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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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Informática y Ciencias de la InformaciónInglés
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It’s been a while since I’ve posted on iPhylo. Since returning from a fun and productive time in Australia there have been a bunch of professional and personal things that have needed attending too. In amongst all this I attended Biodiversity Next in Leiden, a large (by biodiversity informatics standards) conference with the tag line "Building a global infrastructure for biodiversity data.

FreebaseHaystackKnowledge GraphLSIDParallaxInformática y Ciencias de la InformaciónInglés
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While working with linked data and ways to explore and visualise information, I keep coming back to the Haystack project, which is now over a decade old. Among the tools developed was the Haystack application, which enabled a user to explore all sorts of structured data. Below is a screen shot of Haystack showing a sequence for Homo sapiens cyclin T1 (CCNT1), transcript variant a, mRNA.

ALAGithubLinkingMelbourneORCIDInformática y Ciencias de la InformaciónInglés
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I'm doing some work with Nicole Kearney (@nicolekearney) at the Melbourne Museum on the general theme of "linking all the things". It's the end of the first full week we've had, so here's a quick update of what we've been up to. Brainstorming The things we want to do are being captured as a project on GitHub. This is where we come up with ideas, comment on then, then try to figure out which ones can be done.

DggsFrankenplaceGridSearchInformática y Ciencias de la InformaciónInglés
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Quick note on Frankenplace, a cool search tool that displays the geographic distribution of documents that match the user's query as a heatmap. Details of how the tool works are given in: At the heart of the method is a discrete global grid that divides the world up into small areas of the same size.

DBpediaKnowledge GraphNatural LanguageWikidataWikipediaInformática y Ciencias de la InformaciónInglés
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I've tweaked Ozymandias to now include short natural language summaries (snippets) for various taxa. This makes the output a little more friendly and informative. For example, here's a snippet from the page on Cephalodesmius , a dung beetle that makes its own dung. These snippets come from Wikipedia, well actually, from the DBpedia project.

Informática y Ciencias de la InformaciónInglés
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My paper "Ozymandias: A biodiversity knowledge graph" has been published in PeerJ https://doi.org/10.7717/peerj.6739 The paper describes my entry in GBIF's 2018 Ebbe Nielsen Challenge, which you can explore here. I tweeted about its publication yesterday, and got some interesting responses (and lots of retweets, thanks to everyone for those). Carl Boettiger (@cboettig) asked where the triples were, as did Kingsley Uyi Idehen (@kidehen). Doh!

Informática y Ciencias de la InformaciónInglés
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One of the things the biodiversity informatics community has struggled to do is come up with a list of all natural history collections (Taylor, 2016). Most recently GrBio attempted to do this, and appealed for community help to curate the list (Schindel et al., 2016), but this did not emerge, and at the time of writing GrBio is moribund.

ChallengeKnowledge GraphOzymandiasInformática y Ciencias de la InformaciónInglés
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I've written up my entry for the 2018 GBIF Challenge ("Ozymandias") and posted a preprint on Biorxiv (https://www.biorxiv.org/content/early/2018/12/04/485854). The DOI is https://doi.org/10.1101/485854 which, last time I checked, still needs to be registered. The abstract appears below. I'll let the preprint sit there for a little while before I summon the enthusiasm to revisit it, tidy it up, and submit it for publication.

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There's a slow-burning discussion on taxonomic concepts on Github that I am half participating in. As seems inevitable in any discussion of taxonomy, there's a lot of floundering about given that there's lots of jargon - much of it used in different ways by different people - and people are coming at the problem from different perspectives. In one sense, taxonomy is pretty straightforward.