Open Data in biomedical science

Heather (Research Remix) has a most important post on data sharing – she has analysed the data deposition policies of some of the major journals/publishers. Note that this is orthogonal to Open Access – not all these publishers are OA, but many are agressive about requiring data deposition – and that’s good. My comments during and after her post:

Well done Heather. It’s hard work and often depressing. I once tried to read some publishers’ contracts on what authors and readers could do and found them incomprehensible. I thought at the time it was incompetence and out-of-date pages – now I think much of the license area contains deliberate FUD.
I’m interested in the strength of Nature:

Indexed, publicly accessible database, or, where one does not exist, to readers promptly on request. Any supporting data sets for which there is no public repository must be made available [..] any interested reader [..] from the authors directly, [..]. Such material must be hosted on an accredited independent site [..] or sent to the Nature journal at submission [..]. Such material cannot solely be hosted on an author’s personal or institutional web site.

Note that institutional web sites (does that mean repositories) are not good enough for Nature! If you read this as a non-biologist there are precious few sites where you could deposit data. Maybe at somewhere like BMC which offers reposition services. I think there is a great opportunity here for the new semantic web.
… and Science:

Large data sets must be deposited in an approved database and an accession number provided for inclusion in the published paper. Large data sets with no appropriate approved repository must be housed as supporting online material at Science, or when this is not possible, on the author’s web site, provided a copy of the data is held in escrow at Science

What Heather does not mention is what the public access to the data are. Most of the databases are biological and therefore Open.

Approved databases: Worldwide Protein Data Bank ; Research Collaboratory for Structural Bioinformatics, Macromolecular Structure Database (MSD EMBL-EBI), or Protein Data Bank Japan], BioMag Res Bank, and Electron Microscopy Data Bank (MSD-EBI), Cambridge Crystallographic Data Centre {CLOSED). GenBank or other members of the International Nucleotide Sequence Database Collaboration (EMBL or DDBJ) and SWISS-PROT. Gene Expression Omnibus ; ArrayExpress.

The Cambridge Crystallographic Data Centre (no direct connection with PMR) has 350, 000 entries and last time I enquired allows only 25 to be downloaded free (0.01 %). I shall return to this later.
Science is as good as its word – there are many articles with exposed supporting info – here’s a chemistry one and it looks of high technical quality (haven’t read the science):
http://www.sciencemag.org/cgi/content/full/316/5828/1172/DC1
It doesn’t say anything about copyright and I hope that Science can confirm that they do not assert copyright. It would be extremely useful if they suggested (or required)that authors add Science Commons license to the data. This would act as a high-profile encouragement to the others.
Nature is similar – here is
http://www.nature.com/nature/journal/v447/n7144/extref/nature05881-s1.pdf
the supplemental data here has been formatted by Nature – but no copyright has been added – and again I hope that they can take the same approach I have suggested.
Whatever your views on Open access, these two journals have made a good start on Open Data. A long way to go as the data are in the dreaded hamburger PDF (molecules are destroyed by PDFisation), although plaudits for Nature Chemical Biology which sends molecules to Pubchem. We need more semantic data here, please.
Also up in PMR’s good books are Royal Soc. Chemistry and Int. Union of Crystallography which expose all there supplemental data openly and, although muddled, effectively free of copyright.
The ACS is halfway. It does expose supplemental info, but it copyrights them (and I know from first hand intercourse that this is deliberate).
The less satisfactory publishers are harder to be precise about as they hide their information.
Wiley – Hides data for subscribers only and copyrights them aggressively. I suspect that some data are not even required.
Springer – does not seems to manage data itself and hides those that it does get. I have written to my Springer contact asking for clarification but not yet heard back
Elsevier – I suspect they require little data, ut have no hard evidence
It would be EXTREMELY useful for the blogosphere to collect information on these practices. If we all do a little we could cover the whole field. And shame those who need to be shamed.
I shall write more later on supplemental data.