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README.textile

refine-opentree

A extension for Google Refine to display phylogenetic trees from the OpenTreeOfLife.
Developed with Version 2.5 [r2407].

Installation

Copy the opentree folder into the extensions folder of your Google Refine installation. (Note that it may be lost during upgrades – work in progress).

Restart Google Refine.

Usage

Select “Opentree” from the drop-down menu of the column which contains opentree taxonomy IDs (AKA “ott” IDs). For details about how to apply ott_ids to your data see the wiki. (The subdirectory opentree-utils includes a Jython script to help application of ott_ids to data in Google Refine). These will be passed to the OpenTree API to request a Newick format induced subtree, which is displayed using D3.
The induced subtree is calculated based on the current set of filtered rows, so you can facet your dataset in different ways and display phylogenetic trees for each subset.

Build it yourself

Assuming you have installed the “opentree” folder into your Google Refine extensions directory, execute “ant” from there and the extension will be recompiled and repackaged. You will need to restart Google Refine for any changes to take affect.

Credits

The refine-opentree extension was developed as part of the TreeForAll hackathon, Sept 15-19th 2014, supported by Open Tree of Life, Arbor and NESCent HIP.
refine-opentree is based on the sample extension refine-stats developed by Joe Germuska and Christopher Groskopf as part of the Newsapps team at the Chicago Tribune.

The visualisation was developed with reference to examples developed by Jason Davies and kueda.

License

MIT.

About

An extension for Google/Open Refine to display phylogenetic trees from the Open Tree of Life.

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