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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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Quick thoughts on the recent announcement by figshare and F1000 about the new journals being launched on the F1000 Research site. The articles being published have data sets embedded as figshare widgets in the body of the text, instead of being, say, a static table. For example, the article: has a widget that looks like this: You can interact with this widget to view the data.

Published

Was going to post this as a comment on the BHL blog but they use Blogger's native comment system, which is horrible, and it refused to accept my comment (yes, yes, I'm sure it did that on grounds of taste). I read the recent post Building a BHL Africa and couldn't believe my eyes when I read the following: CDs! Really?

Published

Playing with some sequence data I found numerous Plasmodium sequences from the following paper: These sequences (e.g., U43145) give the host as Thamnomys rutilans . You'd think it would be fairly easy to learn more about this animal, given that it hosts a relative of the cause of malaria in humans, and indeed there are a number of biomedical papers that come up in Google, e.g.: Google also tells me that Thamnomys

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The following is a first for iPhylo, a guest post by Bob Mesibov. Rod Page introduced 'dark taxa' here on iPhylo in April 2011. He wrote: Rod suggested that 'quite a lot' of biology can be done without taxonomic names. For the dark taxa in GenBank, that might well mean doing biology without organisms – a surprising thought if you're a whole-organism biologist.

Published

Quick note that Morgan Jackson (@BioInFocus) has written nice blog post Citations, Social Media & Science inspired by the fact that the following paper: Kwong, S., Srivathsan, A., & Meier, R. (2012). An update on DNA barcoding: low species coverage and numerous unidentified sequences. Cladistics, no–no. doi:10.1111/j.1096-0031.2012.00408.x cites my "Dark taxa" in the body of the text but not in the list of literature cited.

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Next week I'm in Copenhagen for GBIC, the Global Biodiversity Informatics Conference. The goal of the conference is to: The collaboration referred to is the agreement to mobilise data and informatics capability to met the Aichi Biodiversity Targets. I confess I have mixed feelings about the upcoming meeting. There will be something like 100 people attending the conference, with backgrounds ranging from pure science to intergovernmental policy.