I think I now "get" the Encylopedia of Life

The Encylopedia of Life (EOL) has been relaunched, with a new look and much social media funkiness. I've been something of an EOL sceptic, but looking at the new site I think I can see what EOL is for. Ironically, it's not really about E. O. Wilson's original vision (doi:10.1016/S0169-5347(02)00040-X:

Imagine an electronic page for each species of organism on Earth, available everywhere by single access on command. The page contains the scientific name of the species, a pictorial or genomic presentation of the primary type specimen on which its name is based, and a summary of its diagnostic traits. The page opens out directly or by linking to other data bases, such as ARKive, Ecoport, GenBank and MORPHOBANK. It comprises a summary of everything known about the species’ genome, proteome, geographical distribution, phylogenetic position, habitat, ecological relationships and, not least, its practical importance for humanity.

We still lack a decent database that does this. EOL tries, but in my opinion still falls short, partly because it isn't nearly aggressive enough in harvesting and linking data (links to the primary literature anyone?), and has absolutely no notion of phylogenetics.

In terms of doing science I don't see much that I'd want to do with EOL, as opposed, say, to Wikipedia or existing taxonomic databases. But thinking about other applications, EOL has a lot of potential. One nice feature is the ability to make "collections". For example, Cyndy Parr has created a collection called Fascinating textures, which is simply a collection of images in EOL (I've included some below):


What is nice about this is that it cuts across any existing classification and assembles a set of taxa that share nothing other than having "fascinating textures". This ability to tag taxa means we could create all sorts of interest sets of taxa based on criteria that are meaningful in a particular context. For example, egotist that I am, I created a collection called Taxa described by Roderic Page, which includes the one crab and 6 bopyrid isopods that I described in the 80's.

Putting on my teaching hat, I'm involved in teaching a course on animal diversity and could imagine assembling collections of taxa relevant to a particular lecture (either taxonomically, or based on some other criteria, such as all parasites of a particular taxon, or all organisms found associated with deep sea vents. Other collections could be built by people or organisations with content. For example, lists of top ten new species, lists of species for which the BBC has content, etc.

In this sense, EOL becomes a tagging service for life, a bit like delicious. The social network side of things is still a little clunky —there doesn't seem to be a notion of "contacts" or "friends", and it needs integration with existing social networks — but I think I now "get" what EOL is for.

iSpecies gets automated tagging

Given that the clones are hot on my heels, I feel the need to add more bells and whistles to iSpecies. The first new feature is automated tagging, and uses Yahoo's Term Extraction API. I send the titles of any papers found, and the Wikipedia snippet, and Yahoo returns keywords ("tags").


As an example, here are the tags for one of my favourite animals, Helice crassa.

mud crabs mangrove estuary muddy sediments mud crab sea coasts mud flats sex ratios habitat preferences activity patterns laboratory conditions estuarine gills burrows endemic respiration original article morphology ventilation dana biology

I think these give a nice sense of what we know about this crab.

I'm storing the tags for future analysis. I think there are some interesting ideas to explore, such as clustering the tags into meaningful groups. I'm also interested in how much we can learn about an organism based on these keywords. Can we automatically infer something about the ecology of the organism?

There is also scope for adding some semantics. Some of these tags are taxon names, and some refer to geographic places. Some are concepts, which could be linked to the relevant page in Wikipedia (Faviki is an example of this approach). At present the tags aren't clickable (i.e., you can't query by tag), but that would be a useful feature. One could get taxa that were tagged with a given term, such as "estuarine". For now, it's a quick way to get a sense of what we know about a taxon.

iPhone, barcodes, and natural history museums

One of my pet peeves is how backward natural history museums are in grasping the possibilities the Internet raises. Most electronic displays in museums have low information content, and are doomed to obsolescence. Traditional media (plaques, labels) have limited space, and also date quickly. For example, the Natural History Museum in London has a skeleton of Diplodocus carnegiei (see photo below by EmLah). This is one of many replicas distributed around the world.


The plaque describing this fossil has fairly minimal information. Wikipedia, however, has a nice article on Diplodocus, which includes a public domain image of the replica skeleton being presented to the trustees of the British Museum of Natural History in 1905.

Given the limitations of physical media, museum labels and plaques will always be small, and will often be out of date. Wikipedia, of course, can be kept current, and anybody can contribute.

So, the trick is to link the physical object to the Internet. This is now trivial thanks to mobile tagging. By pointing a mobile phone with a camera at a 2D barcode, one can go from physical object to web site.


Here is a 2D barcode for the URL of the Wikipedia article on Diplodicus. Imagine taking your iPhone, pointing it at this barcode, and being taken to the Wikipedia page. If museums were clever, they could set out their own Wiki, and mobilise the combined skills of the museum staff, volunteers, and visitors to populate it.

Now that the iPhone has applications, imagine creating an application that read these barcodes. Kevin Chiu at Columbia has a made one, and there are others out there. Museums could build on this, brand it with their logo, and greatly enhance visitor experience.

Wonder if anyone is doing this...?