Tag Archives: journals

Tip of the Week: Creating an Electronic Informed Consent

Informed consent has been a foundation of research, and especially genetics research, in that last few decades though it’s taken quite some time to right past wrongs. And with genomics research and personal genomics generating huge amounts of data, informed consent becomes both more important and more complex. The National Human Genome Research Institute has a pretty good selection of information and regulations surrounding informed consent including the regulations, guidelines, specific NHGRI guidelines and applicable federal legislation. If you are doing human genetics and genomics research it would behoove you to make sure you understand the guidelines and issues. A good paper to read to understand would be the article, “Tailoring the process of informed consent in genetic and genomic research” in Genome Medicine cited below.

Depending on your institution and support, you might not have to ever write up or administer informed consent documentation, but often smaller institutions or projects must. So, let’s get to the nitty gritty logistics of actually creating an informed consent survey and document.

Today’s Tip of the Week is the 4 minute first part of a five part series from iDASH at UCSD on creating an electronic informed consent using LimeSurvey and then using iCONS, iDASH’s Informed Consent Management Tool. iDASH:

“is one of the National Centers for Biomedical Computing (NCBC) under the NIH Roadmap for Bioinformatics and Computational Biology. Founded in 2010, the iDASH center is hosted on the campus of the University of California, San Diego and addresses fundamental challenges to research progress and enables global collaborations anywhere and anytime. Driving biological projects motivate, inform, and support tool development in iDASH. iDASH collaborates with other NCBCs and disseminates tools via annual workshops, presentations at major conferences, and scientific publications.”

There are many ways to create an electronic survey, but this set of tutorials makes it straight forward using LimeSurvey and iCONS. The other short sections are here: Part two, three, four and five.

… and while I have you at iDASH, I suggest you watch this hour talk by Philip Bourne (at UCSD) titled “In the future, will a biological database really be different than a biological journal.” The talk was given just over a month ago and an update to something Dr. Bourne said in 2005. It’s a good corollary to Mary’s (apt and true) oft-repeated mantra: “The data is not in the papers any more.”

(we’ve mentioned iDASH before and a lecture about the cost curation that was interesting)

Quick links:

iDASH: http://idash.ucsd.edu
iCONS: http://idash.ucsd.edu/electronic-informed-consent
iDASH Tutorials: http://www.scivee.tv/user/17631


Charles N Rotimi and Patricia A Marshall (2010). Tailoring the process of informed consent in genetic and genomic research Genome Medicine, 2 (3) : doi:10.1186/gm141

A new BioMed Central feature

Brought to you by OpenHelix and BioMed Central :D. We really like the feature and idea (of course) and thought we’d pass it on.

BioMed Central (BMC) is an open access publisher. BMC along with OpenHelix launched a new feature recently to give readers of BMC journals timely access to relevant genomic resource tutorials. When reading a research article at BMC, researchers are now provided links to online tutorials of many of the genomics resources and tools used or cited in the article. The link takes the reader directly to the training landing page on the OpenHelix site. BMC has a large selection of open access high quality peer-reviewed research journals and much of the research reported today uses and cites many of the resources OpenHelix trains on. Researchers can now quickly find training on the databases and tools used in the research. For example, this recent article Genomewide Characterization of non-polyadenylated RNAs, in BMC’s Genome Biology cites several tools used in their research including GEO, MEME and others. The new feature finds these citations in the article and lists links to the OpenHelix tutorials on those resources as seen in the image.

It can be hard to find a quick link to a relevant resource in papers–the citations are sometimes incomplete, or not linked to the site.

We have plans to expand this feature in several ways to make training on relevant and important genomics resources simpler and quicker for researchers.

We’ve already gotten some great feedback on this–Great idea!

@jytricker Great idea! @BioMedCentral/OpenHelix jv will coach scientists on genomics/bioinformatics tools mentioned in papers http://ow.ly/4eQbG


New to me old news: Dryad data repository

Recently, some major Journals implemented new data archiving policies, including the American Naturalist:

The American Naturalist“The American Naturalist requires authors to deposit the data associated with accepted papers in a public archive. For gene sequence data and phylogenetic trees, deposition in GenBank or TreeBASE, respectively, is required. There are many possible archives that may suit a particular data set, including the Dryad repository for ecological and evolutionary biology data (http://datadryad.org). All accession numbers for GenBank, TreeBASE, and Dryad must be included in accepted manuscripts before they go to Production. Any impediments to data sharing should be brought to the attention of the editors at the time of submission.”

Re: Dryad. This data repository is new to me. Though they are not particularly ‘data-rich’ at the moment (just over 1,000 data files), the idea and purpose behind Dryad seems to have been a long time coming. We have huge data repositories for sequence, structure and the like, but there is so many types data published that reside only at individual journals… or on someone’s hard drive. Dryad’s purpose is a repository for these kinds of evolutionary and ecological data (among others).

It appears that the repository project only got started about two years ago (funded anyway) though I could be wrong, but they’ve made some headway. Nature journals now list Dryad as a recommended option for data repository. And as linked and quoted above, several other large journals now either require or recommend Dryad as a repository.

There is a quick video on how to submit data here. The search capabilities are a bit limited (for example, once you search you can’t alter the original search term without starting all over), but I’m sure with time and funding this will change.

Definitely check it out.

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 :).

Adventures in publishing

A new open access journal, Ideas in Ecology and Evolution, has, well, opened. It’s published at Queen’s College in Canada.

“So?” you ask, “there are lots of journals up starting all the time”.

This one is different. It’s experimenting with a lot of things (ok, so there seem to be a lot of journals experimenting with the model lately). The subject matter is not research per se, but ideas. Having been to my share of ecology and evolution conferences and discussion, I can see this journal has opened itself up to some quite lovely discussions.

As explained by Bob O’hara, there are some interesting review process experiments going on here too. Authors pay to get their ideas published, reviewers are paid, reviewers are not anonymous and they get to publish their views of the article as a companion piece. Bob discusses the issues we’ve all heard about the pros of anonymity (and they are valid ones), but this might work in this case. I also agree with Bob on one point, this structure (reviewers publishing their views) will indeed increase discussion, but I’d too like to see some mechanism for a broader discussion. As it is designed now, it will be like watching TV pundits arguing the finer points of health policy, which I guess is informative, but I’d like to see some mechanism that allows a broader discussion of the article. Something like PLoS has, which I think would actually work better in a journal of ideas like this.

Well, we’ll see. Right now there is nothing there but the editorial. I’ll be watching though.

hat tip: Coturnix

Tip of the Week: Subscribing to journal updates with NCBI

NCBI RSSTwo weeks ago, I showed you how to use HubMed, an alternative search interface to PubMed, to subscribe to a feed for a specific journal, allowing you to stay up-to-date on new articles and issues of that journal. As mentioned earlier, many journals have feeds to their updates, but using PubMed and HubMed are good alternatives if you can not find a feed, want to customize it a bit or just like a single place to go to for all your feeds. This week, I’m going to show you how to do the same thing, subscribe to a feed for a specific journal, using NCBI as suggested by a commenter in the Tip of the Week a couple weeks ago.

Tip of the Week: Subscribing to journal updates with HubMed

hubmed subscriptionsAs one of the tools (along with Connotea, Faculty1000, MyNCBI, HubMed, etc) to keep abreast of the fire hose of literature that is published, I also use RSS feeds to keep up-to-date on the latest publications from journals of interest. There are a lot of journals out there that publish a lot of data interesting to me, but subscribing to them all IRL of course is cost prohibitive (and environmentally unfriendly). Many will send updates by email of new issues, but the last thing I need is another email in my inbox screaming for my attention. Getting an RSS feed from a journal is a good way to keep up-to-date on new issues (if you haven’t used RSS feeds, read up on them here, find a reader here). Many journals include RSS feeds to new content, others don’t. Another way to get RSS feeds to a specific journal is to use HubMed in a nice feature that allows you to get an RSS news feed for a ‘search.’ I’ll show you how to do that here.