I’ve been on holiday to Japan recently, so work came to a halt on this for a while but I think I’ve largely ‘done’ PLOS ONE full text now (excluding supplementary materials). My results are on github: https://github.com/rossmounce/NHM-specimens/tree/master/results – one prettier file without the exact provenance or in-sentence context of each putative specimen entity, and one more extensive file with provenance &

In this post I’ll go through an illustrated example of what I plan to do with my text mining project: linking-up biological specimens from the Natural History Museum, London (sometimes known as BMNH or NHMUK) to the published research literature with persistent identifiers. I’ve run some simple grep searches of the PMC open access subset already, and PLOS ONE make up a significant portion of the ‘hits’, unsurprisingly.

Now I’m at the Natural History Museum, London I’ve started a new and ambitious text-mining project: to find, extract, publish, and link-up all mentions of NHM, London specimens published in the recent research literature (born digital, published post-2000). Rod Page is already blazing a trail in this area with older BHL literature.

Yesterday, I made a journal scraper for the International Journal of Systematic and Evolutionary Microbiology (IJSEM). Fortunately, Richard Smith-Unna and the ContentMine team have done most of the hard work in creating the general framework with quickscrape (open-source and available on github), I just had to modify the available journal-scrapers to work with IJSEM.

April Clyburne-Sherin asked an interesting question on the OpenCon Discussion List recently: Comment: Quite rightly, April does not trust the publisher to make the published work fully open access in perpetuity, and wants to do more as an author, with the publishing agreement (a formal contract) to ensure that the publisher will actually provide the exact services she wants.

Roughly ten days after I first blogged about this (see: Springer caught red-handed selling access to an Open Access article), Springer have now made a curious public statement acknowledging this debacle: Statement on Annals of Forest Science article Berlin, 6 May 2015 A number of tweets posted by Prof.

Today, the author of a paid-for, ‘hybrid’ open access article published in 2009, found that it was wrongly on sale at a Springer website: https://twitter.com/zentree/status/592547039474421760 FWIW it’s still freely available at the original publisher website here.

[Update 5.30PM 2015-03-26: Wiley have now ‘freed’ the wrongly-paywalled articles in response to this. It doesn’t change the fact that these articles were wrongly on sale for 2 months and 26 days.

For those that know me as a biologist it might perhaps surprise you to know that my most cited publication so far is on Open Access and Altmetrics (published in April 2013, 25 cites and counting…) — nothing to do with biology per se! So I took great interest in this new publication: Wang, X., Liu, C., Mao, W., and Fang, Z. 2015. The open access advantage considering citation, article usage and social media attention.

Wiley & Readcube have done something rather sneaky recently, and it’s not escaped the attention of diligent readers of the scientific literature. On the article landing page for some, if not all(?) journal articles at Wiley, in JavaScript enabled web browsers they’ve replaced all links to download the PDF file of the article with links that direct you to Readcube instead.