Friday, January 24, 2014

NCBI taxonomy database now shows type material

›
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

›
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

›
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

›
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"

›
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

›
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)

›
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

›
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!

›
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

›
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

›
Following on from Annotating and cleaning GBIF data: Darwin Core Archive, GitHub, ORCID, and DataCite here's a quick and dirty example ...
Saturday, November 02, 2013

Catalogue of Life and LSIDs: a catalogue of fail

›
I have a love/hate relationship with the Catalogue of Life (CoL). On the one hand, it's an impressive achievement to have persuaded tax...
Friday, November 01, 2013

Annotating and cleaning GBIF data: Darwin Core Archive, GitHub, ORCID, and DataCite

›
This is a quick sketch of a way to combine existing tools to help clean and annotate data in GBIF, particularly (but not exclusively) occurr...
Tuesday, October 15, 2013

What can Global Biodiversity Information Facility (GBIF) do for you?

›
I've recently been appointed Chair of the Science Committee of the Global Biodiversity Information Facility (GBIF) http://www.gbif.org ...
Tuesday, October 08, 2013

Which taxonomic journals should be digitised next?

›
One reason I was able to build BioNames is because a significant fraction of the taxonomic literature for animals is now online, either due...