Here are just two interesting stories I read on other peoples blogs:
First, Jake Young at Pure Pedantry blogs about a recent Cell paper by Sakaue-Sawano et al. who present a clever application of protein ubiquitination for visualizing the cell cycle stage of cells in vivo. Lars Juhl Jensen at Buried Treasure has also picked up this story, and those two blogs provide a lot of detail on the method, including a link to a nice video showing HeLa cells passing through 3 cell cycles. In brief, the authors of this paper exploit the fact that several protein ubiquitination systems are only active during particular phases of the cell cycle. On one hand, there is the APC/Cyclosome system, which degrades target proteins only in late mitosis (APC means Anaphase Promoting Complex) and in G1 phase. Conversely, the SCF-Skp2 system is mainly active in S and G2 phases. By coupling two different dyes to target proteins of APC/C and SCF-Skp2 respectively, it was possible to observe an oscillation between red and green colors as the cells go through the different cell cycle phases.
On a very different note, Peter Murray-Rust blogs about the lack of data mining possibility in the Pubmed Central resource. He goes on to discuss if – in the light of this shortcoming – PMC can still be considered an open access resource. I can understand his concern and would certainly welcome if PMC and other open access scientific repositories can be used for automatic text mining efforts. However, what really struck me was the statement:
When George Bush signed the mandate he clearly envisaged that the information should be used for the benefit of human health…
…and this means text-mining.
I am not sure how serious Peter was when writing this. I hope not too much. I cannot think of a single example where text-mining has ever made a major contribution to solving any real-life biomedical problem. Even if there are such eamples, their number will be small. If we compare the health benefits from text mining efforts to those provided by real (human) scientist reading the literature, I have no doubt that the latter would prevail by a big margin.
There should be no doubt about it, it would clearly be a good thing to enable text-mining on PMC. However, describing the current situation of free access to PMC papers for scientists as useless without added text-mining capabilities appears to be, well, kind of biased.