Friday, September 26, 2008

Half-baked ideas. II. Degree of interest tree of NCBI taxonomy

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Among the many ways to display trees, degree of interest (DOI) trees strike me as one potentially useful way to display trees such as the NC...

Half-baked ideas. I. Wiki for taxonomy

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Next few weeks will be busy with term starting, kids visiting, and other commitments, so time to jot down some ideas. The first is to have ...
2 comments:
Wednesday, September 24, 2008

Displacement activity no. 37 - Wordle

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My delicious tags as a Wordle . In my defense I've not had nearly enough coffee today.
1 comment:
Friday, September 19, 2008

Challenge data

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Just to provide a sense of how much data I want to analyse for the Challenge , I have the XML, PDF, and images for 1687 articles from Molecu...

Postphylogenetics

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Last week I was at NESCent's 2008 Community Summit . As part of that meeting a few of us had a breakout group on "Biodiversity and...
Thursday, September 04, 2008

When ISSN's disappear, taking DOIs with them

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I've been using ISSN's ( International Standard Serial Number ) to uniquely identify journals, both to generate article identifiers,...
4 comments:
Wednesday, September 03, 2008

Hell is other people's data

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Starting to get serious about the Grand Challenge . First step is to parse the XML data Elsevier made available. Sadly this is only for Mol...
Friday, August 29, 2008

Turning Japanese: EUC-JP, UTF-8, and percent-encoding

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In case I forget how to do this, and as an example of how easy it is to get sucked into a black hole of programming micro-details, I spent a...
Tuesday, August 26, 2008

Perceptive Pixel Taxonomy Demo

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Found this while Googling. Demo by Perceptive Pixel of browsing the ITIS classification using their multi-touch technology. I want one...
2 comments:

Vince Smith wins 2008 Ebbe Nielsen Prize

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As spotted by dechronization , GBIF has made public that Vince Smith has won the 2008 Ebbe Nielsen Prize . The award "recognises a rese...
1 comment:
Saturday, August 23, 2008

Reasons text mining will fail. I. UTM Grid References and GenBank accession numbers

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OMG. Playing with extracting identifiers from text, I have a regular expression for GenBank accession numbers that looks something like this...
Thursday, August 21, 2008

Elsevier Grand Challenge

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Elsevier recently announced the 10 semi-finalists for their Grand Challenge . To my consternation, I'm one of them. I wrote a proposal e...
7 comments:
Wednesday, August 20, 2008

NCBI visualisations I - Genbank Timemap

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Time for some fun. In between some tedious text mining I've been meaning to explore some visualisations of NCBI. Here's the first, i...
2 comments:

ZooKeys, DOIs, Open Access, and RSS, but why?

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ZooKeys (ISSN 1313-2970) is a new journal for the rapid publication of taxonomic names, rather like Zootaxa . On first glance it has some n...
3 comments:
Monday, August 18, 2008

DOIs, the good news and the bad news

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The good news is that the merger of Blackwell's digital content with that of Wiley's has not affected the DOIs, which is exactly as...
2 comments:
Friday, August 15, 2008

Freebase Parallax

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Freebase Parallax is a very cool interface to Freebase . Freebase Parallax: A new way to browse and explore data from David Huynh on ...

DBpedia, and integrating taxonomy with the rest of the linked data world

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While biodiversity informatics putters along, generating loads of globally unique identifiers that nobody else uses, perhaps it's time t...
Thursday, August 14, 2008

BNCOD 2008 Workshop

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The proceedings of the BNCOD 2008 Workshop on "Biodiversity Informatics: challenges in modelling and managing biodiversity knowledge...
2 comments:
Tuesday, August 12, 2008

Dinosaurs and the Cretaceous Terrestrial Revolution

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Shameless plug. One of my former PhD students, Katie Davis, is second author on "Dinosaurs and the Cretaceous Terrestrial Revolution...
Thursday, August 07, 2008

Spida of Love

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Systematics makes The Colbert Report . The paper describing Aptostichus stephencolbertio by Jason Bond and Amy Stockman has been published...