An extension for Google/Open Refine to display phylogenetic trees from the Open Tree of Life.
JavaScript Java Python CSS
Switch branches/tags
Nothing to show
Clone or download
Pull request Compare This branch is 12 commits ahead of newsapps:master.
Latest commit 232b7ce Sep 19, 2014
Failed to load latest commit information.
opentree Moved servlet lib Sep 19, 2014
opentreeutils Added util script to help application of ott_ids Sep 19, 2014
.gitignore Initial import. Nov 17, 2010
README.textile Readme mods Sep 19, 2014



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


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.


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.


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.