Half-baked idea time. Thinking about projects such as the Earth Microbiome Project and Genomic Observatories, the recent GBIC2012 meeting (I'm still digesting that meeting), and mulling over the book A Vast Machine I keep thinking about the possible parallels between climate science and biodiversity science.

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.

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?

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

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.

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.

I'm back from Copenhagen and GBIC2012.

For a current project I'm currently working I show organism distributions using data from GBIF, and I display that data on a map that uses the equirectangular projection.

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.

In any discussion of data gathering or data cleaning the term "crowdsourcing" inevitably comes up. A example where this approach has been successful is the Encyclopedia of Life's Flickr pool, where Flickr users upload images that are harvested by EOL.

Just for future reference: