Encyclopedic Tree of Life

Tree of Life image In 1993 I remember discovering the web. It wasn’t much longer after that I discovered the “Tree of Life (ToL).” I was studying for my Ph.D. in evolutionary biology and heard about it by word of mouth. Sometime in 1996 I found it on the web and was intrigued. It has grown since then, though still has a way to go. It’s goal? “… to contain a page with pictures, text, and other information for every species and for each group of organisms, living or extinct.

Today saw the unveiling of the “Encyclopedia of Life (EOL),” which is “an ambitious… project to organize and make available via Encylopedia tree of lifethe Internet virtually all information about life present on Earth.” Carl Zimmer reports on the EOL on his blog and in a NYTimes article.

Those goals overlap a lot it would seem. So I did some checking of the ToL and the EOL for two things that are most interesting to me: genomic information and evolutionary information. A short critique below (with the caveat that EOL is VERY slow today because of the launch):

One species: Drosophila melanogaster. Right off the bat you’ll notice the difference between the two. The Tree of Life is a ‘top down’ approach and the Encyclopedia of Life is a ‘bottom up’ approach. The EOL lists species after species, though at launch they only had 25 “authenticated” species and thousands of nubs. If you were looking for categorization by phylogenetic and evolutionary relationship, you’d be hard-pressed. For example, you can find out the classification for Drosophila melanogaster and related species from the species page, you don’t see much in the way of evolutionary relationships or the ‘big picture’ of evolutionary history (also, bit of a quibble, but taxa are often listed as the ‘generic’ name and not the scientific name, animal instead of animalia. I’d rather see the scientific with the common name in parenthesis). In contrast, the Tree of Life, as it’s name obviously implies, focuses strongly on those evolutionary and phylogenetic relationships. I can work my way down to Drosophila melanogaster by first going to Animalia and a few clicks to Insecta, a few more clicks to Diptera (all the while learning about the taxa and evolutionary relationships) and so on till, well, I could never find the “leaf” of Drosophila melanogaster with all the information about the species and perhaps links to genomic information. Even searches didn’t find a species page, though I know they exist for some species. So, like EOL, it’s lacking in the species page department, but at least I can learn a something about relationships and the taxa.

EOL’s D.m. page does indeed have a lot of information, including links to genomic information (bingo) and more. If that is how the other several million species pages are going to look like, then this will be a wonderful site. The only problem is, this appears that it will be slow going at the moment. Though the EOL does automatic aggregation of data from other sites for it’s pages, the authentication process seems not to be taking advantage of some of the “web 2.0″ possibilities and building community. Several other bloggers have already had their critiques up. Roderic Page over at iPhylo has some words about the lack of content and interaction (no way to download data?) and more. Deepak Singh at bbgm is disappointed that the first release isn’t matching up to the hype the built up to this. I have to say, at this first glance, I’m agreeing with much of the criticism.

With the caveat that there is a lot of potential here.

The Tree of Life group has already shifted to more of a evolutionary and phylogenetic approach. As it says on it’s about page on the overlap of these two sites,

ToL will strengthen its focus on phylogenetic information and the documentation of deeper branches in the tree of life. For the time being, we will still promote the creation of ToL leaf pages, but once the EOL workbench is up and running, we will encourage our contributors to move the development of content for individual species to the EOL platform. The ToL will then import materials for leaf pages from the EOL, while making much of its branch page content and phylogenetic information available for use in the EOL. The EOL has agreed to provide financial assistance to the ToL to support the technical and organizational developments necessary for future ToL/EOL integration.

So perhaps this is a good sign of things to come and more integration and filling out of the data. I hope the take some of the recommendations (community, web 2.0, content, etc) and EOL (and by extension ToL) lives up to the potential.

UPDATE: As Mary comments below, it seems the EOL was so popular today that it was down for at least 2 hours and got over 11.5 million hits in 5 hours according to this article. The article also states that “All the pages have been made by scientists, but in a few months the encyclopedia will start taking submissions from the public, like Wikipedia.” So, perhaps it will be a Wikipedia of Life and use some of that web 2.0 magic. Of course, it will have the downside of trying to figure out how to keep the information quality (unlike the unintentionally hilarious entries of the aboreal octopus or the origins of Kangaroos that was once were or still are entered into the “trustworthy” conservapedia :D ).

PZ Meyers just posted this youtube intro to EOL…

If it lives up to that intro, then it will be pretty cool. I see they had a phylogenetic view… I’ll have to check that once they site is a little less overwhelmed.

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