it actually takes to
> > get into print, because the date of registration (and availability) of
> > the name is *already
> > established* and NOT dependent on the date of printing.
> >
> > That last clause is EXTREMELY significant in regards to the present
> > debate over dating, pre-prints, digital versus paper, and such: if the
> > date a name becomes *available* is the date it is *registered*, then
> > it makes no difference at all when the formal publication takes place,
> > or where, or whether is is e-only, or hard copy only, or privately
> > printed, or printed on demand, etc.
> >
> > I have been arguing for some 20 years now that adopting this approach
> > would be to everyone's collective benefit, for many, many reasons. No
> > longer having to worry about the date of publication (or digital
> > versus paper), is just one of those many reasons.
> >
> > --
> >
> > P.S.: I can imagine several of you immediately leaping forward with
> > questions like "But what if author X takes the manuscript after it is
> > registered, and changes it before it is published?" "What if they
> > never formally publish it?" - and while those are fair questions,
> > superficially, I also think you'll see a few things: first, by virtue
> > of the open review process, there is virtually no reason that there
> > WOULD be any changes between registration and publication. After all,
> > most (if not all!) of the potential referees for the print version
> > will have *already* reviewed the work. No errors should slip through
> > that would require fixing; e.g., if someone's proposed new names are
> > synonyms, or homonyms, or there is some other error regarding
> > Code-compliance (failure to state type depository, etc.), that would
> > *all* *get worked out* before the work could be approved for
> > registration. Second, if changes *are* made, there are several options
> > that could render this a non-problem. Which option people prefer could
> > be a separate topic for discussion, but off the top of my head, (1)
> > declare that only the official registered version of the work has
> > *nomenclatural* standing. I'm not talking about minor changes in the
> > final published version, which would be irrelevant, but something like
> > altering the composition of the type series, changing the spelling of
> > a name, etc. Note that this would, in effect, make the archived
> > registered work the functional equivalent of a digital publication. As
> > such, even if it never got "published" anywhere else, the names and
> > acts in it would still be available, *and* possible to cite. This is
> > one of the main reasons that I advocate that the *entire works* be
> > registered, rather than just a minimalist template. (2) If the author
> > insists that a revised published version *needs* to replace the
> > previously-registered version (e.g., they found a better specimen to
> > be selected as holotype), then - thanks to the entire process being
> > archived - everyone who was involved in the original registration
> > approval could be sent a follow-up e-mail asking whether or not they
> > approve of the revised version; if so, then the revised version
> > replaces the original. This could only be done ONCE, in conjunction
> > with the first post-registration publication. (3) Some publishers might
> be convinced to accept the registered version *as is* and just print it
> without any further review or editorial process.
> >
> > This all could work, and work well.
> >
> > Sincerely,
> >
> > --
> > Doug Yanega      Dept. of Entomology       Entomology Research Museum
> > Univ. of California, Riverside, CA 92521-0314     skype: dyanega
> > phone: (951) 827-4315 (disclaimer: opinions are mine, not UCR's)
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Scott Thomson
Museu de Zoologia da Universidade de São Paulo
Divisão de Vertebrados (Herpetologia)
Avenida Nazaré, 481, Ipiranga
04263-000, São Paulo, SP, Brasil
ORCID: http://orcid.org/0000-0003-1279-2722
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