Wednesday, February 29, 2012

Making biodiversity data sticky: it's all about links

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Sometimes I need to remind myself just why I'm spending so much time trying to make sense of other people's data, and why I go on (a...
Tuesday, February 28, 2012

GBIF specimens in BioStor: who are the top ten museums with citable specimens?

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Brief update on yesterday's post about finding specimens in BioStor . BioStor has some 66,000 articles from BHL, from which I've ex...
Monday, February 27, 2012

Linking GBIF and the Biodiversity Heritage Library

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Following on from exploring links between GBIF and GenBank here I'm going to look at links between GBIF and the primary literature, in ...
Thursday, February 23, 2012

How many specimens does GBIF really have?

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Duplicate records are the bane of any project that aggregates data from multiple sources. Mendeley , for example, has numerous copies of the...
Wednesday, February 22, 2012

Clustering strings

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Revisiting an old idea ( Clustering taxonomic names ) I've added code to cluster strings into sets of similar strings to the phyloinform...

Why LSIDs suck

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I'll keep this short: LSIDs suck because they are so hard to set up that many LSIDs don't actually work. Because of this there seems...
Tuesday, February 21, 2012

Linking GBIF and Genbank

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As part of my mantra that it's not about the data, it's all about the links between the data, I've started exploring matching Ge...
Thursday, February 16, 2012

EOL Phylogenetic Tree Challenge

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The Encyclopedia of Life have announced the EOL Phylogenetic Tree Challenge . The contest has two purposes: It provides a testbed for the Ev...
Friday, February 10, 2012

BLAST a sequence and get a tree and a map

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I've updated the BLAST a sequence and get a tree tool described in a previous post to output additional details, such as a list of the...
Wednesday, February 08, 2012

Automating the creation of geophylogenies: NEXUS + delimited text = KML

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One thing which has always frustrated me about geophylogenies is how tedious they are to create. In theory, they should be pretty straightfo...
Monday, February 06, 2012

Using Google Refine and taxonomic databases (EOL, NCBI, uBio, WORMS) to clean messy data

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Google Refine is an elegant tool for data cleaning. One of its most powerful features is the ability to call "Reconciliation Services...
Thursday, February 02, 2012

Browsing TreeBASE using a genome browser-like interface

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One of the things I find frustrating about TreeBASE is that there's no easy way to get an overview of what it contains. What is it'...
Monday, January 30, 2012

BLAST a sequence and get a tree

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For this weeks sessions of my phyloinformatics course I'm developing some phylogeny tools. The first is a simple AJAX-based BLAST tool....
Thursday, January 26, 2012

Extracting museum specimen codes from text

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Quick note about a tool I've cobbled together as part of the phyloinformatics course , which addresses a long standing need I and others...
Monday, January 23, 2012

Open course on phyloinformatics

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As part of a postgraduate course here at the University of Glasgow I'm teaching five sessions on "phyloinformatics", which I...
Thursday, January 19, 2012

EOL iPad web app using jQueryMobile

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As part of a course on "phyloinformatics" that I'm about to teach I've been making some visualisations of classifications....
Wednesday, January 18, 2012

Yet another reason why we need specimen identifiers, now!

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This message appeared on the TAXACOM mailing list: It is getting more and more necessary for taxonomists to demonstrate that they are usefu...
Tuesday, January 17, 2012

Mendeley as CiteBank: some ideas

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Here are some quick notes on how BHL could use Mendeley as a "CiteBank". As a repository of bibliographic data If the goal is to a...
Tuesday, January 10, 2012

Journals I'd like BHL to scan

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I've recently updated my database of links between animal taxonomic names and literature identifiers , which now has over 280,000 names ...
Monday, December 19, 2011

Towards an interactive taxonomic article: displaying an article from ZooKeys

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One of the things I keep revisiting is the way we display scientific articles. Apart from Nature's excellent iPhone and iPad apps, most...