Friday, February 22, 2013

The end of names? ICZN in financial crisis

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Image by Mr.checker from Wikimedia Commons Science carries a news piece on the perilous state of the International Commission on Zoologica...
Thursday, February 21, 2013

Why are botanists locking away their data in JSTOR Plant Science?

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Somehow I get the feeling that botanists haven't got the "open data" religion. Not only is the list of plant names list behind...
Thursday, February 14, 2013

Rate of description of new animal species and *that* Taxatoy graph

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As part of the discussion on whether legacy biodiversity literature matters a graph from the following paper came up: Sarkar, I., Schenk, R....

Does the legacy biodiversity literature matter?

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I've just come back from a pro-iBiosphere Workshop at Leiden where the role of "legacy literature" became the subject of some...
Friday, January 18, 2013

More GBIF specimen identifier strangeness

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Continuing the theme of trying to map specimens cited in the literature to the equivalent GBIF records, consider the GBIF record http://data...

Thoughts on Mendeley and Elsevier

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Elsevier In Advanced Talks To Buy Mendeley For Around $100M To Beef Up In Social, Open Source Educ... tcrn.ch/W8L5io by @ ingridlunden — Te...
Thursday, January 17, 2013

Tight versus loose coupling

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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 ...
Wednesday, January 16, 2013

Megascience platforms for biodiversity information: what's wrong with this picture?

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The journal Mycokeys has published the following paper: Triebel, D., Hagedorn, G., & Rambold, G. (2012). An appraisal of megascience pl...
Tuesday, January 15, 2013

iDigBio: You are putting identifiers on the wrong thing

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The Integrated Digitized Biocollections (iDigBio) project aims to advance digitising US biodiversity collections. They recently published a...
Friday, December 07, 2012

Elsevier articles have interactive phylogenies

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Say what you will about Elsevier, they are certainly exploring ways to re-imagine the scientific article. In a comment on an earlier post F...
Thursday, December 06, 2012

NEXUS parser and tree viewer in Javascript

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Following on from the SVG experiments I've started to put some of the Javascript code for displaying phylogenies on Github. Not a repos...
Wednesday, December 05, 2012

The Tree of Life

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The following poem by David Maddison was published in Systematic Biology ( doi:10.1093/sysbio/sys057 ) under a CC-BY-NC license. I think th...
Tuesday, December 04, 2012

Viewing phylogenies on the web: Javascript conversion of Newick tree to SVG

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Quick test of an idea I'm playing with. By embedding a Newick-format tree description in HTML and adding some Javascript I can go from t...
Wednesday, November 28, 2012

ZooBank data model

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I'm trying to get my head around the data model used by ZooBank to store taxonomic names. To do this, I've built a graph for the sp...
Tuesday, November 27, 2012

Fuzzy matching taxonomic names using ngrams

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Quick note to self about possible way to using fuzzy matching when searching for taxonomic names. Now that I'm using Cloudant to host C...
Thursday, November 22, 2012

BioStor in the cloud

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Quick note on an experimental version of BioStor that is (mostly) hosted in the cloud. BioStor currently runs on a Mac Mini and uses MySQL ...
Wednesday, November 21, 2012

Species wait 21 years to be described - show me the data

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Benoît Fontaine et al. recently published a study concluding that average lag time between a species being discovered and subsequently desc...
Monday, October 22, 2012

Resolving free-form citations

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We don't need no stinkin' parser- a guide to resolving free-form citations with #CrossRef Metadata Search -> goo.gl/f9a4e — Geof...
Friday, October 19, 2012

The failure of phylogeny databases

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Only 4% of all published phylogenies have data in #treebase or @ datadryad — Karen Cranston (@kcranstn) October 18, 2012 It is well known t...
Wednesday, October 17, 2012

OneZoom

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James Rosindell's OneZoom tree viewer is out and the paper describing the viewer has been published in PLoS One (disclosure, I was a re...