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Add Open Tree of Life resolution #233

Merged
merged 9 commits into from
Apr 27, 2022
Merged

Add Open Tree of Life resolution #233

merged 9 commits into from
Apr 27, 2022

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gaurav
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@gaurav gaurav commented Jan 25, 2022

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

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

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

(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

Base automatically changed from export-as-nquads to master February 15, 2022 23:26
@gaurav gaurav marked this pull request as ready for review February 16, 2022 04:27
@gaurav gaurav requested a review from hlapp February 16, 2022 04:27
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gaurav commented Feb 16, 2022

TODO:

@gaurav gaurav marked this pull request as draft March 29, 2022 06:56
@gaurav gaurav requested review from hlapp and removed request for hlapp March 30, 2022 06:02
@gaurav gaurav marked this pull request as ready for review March 30, 2022 06:02
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Looks good. See one inline suggestion.

src/store/modules/phyx.js Outdated Show resolved Hide resolved
@gaurav gaurav merged commit a9947d1 into master Apr 27, 2022
@gaurav gaurav deleted the add-open-tree branch April 27, 2022 02:34
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