Faculty of 1000 Research recently announced they were almost ready to publish their first articles, and they weren’t kidding. Today marks the publication of its first three papers. Of particular interest to me is a simple benchmark of most modern NGS aligners, with a focus on predictive power to sensitively detect clinically relevant mutations in the BRCA1 gene. Also of interest is an analysis of publicly available methods to interpret direct-to-consumer SNP array data (think 23andMe) and exome sequence from a two-generation pedigree. One disappointing note – the widget F1000 is using for data viewing is silently blocked behind the firewall where I work.

EDIT: the admin for the widget has contacted me, and says they will be working to fix the blocking issue. I think it’s great that F1000 Research is trying to integrate data access into the journal articles.

In a blog post titled “We are almost there!” at the Faculty of 1000 Research site, Rebecca Lawrence writes about the details of the new journal’s first research articles. Specifically, there are a few points that clarify the journal’s policies regarding citations and retractions. Regarding indexing in search engines such as Google Scholar and Pubmed:

“that articles will be indexed at the point at which they have received two or more positive reviews.  If an article fails to achieve this, it will not be indexed.”

This is a reasonable policy, and should quiet most of the concerns about propagating low quality, unreviewed research. What happens if you accidentally cite an article and then it changes drastically?:

“…we have finalised our novel approach to article citation, which will handle the complexities of citing an article that will be in an evolving state of refereeing over time.”

This is a bit vague still, but I am assuming that citing an F1000R article will be a bit like citing the version of a software package. A “pre-release” version of the article might look something like “Shirley et al. 2011a.1″ to denote that the paper you have referenced is unreviewed (“version alpha”), and only exists in one version. Subsequent edits could move the paper toward 2011a.2, for quick changes before it is reviewed, and eventually toward beta and then final versions after there are sufficient reviews. The beta versions of the article would be indexed in search engines, and papers that make it to a final version would demonstrate integrity, since they receive critical positive review.

Update: F1000R has released the full specification for their citation format:

Smith A, Jones B
This is a very interesting article [v3; ref status: Indexed,http://f1000r.es/123456]
F1000 Research 2012, 1: 23, DOI: 10.3410/f1000research.1-23.v3

If the article has not received two or more positive reviews, it will be cited with ref status: Approved X, Not Approved Y where X and Y are the number of positive and negative peer reviews.