Missing/isolated taxa messages (phase 1)

[jimallman]

This includes the static/generic messages for missing and isolated taxa in the synthetic-tree viewer. See screenshots below for examples. Note that I've removed the awkward phrase "not a proper clade" and switched the messages (most likely explanations) shown for the missing vs. isolated taxon.

[kcranston]

I think the messages might be reversed. The disconnected node happens when the taxa is in taxamachine but is not monophyletic in the synthetic tree.

[jimallman]

OK, I've replaced the original messages for missing vs. orphaned taxa. The text for incertae sedis was a little different. Want new screenshots?

[kcranston]

Here are my suggestions for the message text:

• Case 1 (taxon not found / not in treemachine): This taxon is in our taxonomy but not in our tree synthesis database. This can happen for a variety of reasons, but the most probable is that it is flagged as incertae sedis. If you think this is an error, please add link for feedback / issues
• Case 2 (unconnected taxa): This taxon exists in our taxonomy but is not connected to any other taxa in the synthetic tree. This happens when the taxon is non-monphyletic in contributed phylogenies. To contribute a phylogeny that supports monophyly of this taxon, use our link to curation application.

[jimallman]

Updated screenshots with the revisions above:

[kcranston]

Great! thanks!

[jar398]

Should be "taxon", not "taxa", where used as singular.

I don't like "is not connected" because in fact the taxon is connected to
taxa in the synthetic tree; just via links that are not displayed. I prefer
"is not in the synthetic tree" to "is not connected to any other taxa in
the synthetic tree" as it is simpler and more accurate. If you want
something a bit wordier, maybe "is excluded from the synthetic tree".

Should that maybe be "phylogenetic tree" instead of "phylogeny"?

Jonathan

On Tue, Aug 19, 2014 at 6:13 PM, Karen Cranston notifications@github.com
wrote:

Here are my suggestions for the message text:

• Case 1 (taxa not found / not in treemachine): This taxa is in our
  taxonomy but not in our tree synthesis database. This can happen for a
  variety of reasons, but the most probable is that it is flagged as incertae
  sedis. If you think this is an error, please add link for feedback /
  issues
• Case 2 (unconnected taxa): This taxa exists in our taxonomy but is
  not connected to any other taxa in the synthetic tree. This happens when
  the taxa is non-monphyletic in contributed phylogenies. To contribute a
  phylogeny that supports monophyly of this taxa, use our link to
  curation application.

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