Archive for October, 2008

Open access genomes

Open access genomes! (but how is OA protected?), Dave Love, dave love’s blog, October 21, 2008. Excerpt:

We have come a long way in the last 15 years since Craig Venter and his company, Celera, refused to deposit their human genomic sequence in NCBI/GenBank and others who practice gene patenting deflated our collective tyres. I think that PGP understands the benefits of being OA, but I didn’t see anything on their website about a legal backbone to protect that access, such as a Creative Commons copyrights. I hope they will get some advice on this from librarians, lawyers, publishers, and others in the OA community!

For more about the PGP, see: More on the Personal Genome Project, Gavin Baker, Open Access News, October 20, 2008; Profile of the Personal Genome Project, Gavin Baker, Open Access News, August 06, 2008; The Personal Genome Project, George M Church, Mol Syst Biol 2005; 1: 2005.0030 [Epub 2005(Dec 13)].

Modified on October 21, 2008:

See also: From genetic privacy to open consent, Jeantine E Lunshof, Ruth Chadwick, Daniel B Vorhaus and George M Church, Nat Rev Genet 2008(May); 9(5): 406-11. Excerpts from the full text (not OA):

Box 3 | Key features of the Personal Genome Project’s open-consent policy

Open consent as part of the Personal Genome Project implies that research participants accept that:

* Their data could be included in an open-access public database.
* No guarantees are given regarding anonymity, privacy and confidentiality.
* Participation involves a certain risk of harm to themselves and their relatives.
* Participation does not benefit the participants in any tangible way.
* Compliance with monitoring of their well-being through quarterly questionnaires is required.
* Withdrawal from the study is possible at any time.
* Complete removal of data that have been available in the public domain may not be possible.

The moral goal of open consent is to obtain valid consent by effectuating veracity as a precondition for valid consent and effectuating voluntariness through strict eligibility criteria, as a precondition for substantial informed consent.

[End of Box 3]

Open consent. Open consent means that volunteers consent to unrestricted re-disclosure of data originating from a confidential relationship, namely their health records, and to unrestricted disclosure of information that emerges from any future research on their genotype–phenotype data set, the information content of which cannot be predicted. No promises of anonymity, privacy or confidentiality are made. The leading moral principle is veracity — telling the truth — which should precede autonomy. Although, in clinical medicine, veracity is the legal norm in many jurisdictions, physicians may try to justify the withholding of information by invoking the ‘therapeutic privilege’. In research, there is no such privilege, and when seeking informed consent from research subjects, distorted or incomplete information could undermine trust in researchers and in science.

Comment: Those contemplating OA to genetic data need to pay careful attention to the concept of “open consent“, and its emphasis on “telling the truth” and on “voluntariness”. It’s also noted in the full text that “in the PGP potential volunteers are strongly advised to discuss their participation with relatives“.


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Two OA articles about cancer stem cells

A recent article and an earlier review, co-authored by members of the same research group, are currently available from the Journal of Cellular and Molecular Medicine. They are:

1) High aldehyde dehydrogenase and expression of cancer stem cell markers selects for breast cancer cells with enhanced malignant and metastatic ability, by Alysha K Croker and 6 co-authors, including Alison L Allan, J Cell Mol Med 2008(Aug 4). [Epub ahead of print] [PubMed Abstract]. Currently, a PDF version of the full text is gratis OA.

2) Cancer stem cells: implications for the progression and treatment of metastatic disease, a review by Alysha K Croker and Alison L Allan, J Cell Mol Med 2008(Apr); 12(2): 374-90 [PubMed Abstract]. Currently, both the HTML and PDF versions of the full text are gratis OA.

For more about these two articles, and the journal in which they both were published, see: Breast cancer stem cells hard to kill? Cancer Stem Cell News, October 19, 2008.

It’s not clear, either from the articles themselves, or from the PubMed citations, that these articles were intended to be OA.

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Harold Varmus interviewed

Dr Varmus, I presume? By David Worlock, Outsell’s Thinking Out Loud, October 15, 2008. Excerpts:

October 14 was the foundation date for PLoS Biology, as well as the designated Open Access Day, so the 300 STM publishers gathered at the STM Association’s annual meeting on that day at the Frankfurt Book Fair to hear this interview needed no reminder of the significance of Dr Varmus’ work. They may have been surprised, however, when he spoke as a publisher himself and shared some of his five years of experience.


The foundation of PLoS One as a fast track publication mode based on review of technical competence and eligibility, rather than scientific standing or originality, had been a great success, with a high proportion of submissions being accepted at a lower $1200 fee. The peer reviewed journals now had high reputations, and rejected some 90% of submissions, but had needed to raise fees beyond his forecast of five years ago to cover costs.


He is plainly interested by search tools and analysis, and while it remains his conviction that repositories like PubMed are a critical component, he wants to see the urge of scientists to cross search the literature on factors and issues of their own choosing as vital to eventual success, regardless of the conventional structures of current article publishing.


And in terms of new developments, he certainly sees the article as a work in progress, and was particularly strong on the need, where privacy and data regulation permitted, for more of the evidential base to be exposed to allow other scientists to examine the data from which conclusions had been drawn, and subject it to their own analytical techniques.

Recommendation: Read the entire text of the blog post from which these excerpts were taken.

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Cancer Stem Cell News blog

On August 28, 2008, I began editing another blog, entitled: “Cancer Stem Cell News“:

A blog of news items related to cancer stem cells, with an emphasis on recent research and articles that are openly accessible.

It’s a blog of the Cancer Stem Cell Consortium (CSCC):

The Cancer Stem Cell Consortium (CSCC) is a groundbreaking organization founded in 2007 by a group of Canadian funding agencies to support international collaboration on a promising new front in the fight against cancer—research on cancer stem cells, which direct the growth of the many kinds of tumours.

I’m a member of the Board of the CSCC, and have taken initial responsibility for the CSCC blog in order to highlight the advantages of improved access to news and publications about the rapidly-expanding field of research on cancer stem cells. An interim analysis of a randomized controlled trial (BMJ 2008(July 31);337:a568) has already provided additional strong evidence that open access increases the dissemination of scientific articles. See a comment of mine about this trial:

The enhanced transfer of knowledge to those whose access currently is restricted because of price barriers is an important example of the advantages of OA.

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A new OA journal from OUP: Database

A new journal from Oxford University Press (OUP), Database: The Journal of Biological Databases and Curation, will begin publishing research in the coming months. (Thanks to Francis Ouellette, who is an Associate Editor of this new journal).

About the Journal. Excerpt:


All Database content is published under an open access model. Database articles will therefore be freely available to everybody online, upon publication, without the barrier of paid subscription to access.

Under this model, the journal’s costs are covered by author publication charges of £800/€1200/$1600 per article.

It’s of interest to compare these charges with those for hybrid Oxford journals that provide an optional Open Access Model (Oxford Open). See: Optional Author Publication Charges. Excerpts:

For an author based at a subscribing institution:

Regular charge – £900 / $1800 / €1350

For an author based at an institution that does not subscribe:

Regular charge – £1500 / $3000 / €2250

Thus, the charges for Database are lower than the regular charges for the Oxford Open option.

In the right frame of some Database pages, there’s a heading entitled: “Author Self Archiving Policy”. At present, the links that are provided don’t yield any information about this policy. The site currently still appears to be under construction.

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Another Canadian access policy

The National Cancer Institute of Canada (NCIC) supports cancer research in Canada using funds raised by the Canadian Cancer Society and the Terry Fox Foundation. The NCIC now has an Open access policy.  (Version dated 01 August 2008 archived by WebCite® at: Excerpts:

Effective July 2009, all researchers supported in whole or in part through the NCIC are required to make their published results of NCIC supported work publicly available. Researchers are encouraged to make their work publicly available as soon as possible, but must do so no later than six months after the final publication date.


As part of this policy, the NCIC will provide support for any charges levied by publishers that are required to comply with this open access process. Such charges may be included as legitimate research expenses (fully justified as with all other expenses) in the budget of a research grant submission.

See also: Open access policy FAQs. (Version dated 01 August 2008 archived by WebCite® at: Excerpt:

9. What if a journal is compliant with open access, but does not allow the paper to be made freely available until 12 months after publication?
Researchers are able to submit their work to a journal that does not support public availability within six months of the publication date. The NCIC does not wish to compromise the ability of researchers to publish in high-impact journals. However, researchers must inform the NCIC of this limitation and the paper must be made freely available as soon as possible. Please email when this issue arises for monitoring purposes. Like other agencies, the NCIC is applying pressure to non-compliant journals to allow for public availability within six months.

Comment: The NCIC policy is similar to the Policy on Access to Research Outputs of the Canadian Institutes of Health Research (CIHR).

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