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Karen Cranston talks about open licensing and Dryad

Making scientific data available

In case you haven’t seen the video yet, Open Tree of Life investigator Karen Cranston talked about sharing research data in open access data repositories during the Creative Commons 10-year celebration in Raleigh, North Carolina, last December. She mainly focused on the use of CC0 for Dryad, which is a curated general-purpose repository that makes the data underlying scientific publications discoverable and freely reusable. Cranston also mentioned that data availability leads to more citations, which is highly valued in the academic community. You can access the presentation slides as well (link).

Posted by robinblom | April 15, 2013 | Categories: Open data | Tags: CC0, Creative Commons, data repositories, database, digital data, Dryad, open access, open data, open science, open tree of life, science | Leave A Comment »

Interview with Open Tree of Life investigator

Crandall featured on PeerJ blog

Open Tree of Life investigator Keith Crandall is featured on the blog of PeerJ, which is a peer-reviewed, open access journal on the Internet. Crandall is an Academic Editor for PeerJ and is the director of the Computational Biology Institute at George Washington University. He was the editor for the “living fossil” manuscript that got much news media attention last week. Here’s the link to the interview.

Posted by robinblom | April 9, 2013 | Categories: Press releases | Tags: #opentree, fossil, interview, open access, open data, open science, open tree of life, PeerJ, phylogeny | Leave A Comment »

Building an API for the Open Tree of Life database

Do you want an app for this?

The 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. Read the rest of this page »

Posted by robinblom | February 28, 2013 | Categories: Building Open Tree, We need your help! | Tags: #opentree, API, community, database, digital data, evolutionary biology, evolutionary trees, Facebook, graph database, national science foundation, open science, open tree, open tree of life, phylogenies, phylogeny, queries, searching the tree of life, software, species, tree of life, Twitter | 5 Comments »

Connecting millions of data points in a graph database

Creating ‘Facebook’ for species

The 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.” Read the rest of this page »

Posted by robinblom | February 26, 2013 | Categories: Building Open Tree, We need your help! | Tags: #opentree, community, database, digital data, evolutionary biology, evolutionary trees, Facebook, graph, graph database, graph search, neo4j, network, open data, open science, open tree, open tree of life, phylogeny, social media, social network, species, synthesis, tree of evolution, tree of life species, Twitter, What is the Tree of Life | 2 Comments »

“We need a sense of ownership of phylogenetic trees”

Where are the fungi datasets?

A couple thousand fungi phylogeny studies have been published in the past twelve years. Clark University postdoc researcher Romina Gazis has gone through all of them. Now she is working on a bigger challenge: finding all the trees and datasets that were the foundation of those studies.

Ideally, all scientists who publish a phylogenetic tree would also deposit the datasets they used to create such trees at a publicly available online database. That allow other researchers to synthesize data from different sources to advance the knowledge about relationships between certain species and their evolutionary history.

Unfortunately, most of those datasets are not publicly available. Gazis only found datasets for about a quarter of the two-thousand fungi articles she surveyed. “Around 600 studies had tree files available, but not necessarily complete,” she concluded. “Some scientists deposited one but not all the trees.” Read the rest of this page »

Posted by robinblom | January 28, 2013 | Categories: Building Open Tree, We need your help! | Tags: #opentree, community, database, dataset, digital data, evolutionary trees, fungi, journal, national science foundation, open tree of life, phylogeny, science | 4 Comments »

Tree of Life: Are big changes looming on the horizon?

All species like some gadgets

While movie hero James Bond gets his spy gadgets from his loyal developer Q, almost every other species on Earth has to put a little more effort in armoring themselves. But that does not mean they cannot rely on some good ol’ friends to do so. In fact, the acquisition of genes from two or more species through lateral gene transfer can lead to innovations that at times can be painful—sometimes even deadly—to others.

One of those evolutionary novelties is noticeable for certain types of jellyfish that developed the ability to sting after their ancestors acquired a gene from a bacterium and incorporated that material in their own DNA. This gene transmission helped jellyfish to create an innovative defense tool to fend off other species that could endanger them. The result is quite frightening: more humans get killed by jellyfish than sharks. Read the rest of this page »

Posted by robinblom | January 21, 2013 | Categories: Building Open Tree | Tags: #opentree, Archaea, Bacteria, biology, Darwin, DNA, DNA sequencing, domains of life, Eukaryotes, evolution, evolutionary biology, evolutionary trees, frankenstein, horizontal gene transfer, James Bond, jellyfish, lateral gene transfer, lineages, national science foundation, network, open tree of life, phylogeny, research, science, sequencing, species, spider, sushi, tree of life, web | 2 Comments »

Open Tree of Life featured in weekly science journal

Four investigators of the Open Tree of Life project and four postdoc researchers affiliated with the project have published an article in the latest issue of Nature, an international weekly journal of science. They have concluded that, unfortunately, most phylogenetic trees and nucleotide alignments from the past two decades have been irrevocably lost. (“Data deposition: Missing data mean holes in tree of life”)

Click here for the the website of Nature (subscription required).

Posted by robinblom | January 17, 2013 | Categories: Uncategorized | Leave A Comment »

Small portion of phylogenetic data is stored publicly

‘The glass is still pretty empty’

Sometimes you wonder whether the glass is half full or half empty.

But when it is only filled for four percent—the other 96 percent is just air—there is only one conclusion: it is time for more.

At least that is what some scientists in the phylogenetic community argue, because only about four percent of all published phylogenies are stored in places such as TreeBASE or Dryad. Their message is quite simple: it is time to bring together more databases with estimations on how species are possibly related to each other.

Several journals in the evolutionary biology field recently adopted policies that encourage or require contributors to make their data publicly available online. Yet, this only leads to the storage of a very small percentage of ten-thousands of phylogenies that have been constructed in the past few decades.

Of course, there are also other ways to receive data that are not stored on the Internet, but those alternatives are commonly not the most efficient routes. For instance, it is possible to send an email to a scientist who published a phylogenetic tree and “sometimes wait for six months to maybe get a response—either with or without the data,” says Keith Crandall, one of the Open Tree of Life investigators and the founding director of the Computational Biology Institute at George Washington University.

Read the rest of this page »

Posted by robinblom | November 13, 2012 | Categories: Building Open Tree, We need your help! | Tags: database, digital data, Dryad, evolutionary trees, open tree of life, phylogeny, software, TOL, TreeBASE | 2 Comments »

You don’t want to build a new tree from scratch?

‘Let the computer do the work’

Creating a phylogenetic tree is no easy task. It usually involves a complex synthesis of multiple datasets, but it leads to much satisfaction when all work is done—until new data come in.

Then, the process typically starts all over again: building a new tree from scratch.

Mark Holder, a professor of statistical phylogenetics at Kansas University and one of the investigators of the Open Tree of Life project, maintains that there is a real need for scientists to have access to digital tools that save them from doing quite a few labor-intensive procedures.

“In the past, researchers combined information from different trees and then analyzed the data. But they never made good computer systems that allowed for continuous updating. They would not be able to see how an entire tree would look like when they added more data or another individual tree. In that case, they had to start over.”

Read the rest of this page »

Posted by robinblom | October 22, 2012 | Categories: Building Open Tree | Tags: #opentree, database, digital data, evolutionary trees, graph, graph database, network, open tree of life, phylogeny, research, science, social media, software, species | 1 Comment »

Puzzling:

Connecting millions of pieces

Creating the entire tree of life is like completing a jigsaw puzzle with more than two million pieces. And to make it even harder; the illustration of how the solved puzzle would look like is missing.

No one knows precisely how all pieces are related.

This disparity is unmistakably demonstrated by disagreements between evolutionary biologists about how certain species and branches are linked together. Throughout the years they have created a large variety of trees with specific groups of species that contradict each other. For example, one researcher maintains that species A is the closest living relative of species B, but another scientist thinks that species C is actually most closely related to B. Read the rest of this page »

Posted by robinblom | October 15, 2012 | Categories: Building Open Tree, We need your help! | Tags: #opentree, community, conflict, database, digital data, evolutionary trees, hypothesis, open tree of life, phylogeny, research, software, species | 4 Comments »

OPEN TREE OF LIFE Assembling, Visualizing, and Analyzing the Tree of Life