Assembling, Visualizing, and Analyzing the Tree of Life

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Building an API for the Open Tree of Life database

Do you want an app for this?

Screen Shot 2012-08-29 at 9.22.20 PMThe developers of the Open Tree of Life would like to know from the phylogenetic community what kind of information they want to extract from its database when the first draft is released later this year. With those preferences, it is possible to develop an API that gives scientists the opportunity to build their own websites or software packages that use the data.

An API (application programming interface) is a digital tool that allows one website or software program to “talk” to another website to dig up certain pieces of data. For instance, a lot of people use Tweetdeck to navigate the ongoing bombardment of messages in the Twittersphere. In that case, Tweetdeck is connecting to Twitter, through its API, to receive and order the messages according to the preferences of the user.

In case of the Open Tree of Life, an API gives researchers advanced access to the data of about two million species, the phylogenies that have been created to illustrate possible relationships between them, and the underlying data and methods of synthesis. “For example, it will be possible to select smaller trees for specific species or find out how many studies there are for a particular node within the database,” says Karen Cranston, the lead investigator of the project. (more…)


Connecting millions of data points in a graph database

Creating ‘Facebook’ for species

Neo4j screenshotThe Open Tree of Life database is not just a list with about two million species. Information is added about their special characteristics and possible relationships with others as well. “It may become tens or hundreds of million pieces of data when we are all done.”

Stephen Smith, an evolutionary biology professor at the University of Michigan, is working together with the other researchers of the Open Tree of Life project to develop the programs and tools that will be used to construct the full tree of life. Scientists from all over the world can then synthesize all the information in the database.

“We are currently building the back-end of the Open Tree of Life. We need to create software that allows us to put all our information in a graph network, so that we can easily retrieve the information that researchers are specifically looking for.” (more…)


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