University of Glasgow

Roderic Page

![PlaceMark](http://lh3.ggpht.com/-2Qh_vEJA2nc/U_sHMisZTOI/AAAAAAAADg0/EfGJf_w3e0c/placeMark.jpg?imgmax=800 "placeMark.jpg"){border="0"
width="128" style="float:right;"}Note to self for upcoming discussion
with [JournalMap](http://www.journalmap.org).  
  
As of Monday August 25th, [BioStor](http://biostor.org) 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](http://biostor.org/reference/140883)
([doi:10.5479/si.23317515.134.1](http://dx.doi.org/10.5479/si.23317515.134.1)).  
  
The SQL for the queries is
[here](https://gist.github.com/rdmpage/8c2e2b85e3242f5f773d).


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.

Geotagging stats for BioStor

![Circle](http://lh5.ggpht.com/-q70lxecAnsA/U0ZTy2c_mdI/AAAAAAAADUM/G_KCvGXkHls/circle.png?imgmax=800 "circle.png"){border="0"
width="112" height="111" style="float:right;"}  
Following on from earlier posts on annotating biodiversity data
([Rethinking annotating biodiversity
data](http://iphylo.blogspot.com/2014/03/rethinking-annotating-biodiversity-data.html)
and [More on annotating biodiversity data: beyond sticky notes and
wikis](http://iphylo.blogspot.com/2014/04/more-on-annotating-biodiversity-data.html))
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](http://www.inaturalist.org/) observation editor). You can
play with this below or on [on
bl.ocks.org](http://bl.ocks.org/rdmpage/9934629), and the source code is
on GitHub <https://gist.github.com/rdmpage/9951904>.  
  

  
  


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.

User interface to edit a point location

![Square](http://lh3.ggpht.com/-CKCAl6Gx4p8/UxnYygQ_JoI/AAAAAAAADRo/M2cULI8YGjU/square.png?imgmax=800 "square.png"){border="0"
width="128" height="128" style="float:right;"}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](http://www.gbif.org/developer/maps) 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](https://gist.github.com/rdmpage/9411457), and you can see it live
above, and at <http://bl.ocks.org/rdmpage/9411457>.


As part of a project exploring GBIF data I've been playing with displaying GBIF data on Google Maps.

GBIF data overlayed on Google Maps

Following on from the [SVG
experiments](http://iphylo.blogspot.com/2012/12/svg-experiment.html)
I\'ve started to put some of the Javascript code for displaying
phylogenies on Github. Not a repository yet, but as
[gists](https://gist.github.com/), 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](https://gist.github.com/4224658) takes a Newick tree,
parses it and displays a tree. You can try it at
<https://bl.ocks.org/d/4224658/>.  
  
The [second gist](https://gist.github.com/4229068) 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](http://www.treebase.org) such as [tree
Tr57874](http://purl.org/phylo/treebase/phylows/tree/TB2:Tr57874?format=nexus).  
  
![Nexus](http://lh4.ggpht.com/-B_JL6Qw3HJ8/UMEjcu3ISvI/AAAAAAAACT4/h-m2j_wrNU8/nexus.png?imgmax=800 "nexus.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="550" height="441"}**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](http://architects.dzone.com/articles/javascript-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.

Messaggi di Rogue Scholar

Geotagging stats for BioStor

User interface to edit a point location

GBIF data overlayed on Google Maps

NEXUS parser and tree viewer in Javascript