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Add Open Tree of Life resolution #233
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TODO:
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hlapp
approved these changes
Apr 8, 2022
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Looks good. See one inline suggestion.
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This PR adds a "Add Open Tree of Life phylogeny" button to the sidebar, which adds the induced subtree from the Open Tree of Life that includes all named taxa used as specifiers across all phyloreferences. Taxa that don't have OTT IDs are ignored, while OTT IDs that not included in the synthetic are ignored. Closes #40.
This appears as a button in the bottom left corner of the screen labeled "Add Open Tree of Life phylogeny":
![Screen Shot 2022-03-29 at 2 48 44 AM](https://user-images.githubusercontent.com/23979/160550764-717367bd-accb-4f24-8301-dc8f962c5d83.png)
Clicking this button doesn't have any obvious signs that anything is happening (I'm not sure where they would go), but once the API calls have completed, a new phylogeny labeled "Open Tree of Life phylogeny" has been added to the Phyx file:
![Screen Shot 2022-03-29 at 2 49 02 AM](https://user-images.githubusercontent.com/23979/160550933-4ee36450-15d2-42a3-b5c5-7059ecd31756.png)
This phylogeny is the induced subtree of all phylogeny nodes that have Open Tree of Life Taxonomy IDs:
![Screen Shot 2022-03-29 at 2 49 33 AM](https://user-images.githubusercontent.com/23979/160551078-b5719755-36c9-48f4-859a-6e8cbff77bb9.png)
(Please ignore the "Primary Reference phylogeny" field; once we close #133, only the "Reference phylogeny" field will remain, and it'll be renamed to something like "Citation").
With the changes I made in 26f836e, this now includes a citation to the Open Tree of Life synthetic phylogeny, as suggested at https://tree.opentreeoflife.org/about/open-tree-of-life -- I've included both the synthetic tree and taxonomy version numbers as reported by the Open Tree API, but only cited the synthetic tree, since we only use the taxonomy to look up nodes on the synthetic tree.
![Screen Shot 2022-03-30 at 2 01 09 AM](https://user-images.githubusercontent.com/23979/160761967-95af83f7-bff4-4374-bc14-4eea9e655c4a.png)