Month: May 2015
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BMNH specimens used in PLOS ONE
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…
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Text mining for museum specimen identifiers
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. See: Linking specimen codes to GBIF & Design Notes…
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Making a journal scraper
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. How did…
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Agreements between authors and publishers
April Clyburne-Sherin asked an interesting question on the OpenCon Discussion List recently: I am an author on a manuscript that my lab wants to publish in a subscription journal that normally retains the copyright. The manuscript is a desirable one so they are “willing” (haha) to provide it “open access” (that was my stipulation to…
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Springer admits wrongdoing in selling open access article
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. Luis Apiolaza on 27 April, and by…