What’s more important: the publication or the product?

The Nature stable of journals. A byword for quality, integrity, impact. Witness this recent offering from Nature Biotechnology:

Bale, S. et al. (2011)
MutaDATABASE: a centralized and standardized DNA variation database.
Nature Biotechnology 29, 117–118
doi:10.1038/nbt.1772

Unfortunately, although it describes an open, public database, the article itself costs $32 to read without subscription (update: it’s freely available as of one day after this post). Not to be deterred, I went to investigate MutaDATABASE itself.

The alarm bells began to ring right there on the index page (see screenshot, right).
Could that be right? I tried several browsers, in case of a rendering problem. Same result – no contents.
mutashit

There seems to be something missing

Clicking on some of the links in the sidebar, I became more concerned. Here’s an example URL:

http://www.mutadatabase.org/index.php?option=com_content&view=article&id=14&Itemid=17

I recognise that form of URL – it comes from Joomla, a content management system. I’ve had servers compromised only twice in my career – both times, due to Joomla-based websites. Their security may have improved since, I guess – but this smacks of people looking to build a website quickly without investigating the alternatives.

mutashit4

It will be great. Promise.

Then, there are the spelling/grammatical errors, the “coming soons”, the “under constructions”, the news page not updated in almost 5 months. And as Tim Yates pointed out to me:
mutashit5

???

@neilfws The mutaDATABASE logo leads me to believe you are right about it being a joke.. is that someone dropping their sequences in a bin?

Who knows, MutaDatabase may turn out to be terrific. Right now though, it’s rather hard to tell. The database and web server issues of Nucleic Acids Research require that the tools described be functional for review and publication. Apparently, Nature Biotechnology does not.

21 thoughts on “What’s more important: the publication or the product?

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    1. Lars Juhl Jensen

      I think you may well guess wrong. Nature Biotech never publish papers on databases or computational tools as research papers – it is always in the form of a Correspondence, and my experience is that they are peer reviewed. One has to wonder if there was content when it was reviewed, or if the reviewers only looked at the manuscript and completely forgot to check the actual product.

      1. nsaunders Post author

        It seems an odd section of a journal for describing a database. If it isn’t peer reviewed, it should be – even if only by the editors. Or do they simply not care whether a tool/resource works and is useful?

        Incidentally, the article has become freely-available overnight; I don’t know whether this is permanent.

  2. Deepak Singh

    What frustrates me about this is that there is no value given to the work, or to the people doing the work, or at least that seems to be the case.

    1. Cameron Neylon

      Only just had a chance to have a closer look at this. It looks as though it is isn’t possible to actually determine whether this is peer reviewed or not?!? This hadn’t really occurred to me as an issue before but its not even so much here the question of exactly what the editorial policy is on review (and whether it was followed) as whether you can even tell what kind of QA process this has even been through (and then decide on that basis whether you believe in it or not).

  3. rpg

    What Cameron said.

    Either way, it all reflects very badly on Nature Biotech. (Plus the authors. I’m like “What were they THINKING?”)

  4. Duncan

    I contacted the corresponding author, Patrick Willems, and pointed him to this post. Here’s his reply so far:

    1. evidently we cannot dictate the press what to do, or what to charge
    2. The project is just starting : genes will be uploaded from next week on; database is being updated

    we are just at the start, thanks for your interest

    I think the “press” here refers to Neil, but the problem seems to be, should incomplete databases be allowed in a publication as “Correspondence”?

    1. nsaunders Post author

      My issue is not really with the database as such, although I don’t think it’s good to “go live” when your site is not ready. It’s as Duncan says: should publication be allowed when a resource is not functional? As I mentioned in the post, if that site were submitted to the NAR database issue in its current state, it would be rejected.

  5. Pingback: Blind.Scientist » Blog Archive » What’s more important: the publication or the product? The publication.

  6. aviwener

    Hi Neil,

    When you visited the European Biotechnologist Blog you expressed some of the same concerns that you’ve expressed in your post above. While I cannot comment on the use of joomla I did do some poking around and as far as the database is concerned, you need to click on the “launch plaform” button located at the bottom of the menu bar and it will take you to the database. Once you are in the database you can search for any gene that you are interested in (as long as it has been catalogued and you have the correct coordinates). For example, you can search by symbol which will require you to have the officially accepted HGNC Search or OMIM. The HGNC symbol can be found on the HGNC page.
    I tested this by looking up nitric oxide synthase 1 which has an HGNC symbol of NOS1. When entere into the database it retrieved a myriad of results.
    I believe that the database is still in its infancy, but it should prove useful through trial and error and through input and comments of diligent users.
    (for the record I have no connection to the authors of the paper or the mutaDATABASE project)

    1. nsaunders Post author

      Incredible. You have found the missing data! I’d suggest they move that key button to the top of the page, instead of hidden down the bottom.

      The “launch platform” button has been added since I wrote the original post, along with several other changes to the website design. But as I commented earlier my issue is not with the database, but with the premature publication.

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