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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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Scienze informatiche e dell'informazioneInglese
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Reading the GitHub issue Define objective rules for taxon concept identity referred to by Markus Döring in a comment on a previous post, I'm once again struck by the unholy mess generated by any discussion of "taxonomic concepts". The sense of déjà vu is overwhelming.

Scienze informatiche e dell'informazioneInglese
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Following on from my earlier post ("Taxonomic concepts for dummies"), Beckett Sterner commented: iNaturalist is interesting, but I'm not convinced that it is internally consistent. As a quick rule of thumb, I'm looking for patterns of how name changes relate to taxon identifier changes.

ChallengeDNA BarcodingGBIFScienze informatiche e dell'informazioneInglese
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Motivated by the 2020 Ebbe Nielsen Challenge I've put together an interactive DNA barcode browser. The app is live at https://dna-barcode-browser.herokuapp.com. A naturalist from the 19th century would find little in GBIF that they weren’t familiar with. We have species in a Linnean hierarchy, their distributions plotted on a map.

Scienze informatiche e dell'informazioneInglese
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[Work in progress] The "dummy" in this case is me. I'm trying to make sense of how to model taxa, especially in the context of linked data, and projects such as Wikidata where there is uncertainty over just what a taxon in Wikidata actually represents. There is also ongoing work by the TDWG Taxon Names and Concepts Interest Group. This is all very rough and I'm still working on this, but here goes.

Scienze informatiche e dell'informazioneInglese
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This morning, as part of a webinar on persistent identifiers, I gave a live demo of a little toy to demonstrate linking together museum and herbaria specimens with publications that use those specimens. A video of an earlier run through of the demo appears below, for background on this demo see Diddling with semantic data: linking natural history collections to the scientific literature.

Scienze informatiche e dell'informazioneInglese
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The following is a guest post by Bob Mesibov. The first Darwin Core Million closed on 31 March with no winner. Since I'm seeing better datasets this year in my auditing work for Pensoft, I've decided to run the competition every six months. Missed the first Darwin Core Million and don't know what it's about? Don't get too excited by the word "million". It refers to the number of data items in a Darwin Core occurrences table, not to the prize!

FigShareImpact FactorMetricsZootaxaScienze informatiche e dell'informazioneInglese
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So this happened: Zootaxa is a hugely important journal in animal taxonomy: On one hand one could argue that impact factor is a bad way to measure academic impact, so it's tempting to say this simply reflects a poor metric that is controlled by a commercial company using data that is not open.

IdentifiersPLoSTaxon ConceptsTaxonomic DatabasesTaxonomyScienze informatiche e dell'informazioneInglese
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Garnett et al. recently published a paper in PLoS Biology that starts with the sentence "Lists of species matter": This paper (one of a forthcoming series) is pretty much the kind of paper I try and avoid reading.

Scienze informatiche e dell'informazioneInglese
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A couple of weeks ago I was grumpy on the Internet (no, really) and complained about museum websites and how their pages often lacked vital metadata tags (such as rel=canonical or Facebook Open Graph tags). This got a response: Vince's lovely line "diddle with semantic data" is the inspiration for the title of this post, in which I describe a tool to display links across datasets, such as museum specimens and scientific publications.