Hey Nature Publishing Group - When are you going to live up to your promises about "free" genome papers? #opengate #aaaaaarrgh

This is just ridiculous.  Nature Publishing Group in 2007 announced that they were making all papers in their journals that reported genome sequences would be made freely available and would be given a Creative Commons license: Shared genomes : Article : Nature.

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

I think the funniest (and scariest) part may be the corrections and errata that are not freely available. And these are just the articles I found in a 15 minute search. I am sure there are more.  Yes, Nature Publishing Group has made many genome papers freely available.  That is great.  Much better than many other publishers.  But the cracks in your system are large and suggest that nobody there is actually dedicated to seeing through on the promises.  Promises are meaningless.  Follow through is the key.  Come on Nature Publishing Group - how about assigning a "Free access ombudsman" or something like that who will make sure that free means free.  I am sick of writing these posts.  You should do your own QC ...

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 ...