Messages de Rogue Scholar

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Publié in iPhylo

If you compare the impact that BHL and Plazi have on GBIF, then it's clear that BHL is almost invisible. Plazi has successfully in carved out a niche where they generate tens of thousands of datasets from text mining the taxonomic literature, whereas BHL is a participant in name only. It's not as if BHL lacks geographic data.

Publié in iPhylo

It's funny how some images stick in the mind. A few years ago Chris Freeland (@chrisfreeland), then working for Biodiversity Heritage Library (BHL), created a visualisation of BHL content relevant to the African continent. It's a nice example of small multiples. For more than a decade (gulp) I've been extracting articles from the BHL and storing them in BioStor.

Publié in iPhylo

At present BioStor provides a simple display of an article extracted from BHL. You get the page images, and sometimes a map and an altmetric "donut". But we can do better than this. For example, I'm starting to experiment with displaying a list of literature cited by the article.

Publié in iPhylo

Given a big corpus of literature one of the fun things to do is look at how the use of a term has changed over time. When did people first use a particular word? When did one word start to replace another, etc.? Google's Ngram Viewer is perhaps the best known tool for exploring these questions.

Publié in iPhylo

BioStor now has 150,000 articles. When I wrote a paper describing how BioStor worked it had 26,784 articles, so things have progressed somewhat! I continue to tweak the interface to BioStor, trying different ways to explore the articles. Spatial search I've tweaked spatial search in BioStor.

Publié in iPhylo

I've been experimenting with simple spatial search in BioStor, as shown in the demo below. If you go to the map on BioStor you can use the tools on the left to draw a box or a polygon on the map, and BioStor will search it's database for articles that mention localities that occur in that region. If you click on a marker you can see the title of the article, clicking on that title takes you to the article itself.

Publié in iPhylo

One of my pet projects is BioStor, which has been running since 2009 (gulp). BioStor extracts articles from the Biodiversity Heritage Library (details here: http://dx.doi.org/10.1186/1471-2105-12-187), and currently has over 110,000 articles, all open access. The site itself is showing its age, both in terms of performance and design, so I've wanted to update it for a while now.