University of Glasgow

Roderic Page

Following on from my previous [post about
Wikispecies](http://iphylo.blogspot.com/2009/08/wikispecies-is-not-database.html)
(which generated [some discussion on
TAXACOM](http://markmail.org/thread/qvdrqwgm4obge6ra)) I\'ve played some
more with Wikispecies.  
  
AS a first step I\'ve added a Wikispecies RSS feed to my list of [RSS
feeds](http://bioguid.info/rss). This feed takes the [original
Wikispecies RSS feed for new
pages](http://species.wikimedia.org/w/index.php?title=Special:NewPages&limit=100&feed=rss)
(generated by the page **Special:NewPages**) and tries to extract some
details before reformatting it as an ATOM feed. Specifically, I extract
GUIDs such as IPNI and Index Fungorum identifiers, bibliographic
references (which I will later parse to try and extract identifiers such
as DOIs), and latitude and longitude if the Wikispecies page has type
locality information. Having the later means that the RSS feed can be
displayed as a map (Google Maps can take a RSS feed with geotagged items
and display it on a map for you).  
  
The map below is live, so it will show any geotagged items in the
current Wikispecies feed.  
  

::: {.iframe}
::: {#mapDiv}
:::
:::

  
[[View Larger
Map](http://maps.google.com/maps?f=q&source=embed&hl=en&geocode=&q=http:%2F%2Fbioguid.info%2Frss%2Fwikispecies.php&ie=UTF8&ll=-1.533335,37.41665&spn=3.76667,5.1333&t=p){style="color:#0000FF;text-align:left"}]{.small}  
  
  


Following on from my previous post about Wikispecies (which generated some discussion on TAXACOM) I've played some more with Wikispecies. AS a first step I've added a Wikispecies RSS feed to my list of RSS feeds. This feed takes the original Wikispecies RSS feed for new pages (generated by the page
<strong>
 Special:NewPages
</strong>
) and tries to extract some details before reformatting it as an ATOM feed.

Wikispecies RSS feed

[e-Biosphere \'09](http://www.e-biosphere09.org/) kicks off next week,
and features the
[challenge](http://www.e-biosphere09.org/page/30/the-e-biosphere-09-informatics-challenge):  

> Prepare and present **a real-time demonstration** during the days of
> the Conference of the capabilities in your community of practice to
> discover, disseminate, integrate, and explore new biodiversity-related
> data by:  
>
> - Capturing data in private and public databases;
> - Conducting quality assurance on the data by automated validation
>   and/or peer review;
> - Indexing, linking and/or automatically submitting the new data
>   records to other relevant databases;
> - Integrating the data with other databases and data streams;
> - Making these data available to relevant audiences;
> - Make the data and links to the data widely accessible; and
> - Offering interfaces for users to query or explore the data.

  
  
Originally I planned to enter the
[wiki](http://iphylo.blogspot.com/search?q=wiki) project I\'ve been
working on for a while, but time was running out and the deadline was
too ambitious. Hence, I switched to [thinking about
RSS](http://iphylo.blogspot.com/2009/05/integrating-and-displaying-data-using.html)
feeds. The idea was to first create a set of RSS feeds for sources that
lack them, which I\'ve been doing over at <http://bioguid.info/rss>,
then integrate these feeds in a useful way. For example, the feeds would
include images from Flickr (such as [EOL\'s
pool](http://www.flickr.com/groups/encyclopedia_of_life/pool/)),
geotagged sequences from GenBank, the latest papers from
[*Zootaxa*](http://www.mapress.com/zootaxa/content.html), and new names
from [uBio](http://www.ubio.org/index.php?pagename=ubioRSS) (I\'d hoped
to include [ION](http://www.organismnames.com/) as well, but they\'ve
been spectacularly hacked).  
  
After playing with triple stores and SPARQL (incompatible vocabularies
and multiple identifiers rather buggers this approach), and
visualisations based on Google Maps (building on my [swine flu
timemap](http://iphylo.blogspot.com/2009/04/h1n1-swine-flu-timemap.html)),
it dawned on me what I really needed was an eye-catching way of
displaying geotagged, timestamped information, just like David Troy\'s
wonderful [twittervision](http://twittervision.com/) and
[flickrvision.com](http://flickrvision.com). In particular, David took
the [Poly9 Globe](http://globe.poly9.com/) and added Twitter and Flickr
feeds (see [twittervision 3D](http://twittervision.com/maps/show_3d) and
[flickrvision 3D](http://flickrvision.com/maps/show_3d). So, I took
hacked David\'s code and created this, which you can view at
<http://bioguid.info/ebio09/www/3d/>:  
  

  
  
It\'s a lot easier to simply look at it rather than describe what it
does, but here\'s a quick sketch of what\'s under the hood.  
  
[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjev0H6rcpbZP-xSc_8lbTIv-u2jtItU7UhHwqGKr8w6jlxcmJGpSG-KumXJhSR9Ow2Fnxszi3ijzuyn1-DsvIIRh65xWFQsPvFm7VSK2wKaKROzNMoiFxT1iPy5csMnwNwyZBj/s200/geo_logo_medium.jpg){#BLOGGER_PHOTO_ID_5340273170678722322
style="float:right; margin:0 0 10px 10px;cursor:pointer; cursor:hand;width: 200px; height: 67px;"
border="0"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjev0H6rcpbZP-xSc_8lbTIv-u2jtItU7UhHwqGKr8w6jlxcmJGpSG-KumXJhSR9Ow2Fnxszi3ijzuyn1-DsvIIRh65xWFQsPvFm7VSK2wKaKROzNMoiFxT1iPy5csMnwNwyZBj/s1600-h/geo_logo_medium.jpg){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}Firstly,
I take RSS feeds, either the raw geoFeed from Flickr, or from
<http://bioguid.info/rss>. The bioGUID feeds include the latest papers
in *Zootaxa* (most new animal species are described in this journal), a
modified version of uBio\'s new names feed, and a feed of the latest,
geotagged sequences in GenBank (I\'d hoped to use only DNA barcodes, but
it turns out rather few barcode sequences are geotagged, and few have
the \"BARCODE\" keyword). The Flickr feeds are simple to handle because
they include locality information (including latitude, longitude, and
Yahoo [Where-on-Earth Identifiers
(WOEIDs)](http://www.ygeoblog.com/tag/woeids/)). Similarly, the [GenBank
feed](http://bioguid.info/rss/genbank.php) I created has latitude and
longitudes (although extracting this [isn\'t always as straightforward
as it should be](http://iphylo.blogspot.com/2008/01/metacrap.html)).
Other feeds require more processing. The uBio feed already has taxonomic
names, but no geotagging, so I use services from [Yahoo!
GeoPlanet™](http://developer.yahoo.com/geo/geoplanet/) to find
localities from article titles. For the [Zootaxa
feed](http://bioguid.info/rss/zootaxa.php) that I created I use uBio\'s
[SOAP service](http://www.ubio.org/index.php?pagename=soap_tools) to
extract taxonomic names, and Yahoo! GeoPlanet™ to extract localities.  
  
[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiUd7KMJ36C2vL5ZZ74_z_1k9bOWL-Ura9LoNT3f8Fedi-IUozZJ1s6_X5PQfWJGrBGUr__zokjER4GWgEhRd0VsYKyt93_ljKQ5qxb532g7SlvDUdNa-jNMAqBrxlfrBkO0jhT/s400/copepod.png){#BLOGGER_PHOTO_ID_5340266936034990706
style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 359px;"
border="0"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiUd7KMJ36C2vL5ZZ74_z_1k9bOWL-Ura9LoNT3f8Fedi-IUozZJ1s6_X5PQfWJGrBGUr__zokjER4GWgEhRd0VsYKyt93_ljKQ5qxb532g7SlvDUdNa-jNMAqBrxlfrBkO0jhT/s1600-h/copepod.png){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}  
I\'ve tried to create a useful display popup. For Zootaxa papers you get
a thumbnail of the paper, and where possible an icon of the taxonomic
group the paper talks about (the presence of this icon depends on the
success of uBio\'s taxonomic name finding service, the Catalogue of Life
having the same name, and my having a suitable icon). The example above
shows a paper about copepods. Other papers have a icon for the journal
(again, a function of my being able to determine the journal ISSN and
having a suitable icon). Flickr images simply display a thumbnail of the
image.  
  
What does it all mean? Well, I could say all sorts of things about
integration and mash-ups but, dammit, it\'s pretty. I think it\'s a fun
way to see just what is happening in digital biodiversity. I\'ve
deliberately limited the demo to items that came online in the month of
May, and I\'ll be adding items during the conference (June 1-3rd in
London). For example, if any more papers appear in *Zootaxa*, or in the
uBio feeds I\'ll add those. If anybody uploads geotagged photos to
EOL\'s Flickr group, I\'ll grab those as well. It\'s still a bit crude,
but it shows some of the potential of bringing things together, coupled
with a nice visualisation. I welcome any feedback.


e-Biosphere '09 kicks off next week, and features the challenge:  Originally I planned to enter the wiki project I've been working on for a while, but time was running out and the deadline was too ambitious. Hence, I switched to thinking about RSS feeds. The idea was to first create a set of RSS feeds for sources that lack them, which I've been doing over at http://bioguid.info/rss, then integrate these feeds in a useful way.

e-Biosphere Challenge: visualising biodiversity digitisation in real time

Tweets from [@ attilacsordas](https://twitter.com/attilacsordas) and
[@stew](https://twitter.com/stew) alerted me to the [Google Map of the
H1N1 Swine Flu
outbreak](http://maps.google.com/maps/ms?ie=UTF8&hl=en&t=p&msa=0&msid=106484775090296685271.0004681a37b713f6b5950&ll=32.639375,-110.390625&spn=15.738151,25.488281&z=5)
by
[niman](http://maps.google.com/maps/user?uid=114692004255934127817&hl=en).  
  
Ryan Schenk
[commented](http://twitter.com/plasticvicar/status/1620517548): \"It\'d
be a million times more useful if that map was hooked into a timeline so
you could see the spread.\", which inspired me to knock together a
[timemap of swine flu](http://bit.ly/qasp4). The timemap takes the RSS
feed from niman\'s map and generates a timemap using Nick Rabinowitz\'s
[Timemap](http://code.google.com/p/timemap/) library.  
  
[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEheFHyHCkiB3eG1VINZGaMi1A_kTOFXCM9LMDTO0eCfMyOupAy08kt1T7I9_rPsFXMfOKJzazgK7Fu0IWlB_VxZOe60ZUMnp-YxTxSjVPVdZX_6V3-XNY34-rrzUYUxb96paFTn/s400/flu.png){#BLOGGER_PHOTO_ID_5329047124150665314
style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 292px;"
border="0"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEheFHyHCkiB3eG1VINZGaMi1A_kTOFXCM9LMDTO0eCfMyOupAy08kt1T7I9_rPsFXMfOKJzazgK7Fu0IWlB_VxZOe60ZUMnp-YxTxSjVPVdZX_6V3-XNY34-rrzUYUxb96paFTn/s1600-h/flu.png){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}  
  
**Gotcha**  
Although in principle this should have been a trivial exercise (cutting
and pasting into [existing
examples](http://iphylo.blogspot.com/2008/08/ncbi-visualisations-i-genbank-timemap.html)),
it wasn\'t quite so straightforward. The Google Maps RSS feed is a
[GeoRSS](http://georss.org/) feed, but initially I couldn\'t get Timemap
to accept it. The contents of the tag in the Google Maps feed looks like
this:  

``` {style="border:1px solid rgb(199,207,213);margin: 20px 0px; padding: 15px; background: rgb(241,245,249);"}
    
      33.041477 -116.894531
    
```

  
Turns out there\'s a minor bug in the file
[timemap.js](http://code.google.com/p/timemap/source/browse/trunk/timemap.js),
which I fixed by adding `coords= TimeMap.trim(coords);` before [line
1369](http://code.google.com/p/timemap/source/browse/trunk/timemap.js#1369).
The contents of the taginclude leading white space, and because
timemap.js splits the latitude and longitude using whitespace, Google\'s
feed breaks the code.  
  
**Postscript**  
Nick Rabinowitz has [fixed this
bug](http://iphylo.blogspot.com/2009/04/h1n1-swine-flu-timemap.html?showComment=1240768920000#c1962777343550315091).


Tweets from @ attilacsordas and @stew alerted me to the Google Map of the H1N1 Swine Flu outbreak by niman. Ryan Schenk commented: "It'd be a million times more useful if that map was hooked into a timeline so you could see the spread.", which inspired me to knock together a timemap of swine flu. The timemap takes the RSS feed from niman's map and generates a timemap using Nick Rabinowitz's Timemap library.

Messaggi di Rogue Scholar

Wikispecies RSS feed

e-Biosphere Challenge: visualising biodiversity digitisation in real time

H1N1 Swine Flu TimeMap