About a year ago I posted to twitter (using the hashtag #opengate) and my blog about how Nature Publishing Group was not following through on their promises. See for example
- Calling for Nature Publishing Group to return all money charged for articles that were supposed to be free #OpenAccess
- Today is a day to be annoyed with Nature (Publishing Group that is) #NatureFail
- The Tree of Life: Nature's publishing machine really wants you to pay for stuff even if it is supposed to be free.
- The Tree of Life: Please help keep the pressure on Nature ...
and more including some from others
- On science blogs this week: Evolution | ScienceWriters (www.nasw.org)
- The price for Nature Open Access: $32 | Mario's Entangled Bank
Amazingly, and pleasantly, I note, in my complaining I exacted some responses from people from Nature Publishing Group who swore that these were just oversights and they would fix them. Well, alas, the money collecting machine of Nature Publishing Group is back.
For example, currently the following papers are not freely available even though at one point they were or they clearly fit in the "Shared genomes" definition Nature Publishing Group so happily promotes:
- Shewanella oneidensis in Nature Biotech.
- Desulfovibrio vulgaris in Nature Biotech.
- Metagenomic contigs in Nature
- Microbial sequencing review in Nature (this used to be freely available ...).
These above are all papers of mine, so I noticed them first (I noticed this when trying to create a Pintarest Baord for all my papers and not being able to get to a free page for these papers meant I couldn't add them to the Board. Could it be that Nature Publishing Group is just trying to get my goat? Let's see. A brief search found these papers by others - all also not freely available even though all clearly fit Nature's own definition of genome sequencing papers:
Here are some others
- Whole-genome sequencing of multiple Arabidopsis thaliana populations
- The complete sequence of the smallest known nuclear genome from the microsporidian Encephalitozoon intestinal
- Genome sequence of the recombinant protein production host Pichia pastors
- Origins of the Moken Sea Gypsies inferred from mitochondrial hypervariable region and whole genome sequences
- Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum
- Complete genome sequence of the myxobacterium Sorangium cellulose
- Comparative analysis of the complete genome sequence of the plant growth–promoting bacterium Bacillus amyloliquefaciens FZB42
- Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72
- Complete genome sequence of the fish pathogen Flavobacterium psychrophilum
- Complete genome sequence of the erythromycin-producing bacterium Saccharopolyspora erythraea NRRL23338
- Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis
- Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88
- Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale
- Genome sequence of the bioplastic-producing “Knallgas” bacterium Ralstonia eutropha H16
- Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis
- Complete genome sequence of the entomopathogenic and metabolically versatile soil bacterium Pseudomonas entomophila
- The complete genome sequence of the meat-borne lactic acid bacterium Lactobacillus sake 23K
- Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution
- Genome sequence of the chlorinated compound–respiring bacterium Dehalococcoides species strain CBDB1
- Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5
- corrigendum: Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution (awesome how the correction is not freely available)
- Complete genome sequence of the acetic acid bacterium Gluconobacter oxydans
- The complete genome sequence of Francisella tularensis, the causative agent of tularemia
- The genome sequence of the ethanologenic bacterium Zymomonas mobiles ZM4
- Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermopiles
- Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78
- Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas plasters
- The genome sequence of the entomopathogenic bacterium Photorhabdus luminescent
- Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica
- Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis
- Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia
- correction: Initial sequencing and analysis of the human genome
- erratum: Initial sequencing and analysis of the human genome
- Erratum: Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
- Corrections: The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus
UPDATE: see some more recent blog posts of mine about this topic:
- A Solution to Nature Publishing Group's Inability to Keep Free Papers Free: Deposit them in Pubmed Central
- Nature's access absurdity: Human Genome Paper free but access to corrections will costs $64
- Corrections Scamming at Nature: Tantalizing clues, to see errors just pay more money #Seriously?
UPDATE 3-28-12 1 PM PST:
Well, if you look at the comments, Nature is apparently trying to fix this and most of the articles I listed above are now freely available (the corrections are still not free but they claim to be working on it). But a simple search of Nature finds there are still some papers that are closed off that shouldn't be:
- New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing : Nature Communications : Nature Publishing Group
- Genome sequencing reveals agronomically important loci in rice using MutMap
- Predicting phenotypic variation in yeast from individual genome sequence
- Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity
It's not that hard to find these. It baffles me a bit how people at Nature don't seem to be able to find them. But maybe I am just really good at searching ...
On behalf of Nature Publishing Group, we’re sorry that you’ve had to raise this issue again. We’re looking into this as a priority and will post an update here as soon as possible.ReplyDelete
Nature Publishing Group
Thanks Patrick. I hope that there will also be a person assigned to check on this every so often in the future - so I don't have to ---ReplyDelete
If NPG were interested in hiring someone to be its Open Access ombudsman (steward? community liaison?), I'm sure Johnathan would be happy to help you find some pretty fantastic candidates.
It doesn't even need a person to check. It's trivial to write an automated script that checks this sort of thing.ReplyDelete
Jonathan, thanks again for flagging this. All of these articles should now be restored to being free to access (under a Creative Commons license). We're also checking that this hasn't happened to other papers and remedying.ReplyDelete
This was a technical error. I appreciate your frustration.
We're looking into the corrections issue, too. I'll post a comment on your post to explain.
Nature Publishing Group
Thanks Grace. Seems that this technical issue comes up over and over again. What are the odds NPG would do as I suggested and deposit genome papers in Pubmed Central?Delete
Oh and Grace - did someone go through and check other publications in addition to the ones I listed?Delete
We did a lot of that when you raised this with us before. We should have identified most of them, but if we have missed any, if you want to let me know we'll happily ensure the Creative Commons license is applied. Hopefully it should only be a few articles that were published before the policy was applied, but the policy is retrospective and we will apply the CC license to genome sequence papers published before 2007.Delete
Sorry, comments in line don't make clear that I was replying to your question about whether we'd checked.Delete
To your question about PubMed Central, please let me come back to you on that.
I should also clarify that our genome policy applies to Nature and the Nature research journals. It is available here: http://www.nature.com/authors/policies/license.htmlReplyDelete
We also publish journals, including the Journal of Human Genetics, on behalf of societies and organizations. It is at the society's discretion if they implement this policy on their own journals.
Nature Publishing Group
Thanks --- does this mean if a society wanted to do this that NPG would agree to it?Delete