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iPhylo

Rants, raves (and occasionally considered opinions) on phyloinformatics, taxonomy, and biodiversity informatics. For more ranty and less considered opinions, see my Twitter feed.ISSN 2051-8188. Written content on this site is licensed under a Creative Commons Attribution 4.0 International license.
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This is not a post I'd thought I'd write, because OpenURL is an awful spec. But last week I ended up in vigorous debate on Twitter after I posted what I thought was a casual remark: This ended up being a marathon thread about OpenURL, accessibility, bibliographic metadata, and more.

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Following on from my previous post bemoaning the lack of links between biodiversity data sets, it's worth looking at different ways we can build these links. Specifically, data can be tightly or loosely coupled. Tight coupling Tight coupling uses identifiers. A good example is bibliographic citation, where we state that one reference cites another by linking DOIs.

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Yesterday I posted notes on Web Hooks and OpenURL. That post was written when I was already late (you know, when you say to yourself "yeah, I've got time, it'll just take 5 minutes to finish this..."). The Web Hooks + OpenURL project is still very much a work in progress, but I thought a screen cast would help explain why I think this is going to make my life a lot easier.

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For me one of the most frustrating things about online databases is that they often can't be edited. For example, I've recently created a version of the Australian Faunal Directory on CouchDB, which contains a list of all animals in Australia, and a fairly comprehensive bibliography of taxonomic publication on those animals. What I'd like to do is locate those publications online.

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After some fussing and hair pulling I've constructed a demo of linking a journal to the Biodiversity Heritage Library and displaying the results in Zotero (see my earlier post for rationale). After some searching I managed to retrieve metadata for several hundred article from the Bulletin of Zoological Nomenclature . Using a local copy of the BHL metadata, I wrote a script that looked up each article in BHL and found the URL of the

Published

One thing I find myself doing (probably more often than I should) is adding a reference to my Zotero library for an item in the Biodiversity Heritage Library (BHL). BHL doesn't have article-level metadata (see But where are the articles?), so when I discover a page of interest (e.g., one that contains the original description of a taxon) I store metadata for the article containing that page in my Zotero library.