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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/
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Better explanation of "Review conflicting instances" tool #523

Open jimallman opened 9 years ago

jimallman commented 9 years ago

Email from @rgazis:

I might have missed this when the tool was being developed/discussed but I have no idea what this means, “Review all conflicting instances of a mapped taxon and choose an exemplar.”

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It is clear that these taxa are paraphyletic in the tree but I do not know what “Mark as exemplar for mapped taxon means”? The legend does not explain what the curator or contributor should do with the conflict. This section does influence the quality of the study so I think it is important to be clear about this.

image

jimallman commented 9 years ago

For proper synthesis, we need to clarify (choose a single taxon exemplar) whenever a given taxon name is mapped to multiple, non-sibling nodes in a tree (thus "conflicting instances"). The need is described in more detail in this shared document.

This feature was added in pull request #269 and improved in #270. Its use is explained in this announcement to the 'opentree-software' Google group.

As you noticed, unresolved conflicts do affect the "study quality" score, but note that this just provides feedback and encouragement to the curator. This score is not used by treemachine to select studies or trees for synthesis!

I'm not sure how we can make this feature more clear in the curation app, without linking out to a long discussion or the docs above. Suggestions are welcome!

rgazis commented 9 years ago

Hi Jim, thanks for your answer and link to the document.

From what I understood, this case, in which a taxon appears as paraphyletic in a study/tree, the contributor would have to choose the taxon/terminal that corresponds to the true representative of the species/genus (i.e., a lineage representing the type in case this has been included in the analysis, or the clade corresponding to the "sensu stricto".

These cases are very common in fungal studies. Many authors do no revise the problem in the same study, so species are not transferred to their correct placement within the taxonomy. Sometimes the true clade/branch representing the genus/species is not indicated in the figure presented in the publication but in same cases the author does include a annotation.

I think this is an important annotation that the author of the study and hopefully who will be contributing and uploading the tree into the database, will resolve easily. Maybe it should be explained that if taxa appear as paraphyletic the author should select which one terminal/clade represents the "sensu stricto".

Romina