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OneZoom: a fractal explorer for the tree of life.

Rosindell J, Harmon LJ - PLoS Biol. (2012)

View Article: PubMed Central - PubMed

Affiliation: Division of Biology, Imperial College London, Silwood Park Campus, Ascot, Berkshire, United Kingdom. james@rosindell.org

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Our knowledge of the tree of life—a phylogenetic tree summarizing the evolutionary relationships among all life on Earth—is expanding rapidly. “Mega-trees” with millions of tips (species) are expected to appear imminently (for example, see http://www.opentree.wikispaces.com)... Trees with millions of tips, richly embellished with additional data, can now be easily explored within the web browser of any modern hardware with a zooming user interface similar to that used in Google Maps... Recent methods of phylogenetic tree visualization attempt to buy extra space in the paper paradigm—for example, by using walls consisting of multiple displays (see Figure 7a in )... This approach is costly and does not give tree visualization capabilities to the masses, which is what is really needed... Furthermore, expensive display technology does not really solve the problem—according to our estimates, even the most advanced technology, such as NASA's “Hyperwall2” of 128 LCD displays, would not be large enough to clearly display 5,000 tip trees using conventional techniques... Other currently available methods make exploration of phylogenetic trees interactive, enabling the user to expand or magnify parts of the tree that may be too small to see in detail at the scale of the screen... Hyperbolic tree browsers, are a good example of this and they can display large trees, but users do not find them intuitive and we don't see the inclusion of rich metadata as being realistically achievable... Fractals are objects that look similar at different scales and have a dimension that is not a whole number; they often appear in the natural world ,... For example, an effective lung requires a large surface area to be packed into a small a volume—its surface is therefore so convoluted and labyrinthine that at some scales it can be regarded mathematically as having a dimension greater than two (a surface) but less than three (a solid object)... Data is always displayed in both intuitive and raw formats... For example, in the “natural” view of the tree of life (see Figure 3), the balance at each node (indicative of the ratio of species richness in each descendent branch) can be taken in at a glance from the thickness and angles of the branches, but the raw numbers can also be found by zooming in on the nodes... The phylogenetic tree is also the most logical structure within which to explore the breadth of biodiversity on Earth, and so OneZoom could potentially be used to browse existing ecological databases of species such as the Encyclopedia of Life (http://eol.org/)... The logical way to do this is to build around the tree of life visualized using OneZoom; we may yet see the Google Maps equivalent for all life on earth.

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An example IFIG of a 408,135-tip phylogeny of small-subunit RNAs using data from SILVA [9].
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pbio-1001406-g002: An example IFIG of a 408,135-tip phylogeny of small-subunit RNAs using data from SILVA [9].

Mentions: We introduce a new phylogenetic tree viewer that allows interactive display of large trees. The key concept of our solution is that all the data is on one page so that all the user has to do is zoom to reveal it—hence the name OneZoom (http://www.onezoom.org). Our interface is analogous to Google Earth, where one can smoothly zoom into any local landmark from a start page showing the whole globe, recognizing familiar landmarks at different scales along the way (e.g., continents, countries, regions, and towns). Equivalently, OneZoom can zoom smoothly to one tip of the tree of life—say, human beings—passing the familiar clades of animals, vertebrates, mammals, and primates at different scales along the way (see Figure 1, which used data from [8]). Trees with millions of tips may require a page of paper larger than the observable universe to be printed: they break the paper paradigm, but on screen, users can still easily zoom in through the tree to any point of interest (see Figure 2, which used data from [9]).


OneZoom: a fractal explorer for the tree of life.

Rosindell J, Harmon LJ - PLoS Biol. (2012)

An example IFIG of a 408,135-tip phylogeny of small-subunit RNAs using data from SILVA [9].
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3472976&req=5

pbio-1001406-g002: An example IFIG of a 408,135-tip phylogeny of small-subunit RNAs using data from SILVA [9].
Mentions: We introduce a new phylogenetic tree viewer that allows interactive display of large trees. The key concept of our solution is that all the data is on one page so that all the user has to do is zoom to reveal it—hence the name OneZoom (http://www.onezoom.org). Our interface is analogous to Google Earth, where one can smoothly zoom into any local landmark from a start page showing the whole globe, recognizing familiar landmarks at different scales along the way (e.g., continents, countries, regions, and towns). Equivalently, OneZoom can zoom smoothly to one tip of the tree of life—say, human beings—passing the familiar clades of animals, vertebrates, mammals, and primates at different scales along the way (see Figure 1, which used data from [8]). Trees with millions of tips may require a page of paper larger than the observable universe to be printed: they break the paper paradigm, but on screen, users can still easily zoom in through the tree to any point of interest (see Figure 2, which used data from [9]).

View Article: PubMed Central - PubMed

Affiliation: Division of Biology, Imperial College London, Silwood Park Campus, Ascot, Berkshire, United Kingdom. james@rosindell.org

AUTOMATICALLY GENERATED EXCERPT
Please rate it.

Our knowledge of the tree of life—a phylogenetic tree summarizing the evolutionary relationships among all life on Earth—is expanding rapidly. “Mega-trees” with millions of tips (species) are expected to appear imminently (for example, see http://www.opentree.wikispaces.com)... Trees with millions of tips, richly embellished with additional data, can now be easily explored within the web browser of any modern hardware with a zooming user interface similar to that used in Google Maps... Recent methods of phylogenetic tree visualization attempt to buy extra space in the paper paradigm—for example, by using walls consisting of multiple displays (see Figure 7a in )... This approach is costly and does not give tree visualization capabilities to the masses, which is what is really needed... Furthermore, expensive display technology does not really solve the problem—according to our estimates, even the most advanced technology, such as NASA's “Hyperwall2” of 128 LCD displays, would not be large enough to clearly display 5,000 tip trees using conventional techniques... Other currently available methods make exploration of phylogenetic trees interactive, enabling the user to expand or magnify parts of the tree that may be too small to see in detail at the scale of the screen... Hyperbolic tree browsers, are a good example of this and they can display large trees, but users do not find them intuitive and we don't see the inclusion of rich metadata as being realistically achievable... Fractals are objects that look similar at different scales and have a dimension that is not a whole number; they often appear in the natural world ,... For example, an effective lung requires a large surface area to be packed into a small a volume—its surface is therefore so convoluted and labyrinthine that at some scales it can be regarded mathematically as having a dimension greater than two (a surface) but less than three (a solid object)... Data is always displayed in both intuitive and raw formats... For example, in the “natural” view of the tree of life (see Figure 3), the balance at each node (indicative of the ratio of species richness in each descendent branch) can be taken in at a glance from the thickness and angles of the branches, but the raw numbers can also be found by zooming in on the nodes... The phylogenetic tree is also the most logical structure within which to explore the breadth of biodiversity on Earth, and so OneZoom could potentially be used to browse existing ecological databases of species such as the Encyclopedia of Life (http://eol.org/)... The logical way to do this is to build around the tree of life visualized using OneZoom; we may yet see the Google Maps equivalent for all life on earth.

Show MeSH