Monday, March 31, 2014

Rethinking annotating biodiversity data

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TL;DR By using bookmarklets and a central annotation store, we can build a system to annotate any biodiversity database, and display those ...
Thursday, March 13, 2014

Publishing biodiversity data directly from GitHub to GBIF

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Today I managed to publish some data from a GitHub repository directly to GBIF. Within a few minutes (and with Tim Robertson on hand via Sky...
Monday, March 10, 2014

Displaying a million DNA barcodes on Google Maps using CouchDB

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Following on from the previous post on putting GBIF data onto Google Maps , I'm now going to put DNA barcodes onto Google Maps. You can ...
Friday, March 07, 2014

GBIF data overlayed on Google Maps

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As part of a project exploring GBIF data I've been playing with displaying GBIF data on Google Maps. The GBIF portal doesn't use Goo...
Monday, March 03, 2014

GBIF liverwort taxonomy broken

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A quick note to myself to document a problem with the GBIF classification of liverworts (I've created issue POR-1879 for this). While b...
Wednesday, February 19, 2014

Five Stages of Data Grief

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There is a great post by Jeni Tennison on the Open Data Institute blog entitled Five Stages of Data Grief . It resonates so much with my ex...
Monday, February 10, 2014

Mark-up of biodiversity literature

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I gave a remote presentation at a proiBioSphere workshop this morning. The slides are below (to try and make it a bit more engaging than a ...
Friday, January 24, 2014

NCBI taxonomy database now shows type material

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Scott Federhen told me about a nice new feature in GenBank that he's described in a piece for NCBI News . The NCBI taxonomy database now...

VertNet starts issue tracking using GitHub

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VertNet has announced that they have implemented issue tracking using GitHub . This is a really interesting development, as figuring out how...
Wednesday, January 15, 2014

What I'll be working on in 2014: knowledge graphs and Google forests

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More for my own benefit than anything else I've decided to list some of the things I plan to work on this year. If nothing else, it may ...
Thursday, January 09, 2014

Annotating GBIF: some thoughts

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Given that it's the start of a new year, and I have a short window before teaching kicks off in earnest (and I have to revise my phyloin...
Thursday, December 12, 2013

Guest post: response to "Putting GenBank Data on the Map"

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The following is a guest blog post by David Schindel and colleagues and is a response to the paper by Antonio Marques et al. in Science doi:...
Wednesday, December 04, 2013

Towards BioStor articles marked up using Journal Archiving Tag Set

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A while ago I posted BHL to PDF workflow which was a sketch of a work flow to generate clean, searchable PDFs from Biodiversity Heritage Li...
Thursday, November 21, 2013

GBIF, GitHub, and taxonomy (again)

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Quick notes on yet another attempt to marry the task of editing a taxonomic classification with versioning it in GitHub. The idea of dumping...
Wednesday, November 20, 2013

Reaction to taxonomic reactionaries

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There is a fairly scathing editorial in Nature [The new zoo. (2013). Nature, 503(7476), 311–312. doi:10.1038/503311b ] that reacts to a re...
Monday, November 11, 2013

Names and nomenclators: just do it already!

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Quick notes on taxonomic names (again). It's a continuing source of bafflement that the biodiversity community is making a dog's bre...
Wednesday, November 06, 2013

ZooKeys, GBIF, and GitHub: fixing Darwin Core Archives part 2

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Here's another example of a Darwin Core Archive that is "broken" such that GBIF is missing some information. GBIF data set A c...

GBIF and Github: fixing broken Darwin Core Archives

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Following on from Annotating and cleaning GBIF data: Darwin Core Archive, GitHub, ORCID, and DataCite here's a quick and dirty example ...