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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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Published

Despite the well deserved scepticism about dashboards voiced by Shannon Mattern @shannonmattern (see Mission Control: A History of the Urban Dashboard, I discovered this by reading Ignore the Bat Caves and Marketplaces: lets talk about Zoning by Leigh Dodds @ldodds) I'm intrigued by the idea a dashboard for biodiversity. We could have several different kinds of information, displayed in a single place.

Published

Yet another barely thought out project, although this one has some crude code. If some 16,000 new taxonomic names are published each year, then that is roughly 40 per day. We don't have a single place that aggregates these, so any major biodiversity projects is by definition out of date. GBIF itself hasn't had an update list of fungi or plant names for several years, and at present doesn't have an up to date list of animal names.

Published

I need more time to sketch this out fully, but I think a case can be made for a taxonomy-centric (or, perhaps more usefully, a biodiversity-centric) clone of PubMed Central. Why? We already have PubMed Central, and a European version Europe PubMed Central, and the content of Open Access journals such as ZooKeys appears in both, so, again, why?

Published

One of the less glamorous but necessary tasks of data cleaning is mapping "strings to things", that is, taking strings such as "George A. Boulenger" and mapping them to identifiers, such as ISNI: 0000 0001 0888 841X. In case of authors such as George Boulenger, one way to do this would be through Wikipedia, which has entries for many scientists, often linked to identifiers for those people (see the bottom of the Wikipedia page for George A.

Published

Imagine a web site where researchers can go, log in (easily) and get a list of all the species they have described (with pretty pictures and, say, GBIF map), and a list of all DNA sequences/barcodes (if any) that they've published. Imagine that this is displayed in a colourful way (e.g., badges), and the results tweeted with the hastag #itaxonomist.

Published

Note to self about a possible project. This PLoS ONE paper: describes a method for inferring a hierarchy from a set of tags (and cites related work that is of interest). I've grabbed the code and data from http://hiertags-beta.elte.hu/home/ and put it on GitHub. Possible project Use Tibély et al. method (or others) on taxonomic names extracted from BHL text (or other) and see if we can reconstruct taxonomic classifications.