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Open course on phyloinformatics

As part of a postgraduate course here at the University of Glasgow I'm teaching five sessions on "phyloinformatics", which I've decided to define broadly enough to encompass most of biodiversity informatics.

Given that this module is being developed on the fly, and will make use of lots of little "toys" I've developed and discussed on this blog, I've decided to put the course notes online, along with the interactive demos and the source code. So, if you want to follow along for the next couple of weeks, here are the links:



Each course page supports comments (see the bottom of the page), so feel free to add comments, or suggestions. The notes are at a crude stage, and will be developed over the duration of the course (2 weeks). I'm also endeavouring to get all the source code for the demonstration apps into GitHub. None of these demos is polished, but they will hopefully provide some ideas for taking them further. There will be iSpecies-like mashups, iPad webapps, classification visualisations, TreeBASE search tools, geophylogenies and other phylogeny viewers.

EOL iPad web app using jQueryMobile

As part of a course on "phyloinformatics" that I'm about to teach I've been making some visualisations of classifications. Here's one I've put together using jQuery Mobile and the Encyclopedia of Life API. It's pretty limited, but is a simple way to explore EOL using three different classifications. You can view this live at http://iphylo.org/~rpage/phyloinformatics/eoliphone/ (looks best on an iPad or iPhone). Once I've tidied it up I'll put the code online. Meantime here's a quick demo:

Yet another reason why we need specimen identifiers, now!

This message appeared on the TAXACOM mailing list:

It is getting more and more necessary for taxonomists to demonstrate
that they are useful and used. This does not only apply to the
individual scientists, but also to institutions with taxonomic
collections, such as museums and herbaria.

In an attempt to live up to that increasing demand for documentation,
the leadership of the Natural History Museum of Denmark has issued an
order to its curatorial staff - The staff members are requested to
document which publications from 2011, written entirely by external
scientists, that in one way or another are based on material in the
collections of the Museum.


Given that most specimens lack resolvable digital identifiers (a theme I've harped on about before, most recently in the context of DNA barcoding), answering this kind of query ends up being a case of searching publications for text strings that contain the acronym of the collection. The sender of the message, Ib Friis, is alarmed at this prospect:

In publications, material from our herbarium at "C" is normally referred
to in text strings of one of the following forms: "(C)", "(C, ", ", C,"
or " C)". But a search in for example Google Scholar or other search
engines result in overflow of thousands and thousands of hits, even
when these text strings are combined with other relevant words such as
"botany", "plants", etc.


In an earlier paper "Biodiversity informatics: the challenge of linking data and the role of shared identifiers" (http://dx.doi.org/10.1093/bib/bbn022) (free preprint available here: hdl:10101/npre.2008.1760.1) I argued that having resolvable identifiers for specimens could enable measures of "citation" to be computed for specimens (and data derived from those specimens). Just as we have citation counts for articles and impact factors for journals, we could have equivalent measures for specimens and collections. These measures may keep administrators happy, for scientists I think the real benefits will be the ability to trace the provenance of some data, and the fate of data they themselves have collected or published.

For things such as publications it is trivial to track their usage. For example, to find the number of times the article "Biodiversity informatics: the challenge of linking data and the role of shared identifiers" has been cited, I simply enter the DOI into Google Scholar, e.g. http://scholar.google.co.uk/scholar?q=10.1093/bib/bbn022. Imagine being able to do the same for specimens?

For this to happen, museum specimens need digital identifiers. If museums are serious about quantifying the impact of their collections, they should make assigning digital identifiers a priority.