Taxacom: Dates of e-pubs ahead of print?

Tue Sep 6 13:45:44 CDT 2022

> In retrospect, it possibly should have been made impossible to register a 

> journal on ZooBank without specification of an archive, given that doing so serves no useful purpose.

Although I more or less agree with you that the requirement to indicate an intended archive serves little purpose, if indicating an online archive was a requirement for all journals in ZooBank, then how could we facilitate the (optional) registration of paper-printed journals (for which no online archive requirement applies)?  In the same way that we strongly encourage the registration of new names in ZooBank even though this is not required, we also strongly encourage the registration of paper-published works (including historical ones, going back to Linnaeus) even though this is not required.

Indeed, one of the earlier prototypes of ZooBank had a registration workflow that began with the first question: “Will this work be published electronically, or on paper?”  If the “electronic” option was selected, registration could not be completed without the required ISSN/ISBN and intended online archive.  After some initial testing, this workflow was abandoned because most registrations were contributed by authors, rather than journal editors or staff, and most authors had no idea whether a journal they planned to publish in used an archive or not (or which one).  This meant that authors who selected “electronic” either selected ALL of the online archives (not understanding what the purpose of the field was in ZooBank), or switched to registering it as a paper publication (often having no idea whether there was a paper edition or not).  After a fair bit of thought and discussion, the workflow was changed to avoid requiring authors to know whether an archive was used (and which one), and instead a warning is given for all prospective registrations that lacked an archive, letting the author know that the work and the names/acts contained within can only be made available under the Code if an archive is indicated, or from a paper edition of the work.  The hope was that the warning would prompt the author to contact the journal editor and sort it out.  I’m not sure whether that hope was achieved (I’d guess probably not).

This approach is not perfect, but it is the “least-bad” option.  As I’ve mentioned already, there are many ideas for how to improve things for the new paradigm under Code-5, which we hope to capture in the draft that will be released for public commentary.

Aloha,

Rich

Richard L. Pyle, PhD
Senior Curator of Ichthyology | Director of XCoRE

Bernice Pauahi Bishop Museum

1525 Bernice Street, Honolulu, HI 96817-2704

Office: (808) 848-4115;  Fax: (808) 847-8252

eMail: deepreef at bishopmuseum.org

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From: Stephen Thorpe <stephen_thorpe at yahoo.co.nz> 
Sent: Monday, September 5, 2022 11:59 PM
To: 'lynn' <lynn at afriherp.org>; Richard Pyle <deepreef at bishopmuseum.org>
Cc: taxacom at lists.ku.edu
Subject: Re: Taxacom: Dates of e-pubs ahead of print?

PS: I see that it was in fact me who created the ZooBank record for 'New Zealand Entomologist', but back in 2011, shortly before the electronic amendment of the Code. That record appears to have been consistently used since then, but nobody officially involved with the journal ever did anything about the lack of a specified archive (I was not obliged to specify an archive and at the time archives may not have even been implemented yet?) At any rate, those involved in production and editing for this journal seem to leave ZooBank registration purely in the hands of individual authors, some of whom have preregistered articles, but with no specified archive. The danger for examples like this one is that journals might switch to being e-only (i.e. no hard copy) and it could be many articles down the track before someone thinks about checking for a specified archive on ZooBank!

In retrospect, it possibly should have been made impossible to register a journal on ZooBank without specification of an archive, given that doing so serves no useful purpose.

Stephen

On Tuesday, 6 September 2022 at 09:30:19 pm NZST, Stephen Thorpe via Taxacom <taxacom at lists.ku.edu <mailto:taxacom at lists.ku.edu> > wrote: 

What is a bit strange is that you have stated that it would be a threat to nomenclatural stability to disallow journal duplicates without archives, yet there is a much greater threat to stability from the very requirement to specify an archive. For example, the journal 'New Zealand entomologist' has no specified archive, so all 81 registrations of articles therein served no useful purpose. They will still be validly published as hard copy (I assume that they are still printing hard copies, though, as with Zootaxa, it is hard to know for certain). https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fzoobank.org%2FReferences%2FF5B1E166-0CC1-49E7-8E3A-3B7A24A875F5&data=05%7C01%7Ctaxacom%40lists.ku.edu%7Cb38f97f0d62e42b5ace308da903806a7%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637980867691588478%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=OwGwd393SSC9aVPEBdhKJMDvLr1L8012Z1tQ0TuPhko%3D&reserved=0 <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fzoobank.org%2FReferences%2FF5B1E166-0CC1-49E7-8E3A-3B7A24A875F5&data=05%7C01%7Ctaxacom%40lists.ku.edu%7Cb38f97f0d62e42b5ace308da903806a7%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637980867691588478%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=OwGwd393SSC9aVPEBdhKJMDvLr1L8012Z1tQ0TuPhko%3D&reserved=0> &data=05%7C01%7Ctaxacom%40lists.ku.edu%7C2a32962d6ec14394848108da8fea62e8%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637980534095414216%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=88glBbjhXw2PKsYZF5IQYIsy9XRYex8IcOeRvy664Jk%3D&reserved=0
I assume this journal isn't the only one without a specified archive. I wonder how many others?Stephen
    On Tuesday, 6 September 2022 at 09:20:49 pm NZST, Richard Pyle <deepreef at bishopmuseum.org <mailto:deepreef at bishopmuseum.org> > wrote:  

Yes, Code-compliant nomenclature is indeed complicated.  That’s why there are 90 Articles of very legal-sounding-ish text in the Code.

Indeed, one of the top priorities for Code-5 is to simplify things as much as possible.  It’s always going to be complicated accommodating historical names & works, but I think the rules for new names/works can be greatly streamlined. Lucky(?) for us, only about 10% (+/-) of animal species have been named, so the remaining ~90% won’t need to be dealt with following the complicated rules for historical names.

Aloha,

Rich

Richard L. Pyle, PhD
Senior Curator of Ichthyology | Director of XCoRE

Bernice Pauahi Bishop Museum

1525 Bernice Street, Honolulu, HI 96817-2704

Office: (808) 848-4115;  Fax: (808) 847-8252

eMail: deepreef at bishopmuseum.org <mailto:deepreef at bishopmuseum.org> 

BishopMuseum.org

Our Mission: Bishop Museum inspires our community and visitors through the exploration and celebration of the extraordinary history, culture, and environment of Hawaiʻi and the Pacific.

From: Stephen Thorpe <stephen_thorpe at yahoo.co.nz <mailto:stephen_thorpe at yahoo.co.nz> > 
Sent: Monday, September 5, 2022 11:15 PM
To: 'lynn' <lynn at afriherp.org <mailto:lynn at afriherp.org> >; Richard Pyle <deepreef at bishopmuseum.org <mailto:deepreef at bishopmuseum.org> >
Cc: taxacom at lists.ku.edu <mailto:taxacom at lists.ku.edu> ; 'Paul van Rijckevorsel' <dipteryx at freeler.nl <mailto:dipteryx at freeler.nl> >
Subject: Re: Taxacom: Dates of e-pubs ahead of print?

Which kind of proves my point about the matter being "complicated"! The level of complexity of Rich's replies is going up on a steep tangent!

On Tuesday, 6 September 2022 at 08:48:28 pm NZST, Richard Pyle <deepreef at bishopmuseum.org <mailto:deepreef at bishopmuseum.org> > wrote: 

Hi Lynn,

I think we are in agreement. I'm just not sure I know what you mean by:

> Not doing so would appear to invalidate nomenclatural acts in earlier issues of

> the journal or am I wrong in this opinion?

Just to walk through the scenarios here:

1. On 1 April 2022 I register a new article ("A") in ZooBank, and create a new Journal ("Jx") for it, but without indicating an online archive for either the article or the new journal. This article fulfills all other requirements of the Code on 2 April 2022, except that it's only issued in electronic form, and is thus not published in the sense of the Code (because there's no online archive indicated).

2. After being admonished by my colleagues for failing to comply with the Code, I log in to ZooBank on 15 April 2022 and indicate Zenodo as the online archive for the article ("A").  

3. On 1 May 2022 I register another Article ("B"), within my existing Journal "Jx", and it fulfills all other requirements of the Code on 2 May 2022.  However, it's not available as a published work, because (again) there is no indicated online archive in ZooBank (recall that the archive for Article "A" was directly linked to the article, not to the parent journal).

4. I am again admonished by my colleagues, so I contact the Editor of the journal "Jx" and ask what online archive they routinely use.  I get a reply the same day that "Jx" has been using Biotaxa for the past 5 years.  I update the ZooBank record for the journal "Jx" on 15 May 2022, to indicate that all articles published in this journal inherit Biotaxa as the online archive.

5. On 1 June 2022, another colleague of mine (we'll call him "Stephen") registers another Article ("C") that he submits to the journal "Jx".  However, there is a glitch in the ZooBank software such that existing journals with titles shorter than 3 characters in length do not show up in the Journal drop-down list.  Thus, "Stephen" is understandably unaware that "Jx" is already in ZooBank, so he creates a duplicate copy of the Journal.  He doesn't assign it an online archive, because he believes that the journal will be published on paper.  This article ("C") is published electronically, and fulfills all other requirements of the Code, on 15 June 2022, except that it's only issued in electronic form, and is thus not published in the sense of the Code (because there's no online archive indicated).

6. Those mean old colleagues now direct their ire at "Stephen" for having created yet another unpublished work.  But "Stephen" has been using ZooBank extensively for years, and knows all the tricks to work around the bugs and glitches, and after taking a closer look he discovers there are indeed two copies of the journal "Jx" in ZooBank, and that the one he created was a duplicate.  He contacts the ZooBank Administrator about the problem, who then eventually corrects the inadvertent error by merging the two duplicate journals on 1 July 2022 (the Zoobank Admin was travelling to attend a wedding that week, so was slow in responding to Stephen's request).

In my interpretation:

- Article "A" was published in the sense of the Code on 15 April 2022 (when all Code-required criteria for electronic publication were fulfilled).

- Article "B" was published in the sense of the Code on 15 May 2022 (when all Code-required criteria for electronic publication were fulfilled; in this case, when an online archive was indicated for the parent journal).

- Article "C" was published in the sense of the Code on 15 June 2022 (following the logic explained in my previous email to a different "Stephen", whereby the duplicate journal "Jx" is considered an inadvertent error, and would have been selected as the correct parent journal had there not been a glitch in the ZooBank website software code).

Addressing your point, even though the Journal "Jx" has been using Biotaxa as an online archive for 5 years, it cannot have published any electronic works earlier than 15 May 2022, unless the individual Articles were registered and assigned directly to an online archive prior to that date.

Continuing the example, suppose that during one of his routine sweeps for duplicate journals, the ZooBank Admin discovers that the Journal "Jy" was registered five years earlier, on 15 November 2017.  Because it was accidentally misspelled, nobody realized that it was the same as the journal "Jx".  When "Jy" was registered in 2017, it was assigned to Biotaxa as the online archive.  In this scenario, my Article "A" would have been published in the sense of the Code on 2 April 2022, and my Article "B" wuld have been published in the sense of the Code on 2 May 2022.  It's just that nobody knew that to be true until the inadvertent duplication of Jy/Jx journal was discovered.

Again, in an ideal world there would be no gap between "truth" and what is visible from the work and/or ZooBank record.  But in this ideal world, I wouldn't have spent my entire 3-day weekend doing ZooBank stuff, etiher... 

:-)

Aloha,

Rich

Richard L. Pyle, PhD

Senior Curator of Ichthyology | Director of XCoRE

Bernice Pauahi Bishop Museum

1525 Bernice Street, Honolulu, HI 96817-2704

Office: (808) 848-4115;  Fax: (808) 847-8252

eMail: deepreef at bishopmuseum.org <mailto:deepreef at bishopmuseum.org> 

BishopMuseum.org

Our Mission: Bishop Museum inspires our community and visitors through the exploration and celebration of the extraordinary history, culture, and environment of Hawaiʻi and the Pacific.

> -----Original Message-----

> From: lynn <lynn at afriherp.org <mailto:lynn at afriherp.org> >

> Sent: Sunday, September 4, 2022 10:17 PM

> To: Stephen Thorpe <stephen_thorpe at yahoo.co.nz <mailto:stephen_thorpe at yahoo.co.nz> >

> Cc: taxacom at lists.ku.edu <mailto:taxacom at lists.ku.edu> ; Paul van Rijckevorsel <dipteryx at freeler.nl <mailto:dipteryx at freeler.nl> >; Richard

> Pyle <Deepreef at bishopmuseum.org <mailto:Deepreef at bishopmuseum.org> >

> Subject: Re: Taxacom: Dates of e-pubs ahead of print?

> 

> Stephen,

> I think you are confusing the article record with the journal record. Rich is quite

> correct in using the earliest compliant registration record of the journal.

> Not doing so would appear to invalidate nomenclatural acts in earlier issues of

> the journal or am I wrong in this opinion?

> I  am sure that it would help Rich if anyone noticing duplicate journal

> registrations would let him know about them.

>  Lynn Raw

> 

> > On 5 Sep 2022, at 04:18, Stephen Thorpe via Taxacom

> <taxacom at lists.ku.edu <mailto:taxacom at lists.ku.edu> > wrote:

> >

> >  Rich,So, is it to be in some sense "understood" that duplicate

> > journal records all defer to the first archive associated with any of

> > them, even before you get around to actually merging them? It could

> > take years, in theory, for you to notice and merge a duplicate. Anyone

> > trying to verify the date of availability before you merge will find

> > no archive associated with the journal record actually used, which has

> > not yet been merged. It will only retrospectively become available (if

> > published online first) when the merge is actually done. I can imagine

> > some hypothetical taxonomists trying to claim priority because the

> > earlier name by some rival is not associated with a specified archive,

> > even though it would gain retrospective priority after the merge. In

> > my opinion, the archive date should be the date of the merge, not the

> > date associated with the earliest duplicate with a specified archive,

> > so there is some room for argument about your "most appropriate

> > means".Cheers, Stephen

> >>    On Monday, 5 September 2022 at 10:49:54 am NZST, Richard Pyle

> <deepreef at bishopmuseum.org <mailto:deepreef at bishopmuseum.org> > wrote:

> >>

> >> One complication here is that many people preregistering publications

> >> on ZooBank create a new record for the journal, even though one may

> >> already exist with a specified archive. If they don't specify an

> >> archive for the new duplicate journal record, then we have a

> >> situation where there is no specified archive for the journal record

> >> associated with the publication, but Rich Pyle can at any stage merge

> >> the duplicate record with the original journal record with a

> >> specified archive. I forget what the  consquences are of this, in

> >> terms of the date of specified archived, but it all gets a bit too complicated!

> >

> > Stephen is correct that people sometimes create a duplicate copy of a Journal

> that lacks a reference to an online archive.  When such errors are discovered,

> they are corrected by the most appropriate means.  The way it works is that

> when duplicate journal records are merged, the earliest date on which one of

> the journals was linked to an archive is taken as the date on which the indication

> was made in ZooBank. The same applies to ISSN/ISBN assignment.

> >

> > Not really all that complicated, actually.

> >

> > Aloha,

> > Rich

> >

> > Richard L. Pyle, PhD

> > Senior Curator of Ichthyology | Director of XCoRE Bernice Pauahi

> > Bishop Museum

> > 1525 Bernice Street, Honolulu, HI 96817-2704

> > Office: (808) 848-4115;  Fax: (808) 847-8252

> > eMail: deepreef at bishopmuseum.org <mailto:deepreef at bishopmuseum.org> 

> > BishopMuseum.org

> > Our Mission: Bishop Museum inspires our community and visitors through the

> exploration and celebration of the extraordinary history, culture, and

> environment of Hawaiʻi and the Pacific.

> >

> >

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