Some notes to self about future directions for the "million DNA barcodes map" http://iphylo.org/~rpage/bold-map/. At the moment we have an interactive map that we can pan and zoom, and click on a marker to get a list of one or more barcodes at the location. We can also filter by major taxonomic group. Here are some ideas on what could be next. Search At the moment search is simply browsing the map.
A little over a week ago I was at the 6th International Barcode of Life Conference, held at Guelph, Canada. It was my first barcoding conference, and was quite an experience. Here are a few random thoughts. Attendees It was striking how diverse the conference crowd was. Apart from a few ageing systematists (including veterans of the cladistics wars), most people were young(ish), and from all over the world.
On a recent trip to the Natural History Museum, London, the subject of DNA barcoding came up, and I got the clear impression that people at the NHM thought classical DNA barcoding was pretty much irrelevant, given recent developments in sequencing technology. For example, why sequence just COI when you can use shotgun sequencing to get the whole mitogenome? I was a little taken aback, although this is a view that's getting some traction, e.g.
If we view biodiversity data as part of the "biodiversity knowledge graph" then specimens are a fairly central feature of that graph. I'm looking at ways to link specimens to sequences, taxa, publications, etc., and doing this across multiple data providers. Here are some rough notes on trying to model this in a simple way.
Following on from the previous post on putting GBIF data onto Google Maps, I'm now going to put DNA barcodes onto Google Maps. You can see the result at http://iphylo.org/~rpage/bold-map/, which displays around 1.2 million barcodes obtained from the International Barcode of Life Project (iBOL) releases.
The following is a guest blog post by David Schindel and colleagues and is a response to the paper by Antonio Marques et al. in Science doi:10.1126/science.341.6152.1341-a. Marques, Maronna and Collins (1) rightly call on the biodiversity research community to include latitude/longitude data in database and published records of natural history specimens.
Quick note to highlight the following publication: This paper outlines the methods used by the BOLD project to cluster sequences into "BINS", and touches on the issue of dark taxa (taxa that are in GenBank but which lack formal scientific names). Might be time to revisit the dark taxa idea, especially now that I've got a better handle on the taxonomic literature (see BioNames) where the names of at least some dark taxa may lurk.
Came across this paper recently: Despite QR Codes being uncool, there's something appealing about the idea of compressing a DNA barcode sequence into a small image.
Dark taxa have become even darker. NCBI has pulled the plug on large numbers of DNA barcode sequences that lack scientific names. For example, taxon Cyclopoida sp. BOLD:AAG9771 (tax_id 818059) now has a sparse page that has no associated sequences. From an earlier download of EMBL I know that this taxon is associated with at least 5 sequences, such as GU679674. But if you go to that sequence you get this: So the the sequence is hidden.
Given various discussions about identifiers, dark taxa, and DNA barcoding that have been swirling around the last few weeks, there's one notion that is starting to bug me more and more.