Mapping evolutionary biology: @evoldir and #ProjectEvoMap

Robert M. Griffin (@GriffinEvo) has launched ProjectEvoMap. Rob explains:

I have decided this week to try to create a resource where evolutionary
biologists can find info on labs and groups from all around the world. I
have created a collaborative Google map online which evolutionary biology
research groups can pin their labs to with a brief description of their
interests. Others can then browse the map to look for labs in specific
areas – for example, if someone wants to find suitable labs in their
current country for work they can see all the labs in that area, likewise
anyone looking for work in a specific region or who needs access to labs
while on fieldwork can look for nearby groups which may be able to help.

Below is a screen shot of part of the map. If you're working on evolutionary biology now is your chance to literally put your lab on the map.


In parallel I'm experimenting with adding a map to the venerable EvolDir mailing list, for which I run a twitter stream (@evoldir). Using some terribly crude code to extract what looks like an address from EvolDir posts, then calling Google's Geocoding API results in a map of recent posts. You can see the live map at http://bioguid.info/services/evoldir/. This service compliments Rob's by giving a sense of current activity in the community (e.g., conferences, courses, jobs).

Deep zooming a large 2D tree

Here's a quick demo of a 2D large tree viewer that I'm working on. The aim is to provide a simple way to view and navigate very large trees (such as the NCBI classification) in a web browser using just HTML and Javascript. At the moment this is simply a viewer, but the goal is to add the ability to show "tracks" like a genome browser. For example, you could imagine columns appearing to the right of the tree showing you whether there are phylogenies available for these taxa in TreeBASE, images from Wikipedia, sparklines for sequencing activity over time, etc. I'll blog some more on the implementation details when I get the chance, but it's pretty straightforward. Image tiles are generated from SVG images of tree using ImageMagick, labelling is applied on the fly using GIS-style queries to a MySQL database that holds the "world coordinates" of the nodes in the tree (see discussion of world coordinates on Google's Map API pages), and the zooming and tile fetching is based on Michal Migurski's Giant-Ass Image Viewer. Once I've tidied up a few things I'll put up a live demo so people can play with it.

Deep tree zooming from Roderic Page on Vimeo.

Viewing scientific articles on the iPad: browsing articles

In previous articles I've looked at how various apps display scientific articles. The apps I looked at were:

• PLoS Reader
• Nature
• Papers
• Mendeley

So, where next? As Ian Mulvany noted in a comment on an earlier post, I haven't attempted to summarise the best user interface metaphors for navigation. Rather than try and do that in the abstract, I'd like to create some prototypes to play with various ideas. The Sencha Touch framework looks a good place to start. It's web-based, so things can be prototyped rapidly (I'm not going to learn Objective C anytime soon). There's a moderately steep learning curve, unless you've written a lot of Javascript (I've done some, but not a lot), but it seems to offer a lot of functionality. Another advantage of developing a web app is that it keeps the focus on making the content accessible across devices, and using the web as the means to display and interact with content.

Then there is also the issue (in addition to displaying an individual article) of how to browse and find articles to view. Here are some possibilities.

Publisher's stream
Apps such as the Nature app and the PLos Reader provide you with a stream of articles from a single publisher. This is obviously a bit limiting for the reader, but might have some advantages if the publisher has specifically enhanced their content for devices such as the iPad.

Personal library
Apps such as Mendeley and Papers provide articles from your personal library. These are papers you care about, and one you may make active use of.

Social
Social readers such as Flipboard show the power of bringing together in one place content derived from social streams, such as Twitter and Facebook, as well as curated sources and publisher streams. Mendeley and other social bookmarking services (e.g., CiteULike, Connotea) could be used to provide social similar streams of papers for an article viewer. Here the goal is probably to find out what papers people you know find interesting.

Spatial
In an earlier post I used a map to explore papers in my BioStor archive. This would be an obvious thing to add to an iPad app, especially as the iPad knows where you are. Hence, you could imagine browsing papers about areas that are near you, or perhaps by authors near you. This would be useful if, say, you wanted to know about ecological or health studies of the area you live in. If the geographic search was for people rather than papers, you could easily discovering what kind of research is published by universities or other research bodies that are near your current location.

Of course, Earth is not the only thing we can explore spatially. Google maps can display other bodies in the solar system, (e.g., Mars), as well as the night sky. Imagine being interested in astronomy and being able to browse papers about specific planetary or stellar objects. Likewise, genomes can be browsed using Google maps-inspired browsers (e.g., jBrowse), so we could have an app where you could easily retrieve articles about a particular gene or other region of a genome.

Categories
Another way to browse content is by topic. Classifying knowledge into categories is somewhat fraught, but there are some obvious wasy this could be useful. A biologist might want to navigate content by taxonomic group, particularly if they want to browse through the 1000's of articles published in a journal such as Zootaxa (hence my experiments on browsing EOL). Of course, a tree is not the only way to navigate hierarchical content. Treemaps are another example, and I've played with various versions in the past (see here and here).



I have a love-hate relationship with treemaps, but some of the most interesting work I've seen on treemaps has been motivated by displaying information on small screens, e.g. "Using treemaps to visualize threaded discussion forums on PDAs" (doi:10.1145/1056808.1056915).

Summary
These notes list some of the more obvious ways to browse a collection of articles. It would be fun to explore these (and other approaches) in parallel with thinking about how to display the actual articles. These two issues are related, in the sense that the more metadata we can extract from the articles (such as keywords, taxonomic names and other named entities, geographic localities, etc.) the richer the possibilities for finding our way through those articles.

Browsing a digital library using a map

Every so often I revisit the idea of browsing a collection of documents (or specimens, or phylogenies) geographically. It's one thing to display a map of localities for single document (as I did most recently for Zootaxa), it's quite another to browse a large collection.

Today I finally bit the bullet and put something together, which you can see at http://biostor.org/maps/. The website comprises a Google Map showing localities extracted from papers in BioStor, and a list of the papers that have one or more points visible on the map.

In building this I hit a few obstacles. The first is the number of localities involved. I've extracted several thousand point localities from articles in BioStor. Displaying all these on a Google Map is going to be tedious. Fortunately, there's a wonderful library called MarkerCluster, part of the google-maps-utility-library-v3 that handles this problem. MarkerCluster cluster together markers based on zoom level. If you zoom out the markers cluster together, as you zoom in these clusters will start to resolve into their component points. Very, very cool.

The second challenge was to have the list of references update automatically as we move around or zoom in and out on the map. To do this I need to know the bounding box currently being displayed in the map, I can then query the MySQL database underlying BioStor for the localities within the bounding box, using MySQL's spatial extensions. The query is easy enough to implement using ajax, but the trick was knowing when to call it. Initially, listening for the bounds_changed event seemed a good idea. However, this event is fired as the map is being moved (i.e., if the user is panning or dragging the map a whole series of bounds_changed events are fired), whereas what I want is something that signals that the user has stopped moving the map, at which point I can query the database for articles that correspond to the region that map is currently displaying. Turns out that the event I need to listen for is idle (see Issue 1371: map.bounds_changed event fires repeatedly when the map is moving), so I have a function that captures that event and loads the corresponding set of articles.

Another "gotcha" occurs when the region being viewed crosses longitude 180° (or -180°) (see diagram below from http://georss.org/Encodings).

In this case the polygon used to query MySQL would be incorrectly interpreted, so I create two polygons, each with 180° or -180° as one of the boundaries, and merge the articles with points in either of those two polygons.

I've made a short video showing the map in action. Although I've implemented this for BioStor, the code is actually pretty generic, and could easily be adapted to other cases where we want to navigate through a set of objects geographically.

Browsing a digital library using a map from Roderic Page on Vimeo.

Wikispecies RSS feed

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 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.


View Larger Map

H1N1 Swine Flu TimeMap

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.



Gotcha
Although in principle this should have been a trivial exercise (cutting and pasting into existing examples), it wasn't quite so straightforward. The Google Maps RSS feed is a GeoRSS feed, but initially I couldn't get Timemap to accept it. The contents of the <georss:point> tag in the Google Maps feed looks like this:

    <georss:point>
      33.041477 -116.894531
    </georss:point>

Turns out there's a minor bug in the file timemap.js, which I fixed by adding coords= TimeMap.trim(coords); before line 1369. The contents of the <georss:point> 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.