Monday, January 25, 2016

iSpecies is back: mashing up species data

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A decade ago (OMG, that can't be right, an actual decade ago) I created "iSpecies", a simple little tool to mashup a variety o...
Wednesday, January 13, 2016

Surfacing the deep data of taxonomy

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My paper "Surfacing the deep data of taxonomy" (based on a presentation I gave in 2011) has appeared in print as part to a special...
Thursday, December 17, 2015

Will JSON, NoSQL, and graph databases save the Semantic Web?

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OK, so the title is pure click bait, but here's the thing. It seems to me that the Semantic Web as classically conceived (RDF/XML, SPARQ...
Wednesday, December 09, 2015

Visualising the difference between two taxonomic classifications

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It's a nice feeling when work that one did ages ago seems relevant again. Markus Döring has been working on a new backbone classificatio...
Tuesday, December 01, 2015

Frontiers of biodiversity informatics and modelling species distributions #GBIFfrontiers @AMNH videos

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For those of you who, like me, weren't at the "Frontiers Of Biodiversity Informatics and Modelling Species Distributions" held...

Guest post: 10 years of global biodiversity databases: are we there yet?

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This guest post by Tony Rees explores some of the themes from his recent talk 10 years of Global Biodiversity Databases: Are We There Yet? ...
Wednesday, November 18, 2015

Comments on "Widespread mistaken identity in tropical plant collections"

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Zoë A. Goodwin ( @Drypetes ) and collegagues have published a paper with a title guaranteed to get noticed: Goodwin, Z. A., Harris, D. J.,...
Wednesday, September 23, 2015

Visualising big phylogenies (yet again)

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Inspired in part by the release of the draft tree of life ( doi:10.1073/pnas.1423041112 by the Open Tree of Life, I've been revisiting ...
Friday, September 18, 2015

Towards an interactive web-based phylogeny editor (à la MacClade)

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Currently in classes where I teach the basics of tree building, we still fire up ancient iMacs, load up MacClade, and let the students have...
Thursday, September 17, 2015

On having multiple DOI registration agencies for the same journal

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On Friday I discovered that BHL has started issuing CrossRef DOIs for articles, starting with the journal Revue Suisse de Zoologie . The me...
Friday, September 11, 2015

Possible project: natural language queries, or answering "how many species are there?"

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Google knows how many species there are. More significantly, it knows what I mean when I type in "how many species are there". Wo...
Monday, September 07, 2015

Wikidata, Wikipedia, and #wikisci

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Last week I attended the Wikipedia Science Conference (hashtag: #wikisci ) at the Wellcome Trust in London. it was an interesting two days ...
Wednesday, September 02, 2015

Hypothes.is revisited: annotating articles in BioStor

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Over the weekend, out of the blue, Dan Whaley commented on an earlier blog post of mine ( Altmetrics, Disqus, GBIF, JSTOR, and annotating b...
Tuesday, September 01, 2015

Dark taxa, drones, and Dan Janzen: 6th International Barcode of Life Conference

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A little over a week ago I was at the 6th International Barcode of Life Conference , held at Guelph, Canada. It was my first barcoding conf...
Friday, August 14, 2015

Possible project: NameStream - a stream of new taxonomic names

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Yet another barely thought out project, although this one has some crude code . If some 16,000 new taxonomic names are published each year, ...

Possible project: A PubMed Central for taxonomy

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I need more time to sketch this out fully, but I think a case can be made for a taxonomy-centric (or, perhaps more usefully, a biodiversity...
Monday, August 10, 2015

Demo of full-text indexing of BHL using CouchDB hosted by Cloudant

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One of the limitations of the Biodiversity Heritage Library (BHL) is that, unlike say Google Books, its search functions are limited to sea...

Possible project: mapping authors to Wikipedia entries using lists of published works

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One of the less glamorous but necessary tasks of data cleaning is mapping "strings to things", that is, taking strings such as ...
Sunday, August 09, 2015

More Neo4J tests of GBIF taxonomy: Using IPNI to find objective synonyms

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Following on from Testing the GBIF taxonomy with the graph database Neo4J I've added a more complex test that relies on linking taxa to...

Possible project: #itaxonomist, combining taxonomic names, DOIs, and ORCID to measure taxonomic impact

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Imagine a web site where researchers can go, log in (easily) and get a list of all the species they have described (with pretty pictures and...