Tag Archives: plos

Friday SNPpets

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

Impact Factor

I remember considering the “Impact Factor” of journals when submitting research papers, and wondering what the impact factor of a specific paper I published might be out of curiosity. Not particularly seriously, my field was narrow enough in my Ph.D. research that there were just a few journals to even consider, so it was usually pretty simple choosing. And for individual articles, I am pretty sure I knew the 4 people in the world outside my lab that were interested in my research (I jest, a little). During my postdoc, my PI was pretty good and choosing journals based on the article, the journal’s audience… and impact factor.

But impact factor measuring has it’s issues (Article-Level Metrics and the Evolution of Scientific Impact, Neylon and Wu. PLoS Biol 7: e1000242), and there is always a search to measure the impact of journals and individual articles better, or at least differently. Well, one of my favorite science sites and one of my favorite journal publishers ResearchBlogging.org and PLoS, have worked together to measure the impact of journal articles. PLoS has a lot of metrics to see what the ‘impact’ of an article might be, and now they’ve added a metric to see how many times it’s been written about on blogs using blog aggregators like Postgenomic, Blog Lines and Nature Blogs, and now ResearchBlogging.

I like the partnership with ResearchBlogging specifically because whereas the other blog aggregators are not necessarily picking up articles that discuss the science of the article (Postgenomic) or aggregate only a subset of science blogs out there (Nature Blogs), ResearchBlogging is specifically blogs posts discussing the research of  peer-reviewed articles.

Of course I don’t find this particularly useful to compare one article against another (the best articles aren’t always written about, and those that are might not be in the blog aggregators), but I do think this will be great way to carry on the conversation and dig deeper into the research topic.

You can view that metric at PLoS of any article, for example the one I link to above, click on the “metric” tab, scroll down a bit until you see the heading “Blog Coverage.” For that article, you’ll see two ResearchBlogging posts (as of this writing), a metric for this paper about metrics :).

Teaching and annotating at the same time

plos teaching paperA recent paper (couple weeks ago) in PLoS Biology from Hingamp et al. had me intrigued. Entitled Metagenome Annotation Using a Distributed Grid of Undergraduate Students, the lecturers put together a system to teach bioinformatics to undergraduates that uses new unannotated sequences from metagenome projects. As stated in the announcement,

This method asks students to randomly pick and analyze unknown metagenomic DNA fragments from a real research sequence stockpile. The student’s mission, using Internet tools only, is to figure out from which organism the DNA comes from, and what biological function it might have. As well as gaining confidence and proficiency in bioinformatics, students experience the authentic research process of weighing the arguments, establishing prediction reliability, building hypotheses, and maintaining rigorous disourse.

The lecturers have put together  a teaching-annotation procedure in a publicly accessible “annotation environment” they call “Annotathon.” This web interface walks the student through the annotation process in a procedure as you see in the figure here. Since you can join and use this interface, I thought I’d give it a test drive.

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Happy Open Access day! (Oct 14th)

openacess_day_logo.jpgAccording to this BioMed Central blog, tomorrow is Open Access day – how shall we celebrate? Maybe read an extra open access article or two? Attend one of the events? Your blog on Oct 14th about the importance of open access to you could win you a ‘bag of swag’ PLoS ‘Synchroblogging competition – get writing this weekend’ competition. Another option is to join the BioMed Central Facebook fan club. As you can see there are LOTS of ways to support OpenAcess – let us know what you do to celebrate this important movement.

Gene Wiki?

ResearchBlogging.org PLoS Biology has an article out today entitled “A Gene Wiki for Community Annotation of Gene Function.” The article describes the authors attempts to create a comprehensive gene wiki of gene functions by ‘seeding’ Wikipedia with a foundation of ‘stub’ articles with information from existing databases (such as Entrez Gene). This foundation would then be built upon in Wikipedia fashion by community editing.

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Open Access Publishing

The Public Library of Science was founded in 2001 and published a letter urging publishers to open access to research published in their journals (I remember this letter being presented at an ISMB conference then). PLOS launched a series of open access journals when the response wasn’t particularly enthusiastic from the publishers. Those PLOS journals have had some success since, as have those at Biomed Central, another open access publisher.

There has been resistance from scientific publishers to the open access movement. Some fully opposing it, others like Nature Publishing Group’s official opinion is that it has no position, but that the business model is unproven and peer review an expensive endeavor. Nature has been experimenting with open source models though through the Molecular Systems Biology (an open access Nature journal) supporting self-archiving through public repositories, making an exception for papers reporting genomes and their open text mining initiative.

And now a new development: Wednesday, President Bush signed the Consolidated Appropriations Act of 2007 (H.R. 2764), which requires all NIH-funded published research to be deposited into PubMed Central (and thus open access) within 12 months of publication. Continue reading