rplos is an R package to facilitate easy search and full-text retrieval from all Public Library of Science (PLOS) articles, and we have a little feature which aren’t sure if is useful or not. I don’t actually do any text-mining for my research, so perhaps text-mining folks can give some feedback. You can quickly get a lot of results back using rplos, so perhaps it is useful to quickly browse what you got.

A few bits and pieces about the PLOS Collection on sauropod gigantism that launched yesterday. First, there’s a nice write-up of one of our papers (Wedel and Taylor 2013b on pneumaticity in sauropod tails) in the Huffington Post today. It’s the work of PLOS blogger Brad Balukjian, a former student of Matt’s from Berkeley days.

I just read Mick Watson’s post Why I resigned as PLOS ONE academic editor on his blog opiniomics. Turns out his frustration with PLOS ONE is not to do with his editorial work but with the long silences he faced as an author at that journal when trying to get a bad decision appealed. I can totally identify with that, though my most frustrating experiences along these lines have been with other journals.

A while back, Elsevier launched its journal finder, tagged “Find the perfect journal for your article”. Since our priorities in choosing a journal are a bit different from Elsevier, here is the SV-POW! journal finder. (That’s version 2, by the way.

We recently had a paper come out in a special issue on article-level metrics in the journal Information Standards Quarterly. Our paper basically compared article-level metrics provided by different aggregators. The other papers covered various article-level metrics topics from folks at PLOS, Mendeley, and more. Get our paper.

Quick note to highlight the following publication: This paper outlines the methods used by the BOLD project to cluster sequences into "BINS", and touches on the issue of dark taxa (taxa that are in GenBank but which lack formal scientific names). Might be time to revisit the dark taxa idea, especially now that I've got a better handle on the taxonomic literature (see BioNames) where the names of at least some dark taxa may lurk.

Jonathan Eisen recently wrote that the PLOS Hub for Biodiversity is soon to be retired, and sure enough it's vanished from the web (the original URL hubs.plos.org/web/biodiversity/ now bounces you straight to http://www.plosone.org/, you can still see what it looked like in the Wayback Machine).Like Jonathan, I was involved in the hub, which was described in the following paper:In retrospect PLoS's decision to pull the hub is not surprising.

Christopher W. Schadt tells a distasteful story over on his blog, about how a PLOS ONE paper that he was a co-author on was republished as part of a non-PLOS printed volume that retails for $100. The editors and publishers of this volume neither asked the authors’ permission to do this (which is fair enough, it was published as CC By), nor even took the elementary courtesy of informing them.

Here at SV-POW!, we are an equal-opportunity criticiser of publishers: Springer, PLOS, Elsevier, the Royal Society, Nature, we don’t care. We call problems as we see them, where we see them. Here is one that has lingered for far too long.

Because I am preparing this paper from PLOS ONE, with its stupid numbered-references system, I am finally getting to grips with a reference-management system. Specifically, Zotero, which is both free and open source, which means it can’t be taken over by Elsevier. As a complete Zotero n00b, I’ve run into a few issues that more experienced users will no doubt find laughable. Here are two of them.