Friday, January 20, 2017

A changing of the times...?

With a title like this on a day like this, you probably think I'm talking about something happening in about an hour from me in Washington.

Don't worry, my level of denial regarding that series of events is nearing 100.000%. I don't even know what you might be implying.

What I'm actually thinking about is the abundance of these pre-print articles that keep popping up in fields outside of our own!

This is the topic of this article in this month's The Scientist (my 4th favorite magazine stacked in my bathroom -- and probably yours!)

I know this is controversial -- and there are big 'ol weaknesses to preprints -- like -- THEY HAVEN'T BEEN PEER-REVIEWED YET!  -- but -- the up-sides can't be ignored either. It doesn't seem uncommon for a traditionally published article to be in some stage of review/revision for 2 years, right? I'm seeing quite a few. could maybe argue...that these kinds of lags aren't exactly allowing science to always proceed at the rocket pace other areas of technology might be able to (and maybe that is a good thing...but....)

I figured it was time to start talking about this when one of my favorite recent studies in our field went the open / pre-print route!

F1000 is an open and transparent publication system.  It works like this:

In the case of this paper from Breckels et al., I can see exactly where they are in the review process. As of this morning, 2 reviewers have checked in and it looks to me like it is about to be accepted with some revisions. I also know who is reviewing it, and I can read their comments. This is just a little different than what we're used to. Is it the right system? I dunno...but it sure is fast!

The thing I'm seeing a lot more of...but not proteomics yet (well...some nice meta-analyses) is biorXiV (not sure I capitalized the right stuff).

This resource from CSHL is a hybrid system. It allows the posting of research and comments before the study goes to a journal for publication. It allows you to have a place holder for your findings to some degree while the final work is finding a permanent home. Your data gets out there, allowing the next person to build on it, but you can definitely stake your claim that it was your development.

The next question, of course, is this nice statement we see a lot of the times when our we submit and article for review:

If you read the beginning (this is for MCP) it sounds like you can't use a pre-print service, but if you keep digging you'll find this isn't the case at all! You just need to disclose all the info (further down in the highlighted zone).


You have to download the JPR author guidelines PDF to find that that they're already prepared for this revolution in proteomic data dissemination

(WOOHOO!!) ...which definitely makes it seem like I'm the one who is behind the times!

1 comment:

  1. I am starting to see a lot more in bioRxiv, and like you said, the journals allow it. I have colleagues that submit pre-print on bioRxiv just before starting the submission to a journal to ensure immediate dissemination of results.