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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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GithubJavascriptJQueryMobileNatureInformatikEnglisch
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One thing I'm increasingly conscious of is that I've a lot of demos and toy projects hanging around and the code for most of these isn't readily available. So, I plan to clean these up and put them in GitHub so others can explore the code, and reuse it if they see fit.First up is the code to create a HTML+Javascript clone of Nature's iPhone app, as described in an earlier post.There's a live version of the clone here here.

Biodiversity InformaticsICZNIONOpen AccessSherbornInformatikEnglisch
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Here is my presentation from today's Anchoring Biodiversity Information: From Sherborn to the 21st century and beyond meeting. Open taxonomy View more presentations from Roderic PageAll the presentations will be posted online, along with podcasts of the audio. Meantime, presentations by Dave Remsen and Chris Freeland are already online.

ChallengeGeographyRDFTDWGInformatikEnglisch
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Quick final comment on the TDWG Challenge - what is RDF good for?. As I noted in the previous post, Olivier Rovellotti (@orovellotti) and Javier de la Torre (@jatorre) have produced some nice visualisations of the frog data set:Nice as these are, I can't help feeling that they actually help make my point about the current state of RDF in biodiversity informatics.

ChallengeConservation StatusDBpediaDOIFrogsInformatikEnglisch
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This is a follow up to my previous post TDWG Challenge - what is RDF good for? where I'm being, frankly, a pain in the arse, and asking why we bother with RDF? In many ways I'm not particularly anti-RDF, but it bothers me that there's a big disconnect between the reasons we are going down this route and how we are actually using RDF.

Bio2RDFCrossrefDOIGenbankIntegrationInformatikEnglisch
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Last month, feeling particularly grumpy, I fired off an email to the TDWG-TAG mailing list with the subject Lobbing grenades: a challenge . Here's the email:In the context of the TDWG meeting (happening as we speak and which I'm following via Twitter, hashtag #tdwg) Joel Sachs asked me whether I had any specific data in mind that could form the basis of a discussion. So, here goes.

Business ModelDeepDyveDigitisationITunesLong TailInformatikEnglisch
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Bit late, but I stumbled across DeepDyve, which provides rental access to scientific papers for as little as $0.99. The pitch to publishers is:Renting a paper means you get to read it online, but you can't print or download it, and access is time limited (unless you purchase the article outright). You can also purchase monthly plans (think Spotify for papers).It's an interesting model, and the interface looks nice.

AppleDesignIBookJoySteve JobsInformatikEnglisch
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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 FineInformatikEnglisch
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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 SpeciesTaxonomyWoRMSInformatikEnglisch
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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 FrancisInformatikEnglisch
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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.