Geotagging stats for BioStor

Note to self for upcoming discussion with JournalMap.

As of Monday August 25th, BioStor has 106,617 articles comprising 1,484,050 BHL pages. From the full text for these articles, I have extracted 45,452 distinct localities (i.e., geotagged with latitude and longitude). 15,860 BHL pages in BioStor pages have at least one geotag, these pages belong to 5,675 BioStor articles.

In summary, BioStor has 5,675 full-text articles that are geotagged. The largest number of geotags for an article is 2,421, for Distribución geográfica de la fauna de anfibios del Uruguay (doi:10.5479/si.23317515.134.1).

The SQL for the queries is here.

User interface to edit a point location

Following on from earlier posts on annotating biodiversity data (Rethinking annotating biodiversity data and More on annotating biodiversity data: beyond sticky notes and wikis) I've started playing with user interfaces for editing data.

For example, here's a simple interface to edit the location of a specimen or observation (inspired by the iNaturalist observation editor). You can play with this below or on on bl.ocks.org, and the source code is on GitHub https://gist.github.com/rdmpage/9951904.

GBIF data overlayed on Google Maps

As part of a project exploring GBIF data I've been playing with displaying GBIF data on Google Maps. The GBIF portal doesn't use Google Maps, which is a pity because Google's terrain and satellite layers are much nicer than the layers used by GBIF (I gather there are issues with the level of traffic that GBIF receives is above the threshold at which Google starts charging for access).

But because the GBIF developers have a nice API it's pretty easy to put GBIF data on Google maps, like this (the map is live):



The source code for this map is available as a gist, and you can see it live above, and at http://bl.ocks.org/rdmpage/9411457.

NEXUS parser and tree viewer in Javascript

Following on from the SVG experiments I've started to put some of the Javascript code for displaying phylogenies on Github. Not a repository yet, but as gists, little snippets of code. Mike Bostock has created http://bl.ocks.org/ which makes it possible to host gists as working examples, so you can play with the code "live".

The first gist takes a Newick tree, parses it and displays a tree. You can try it at https://bl.ocks.org/d/4224658/.

The second gist takes a basic NEXUS file containing a TREES block and displays a tree (try it at http://bl.ocks.org/d/4229068/ ). You can grab examples NEXUS tree files from TreeBASE such as tree Tr57874.

Why am I doing this?
Apart from "because it's fun" there are two reasons. The first is that I want a simple way to display phylogenetic trees in web pages, and doing this entirely in the web browser (Javascript parses the tree and renders it in SVG) saves me having to code this on my server. Being able to do this in the browser opens up the opportunity to embed tree descriptions in HTML, for example, and have the browser render the tree. This means the same web page can have machine-readable data (the tree description) but also generate a nice tree for the reader. As an aside, it also shows that TreeBASE could display perfectly good, interactive trees without resorting to a Java appelet.

The other reason is that the web seems to be moving to Javascript as the default language, and JSON as the standard data format. Instead of large chunks of "middleware" (written in a scripting language such as Perl, PHP, or, gack, Java) which is responsible for talking to databases on the server and sending static HTML to the web browser, we now have browsers that can support sophisticated, interactive interfaces built using HTML and Javascript. On the server side we have databases that speak HTTP (essentially removing the need for middleware), store JSON, and use Javascript as their programming language (e.g., CouchDB). In short, it's Javascript, Javascript, everywhere.