Field of Science

O Zoobank, Where Art Thou?

Does anyone reading this have experience with registering publications, etc. on ZooBank? Can you clarify how the process works?

In the comments for yesterday's post, two readers brought up a potential issue with ZooBank's records. A number of taxa published recently in PLoS One that were supposed to have been registered with ZooBank, such as Mochlodon vorosi, are not coming up in searches there. However, the original publications for these taxa cite LSIDs, the unique identifier assigned to any ZooBank registration, for them. If these taxa were never registered with ZooBank, how could there have been an LSID to cite? I ran a search of my own for two taxa recently published in a different journal, ZooKeys: Calliostoma tupinamba and Angelopteromyia korneyevi. Same result: cited LSIDs, but no results in a ZooBank search.

So what's happening here? If a paper is registered prior to being published (as must have been the case here, for the LSID to be cited in the published papers), does the registrant have to confirm publication later for that record to be visible to the public? Could these records have simply not yet been made public? Or is there a bigger problem here?

8 comments:

  1. I've had no issue with ZooBank.

    But, when adding new nomenclatural acts you have the option of stating whether the paper/book is published or 'in press'. (Currently ZooBank is only allowing registration of new names: species, genera, family group.)

    If the nomenclatural act is 'in press' it cannot be viewed by anyone else but yourself (when logged in). I've just checked this with 'in press' taxa I've previously added to ZooBank.

    My guess is the author(s) who registered the names you mention above have forgotten to switch the nomenclatural act to being published.

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  2. Mark,

    That make sense, but it is weird that none of the paleontology-related taxa published in PLoS One can be found on ZooBank. Would be weird that all paleontologists make this mistake!

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  3. Thank you Mark, that does make sense. I can see problems potentially arising from this in future, though, when someone assumes that something they can't find the record for on ZooBank has not been validly published.

    Would be weird that all paleontologists make this mistake!

    My guess is that it's not the authors that have been registering the taxa, but someone working for PLoS One who's consistently forgotten (or been unaware that they needed to).

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  4. Hi Chris,

    I just discovered your blog here -- great stuff! Thank you for raising these sorts of issues.

    I am the person in charge of developing and maintainign the ZooBank Website, and I want to confirm that Mark Young is exactly right in answering your question. One of the things we have wrestled with (and continue to wrestle with) is how to efficiently manage the workflow for "prospective" registrations (i.e., registrations that happen prior to publication; as all such registrations must be for electronic works under the amended Code). We're experimenting with several models (e.g., registration done by the publisher, vs. registration by an author vs. registration by a third party). It will probably be several months (at the soonest) before we have enough real-world ZooBank usage data to understand how best to ensure that records are updated with the correct publication date after publication.

    In the case of PLoS ONE, I am the person most to blame. PLoS has been a tremendous advocate of ZooBank for years, and as such has required that all of its works containing Code-governed acts (new names) be registered in ZooBank -- since long before the new public release last month. In the past, authors publishing such acts have contacted me to do the registrations for them, which I have been more than happy to do. However, we don't yet have an effective mechanism for updating the ZooBank record with the publication date, after its published.

    As the person who created the registrations, this is really my responsibility. However, I have been so overwhelmed with getting the new ZooBank ready for public release, that I simply have not had time to follow-up on updating these registrations with the publication date.

    However, now that the dust is settling a bit after the public ZooBank launch, I have some more time to take a look at these sorts of issues. I've already updated the ones you indicated, so they should now be publicly visible. And because of of your blog post, I am now motivated to write some scripts to identify all the works I have registered that are still indicated as "In Press", and then update them accordingly. This will evolve into a feature that we have long planned where any user will get a prompting (either email, or on the ZooBank site, or both) of items that are registered but remain as "In Press", as a way to encourage and remind people to keep the records updated.

    Sorry for the long comment, but I really do appreciate these issues being discussed on an open forum, and I'm glad it's done in a way that allows me to post feedback.

    Aloha,
    Richard Pyle

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  5. Thanks very much for your response, Richard. And keep up the good work!

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  6. Stephen Thorpe10 October 2012 12:32

    Actually, Mark is not exactly correct! He stated: [quote] If the nomenclatural act is 'in press' it cannot be viewed by anyone else but yourself (when logged in) [unquote] Actually, in press records can be viewed by all ZooBank users with the status of 'editor' (like myself) ...

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  7. press records can be viewed by all ZooBank users with the status of 'editor'

    That sounds like a good idea. It means that 'in press' records could be updated when necessary, even if the original registrant is, for some reason, unable to do so themselves.

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  8. Yes, Stephen is correct, of course. We are currently reviewing a draft Policy on ZooBank user levels and authorizations. A brief overview is included on the ZooBank Help page (http://zoobank.org/Help), under the 'Editing Content' section.

    Aloha,
    Rich

    P.S. Prompted by the earlier exchange, I have gone back and updated the publication date for all the PLoS articles that have already been published, so they are now publicly visible. Now we just need a clever mechanism to make it easy to stay on top of this -- not just for PLoS, but for all prospectively registered works in ZooBank.

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