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OpenTreeOfLife / opentree

Opentree browsing and curation web site. For overarching or cross-repo concerns, please see the 'germinator' repo.
http://tree.opentreeoflife.org/
BSD 2-Clause "Simplified" License
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"choose an exemplar" option #766

Open rgazis opened 8 years ago

rgazis commented 8 years ago

Hi When curating a study and trying to address the issues that pop-up in red such as:

Review all conflicting instances of a mapped taxon and choose an exemplar.

If the terminal/label causing the issue is paraphyletic e.g.

https://tree.opentreeoflife.org/curator/study/edit/pg_1669/?tab=trees&tree=tree5902

In the case of Epichloe amarillans is fine because the taxa itself is monophyletic.

screen shot 2015-09-28 at 3 02 43 pm

But in the case of Epichloe typhina, this taxa is paraphyletic, therefore when selecting an exemplar terminal to represent that taxa we are favoring some phylogenetic relationship/placement over other.

screen shot 2015-09-28 at 3 05 29 pm

I am assuming that the terminals that are not selected as exemplars and appear more than once in the tree are pruned?
I think this might create confusion for people uploading studies with redundant and polyphyletic taxa.

Romina

rgazis commented 8 years ago

Example in which the MRCA "test" pinpoints problems in the tree

https://tree.opentreeoflife.org/curator/study/edit/pg_1165/?tab=trees

The MRCA of the taxa in the tree should be Nectriaceae even Dactylella ambrosia, since it is the current name for Fusarium ambrosium

screen shot 2015-09-28 at 5 21 02 pm

BUT when searching IF for Dactylella ambrosia, this is classified as screen shot 2015-09-28 at 5 24 40 pm

SO…I guess OTT follows the second one because the MRCA test gives "Pezizomycotina" as result and not Nectriaceae. Could this be introducing conflict and not allowing the trees to pass through tree machine?

Romina