Tuesday, September 17, 2013

Really? Nature put the #HeLa genome paper behind a paywall? Time for Nature Publishing Group to return ALL money obtained from genome papers

This is just fucking ridiculous.  As I have written about many many times - Nature Publishing Group many years ago promised to make papers reporting genome sequence data freely available.  They do not generally live up to this promise well.  See for example
Today I discovered that not only are some important genome papers not freely available but one for the ages - the paper on the HeLa genome - reported with much fanfare recently as a triumph of an agreement with the family of Henrietta Lacks - is only available if you pay.



Once again I call on Nature Publishing Group to publicly disclose all financial gains that have come from people paying for the these genome papers and for the money to be returned.

13 comments:

  1. The Nature policy applies only to papers that report an organism's genome for the first time. Doesn't apply to this paper.

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    1. You tell the Lacks family the cells are a new species....

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    2. Yes, I was not serious about the new species thing. But Nature says "In December 2007, NPG introduced the Creative Commons attribution-non commercial-share alike unported licence for those articles in Nature journals that are publishing the primary sequence of an organism's genome for the first time." I would define organism as any separate living entity. I am an organism. You are an organism. Henrietta Lacks was an organism. Therefore I think the policy applies to the HeLa genome.

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    3. Michael's interpretation of our policy is correct - it applies to "those articles in Nature journals that are publishing the primary sequence of an organism's genome for the first time". So this article does not fall under that policy.

      Clearly there is still some confusion about this policy, so we'll work on an unambiguous explanation. In the meantime, please may I reiterate that no APCs are paid for these articles and authors of *all* research articles are encouraged to self-archive, including in PMC, the accepted manuscript 6 months after publication. Anyone who wishes to read the policy for themselves can do so here: http://www.nature.com/authors/policies/license.html

      Grace Baynes, Nature Publishing Group

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    4. Grace - the general interpretation of the word organism seems pretty clear to me. It is any separate living entity. If Nature wants this policy to apply to "the first genome for any species" then it should say that and that would certainly be much clearer. But as it is now, it is pretty clear - it says it applies to each organism and organism does not have any taxonomic specificity to the term.

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    5. From the MacMillan Dictionary organism is " a living thing such as a person, animal, or plant, especially an extremely small living thing"

      From the Cambridge Dictionary Online: "a single living plant, animal, virus, etc.:"

      Or from an article in pubmed about expanding the definition "Most biologists implicitly define an individual organism as "one genome in one body."

      I think it is pretty clear - organism = one individual. So now Grace you are saying "we meant something else". Well, my goodness, please figure out out Nature means and describe it somewhere accurately.

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  2. NPG and Nature have very clear guidelines on what this policy applies to, and have had from the outset. I agree it could be more clearly explained for our authors and readers, and we will do so as we don't wish for this confusion to continue.

    I could point you to other definitions of 'organism' that refer to genus + species, which is what the policy refers to, as Michael correctly interprets above. But I'm not a biologist, and I wouldn't be impertinent enough to argue with you and your colleagues on this point. So I will work with my editorial colleagues to clarify our policy definitively so that we can avoid future confusion about whether articles are subject to it.

    And just to be totally clear, what we mean by the 'primary sequence of an organism' is the genome of the species, not sub-species. We'll make sure that is spelled out in the clarification of the policy, too.

    Thanks as ever for keeping us honest, even if it is sometimes frustrating to be so often chastised for a policy that was established to do "the right thing".

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    1. Thanks Grace for the response. I note - I started on this because I myself told lots of people about the open policy for genome papers and then was embarrassed when people would say "well, why isn't this paper of yours open" or "what about this paper". So - I tried to promote the policy and to give Nature credit for (in this case) doing a good thing in terms of openness. So I then pointed people to the "clarified" wording and it is pretty clear to me in the biological literature of my field at least that "organism" refers to individuals. I personally thought this wording was meant to exclude metagenomic data which does not necessary get mapped to a specific organism ... and thus I thought any new genome sequence of some organism one could identify (e.g., a person, a cell line) would be OK.

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    2. Jonathan, thanks for continuing to discuss this with me. I'll make sure all of this is noted and fed back.

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  3. Regardless of the definition of an "organism", paywalling the HELA genome seems against spirit of the Nature editorial on the release of (human) genome data http://www.nature.com/nature/journal/v450/n7171/full/450762b.html .

    Graham Coop

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  4. Maybe it's time scientists step up and boycott submitting to these journals riddled with paywalls. Get published in open access journals. Journals like Nature can either jump on board or they can become extinct. I understand there is a lot of stigma to submitting to open access because they tend to be less selective and therefore have a lower impact factor. But whose fault is that? If we want to break the cycle, we actually have to participate. And we need to realize it's not a something that will be corrected over night.

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    1. I am with you... that is basically the notion behind the origins of the Public LIbrary of Science ...

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