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iPhylo

Rants, raves (and occasionally considered opinions) on phyloinformatics, taxonomy, and biodiversity informatics. For more ranty and less considered opinions, see my Twitter feed.ISSN 2051-8188. Written content on this site is licensed under a Creative Commons Attribution 4.0 International license.
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AppleDesignIBookJoySteve JobsComputer and Information Sciences
Published

In light of today's news here's my favourite Mac, the original iBook.In many ways, it wasn't the machine itself so grabbed me (cool as it was), it was the experience of unpacking it when it arrived in my office over a decade ago. In the box with the computer and the mains cord was a disc about the size of a hockey puck (on the right in the image above). I looked at it and wondered what on Earth it was.

TaxonomistsTaxonomyWe Feel FineComputer and Information Sciences
Published

Following on from the last post How many species are there, and why do we get two very different answers from same data? another interesting paper has appeared in TREE:The paper analyses the "ecology and social habits of taxonomists" and concludes:Queue flame war on TAXACOM, no doubt, but it's a refreshing conclusion, and it's based on actual data. Here I declare an interest.

Biodiversity InformaticsCatalogue Of LifeNumber Of SpeciesTaxonomyWoRMSComputer and Information Sciences
Published

Two papers estimating the total number of species have recently been published, one in the open access journal PLoS Biology :the second in Systematic Biology (which has an open access option but the authors didn't use it for this article): The first paper has gained a lot of attention, in part because Jonathan Eisen Bacteria &

AtyponCrossrefDOIFailTaylor And FrancisComputer and Information Sciences
Published

DOIs are meant to be the gold standard in bibliographic identifier for article. They are not supposed to break. Yet some publishers seem to struggle to get them to work. In the past I've grumbled about BioOne, Wiley, and others as cuplrits with broken or duplicate or disappearing DOIs.Today's source of frustration is Taylor and Francis Online.

CiNiiCrossrefLinked DataMetadataRDFComputer and Information Sciences
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OK, a bit of hyperbole in the morning. One of the goals of RDF is to create the Semantic Web, an interwoven network of data seamlessly linked by shared identifiers and shared vocabularies. Everyone uses the same identifiers for the same things, and when they describe these things they use the same terms. Simples. Of course, the reality is somewhat different.

CrossrefDOIEntomologica ScandinavicaGraphvizInsect Systematics And EvolutionComputer and Information Sciences
Published

I've been spending a lot of time recently mapping bibliographic citations for taxonomic names to digital identifiers (such as DOIs). This is tedious work at the best of times (despite lots of automation), but it is not helped but the somewhat Orwellian practices of some publishers. Occasionally when an established journal gets renamed the publisher retrospectively applies that name to the previous journal.

Biodiversity InformaticsCharles SherbonNHMSpeakingTaxonomyComputer and Information Sciences
Published

Charles Davies Sherborn, the Natural History Museum's 'magpie with a card-index mind’Next month I'll be speaking in London at The Natural History Museum at a one day event Anchoring Biodiversity Information: From Sherborn to the 21st century and beyond.

EOLSocial MediaTaggingComputer and Information Sciences
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The Encylopedia of Life (EOL) has been relaunched, with a new look and much social media funkiness. I've been something of an EOL sceptic, but looking at the new site I think I can see what EOL is for. Ironically, it's not really about E. O. Wilson's original vision (doi:10.1016/S0169-5347(02)00040-X:We still lack a decent database that does this.

DuplicationErrorMatchingMendeleyMergingComputer and Information Sciences
Published

Browsing Mendeley I found the following record: http://www.mendeley.com/research/description-larva/. This URL is for a paperwhich apparently has the DOI doi:10.1645/GE-2580.1. This is strange because Zootaxa doesn't have DOIs. The DOI given resolves to a paper in the Journal of Parasitology :Now, this paper has it's own record in Mendeley.OK, so this is weird..., but it gets weirder.

BioStorCitationCitation MatchingMatchingMetadataComputer and Information Sciences
Published

Some quick half-baked thoughts on citation matching. One of the things I'd really like to add to BioStor is the ability to parse article text and extract the list of literature cited.

APIBHLBioStorFlickrInterfaceComputer and Information Sciences
Published

Following on from my previous post on BHL apps and a Twitter discussion in which I appealed for a "sexier" interface for BHL (to which @elywreplied that is what BHL Australia were trying to do), here are some further thoughts on improving BHL's web interface. Build a new interface A fun project would be to create a BHL website clone using just the BHL API.