behaviour of find_trees based on OTT names or OTT IDs

[kcranston]

In the find_trees method using OTT IDs or names, we return a tree in the results if there is at least one overlapping taxa in these two sets:

• the tips on the tree
• the search taxon and all descendents of the search taxon in OTT

This ends up being very liberal. For example, when searching for trees matching Balaenopteridae, we get 14 matched trees. Ignoring two of the results (TimeTree, and a tree that appears to have been uploaded in error), we see:

• 5 trees that have more than one tip in Balaenopteridae
• 4 large mammal trees that have a single overlapping tip in the ingroup (often a higher taxa)
• 3 trees (lemurs, primates, and fairy armadillos) that have a single Balaenopteridae in the outgroup

Question for folks. What would you expect from this method? Trees with any amount of overlap? Only trees with more than one taxon? Only matches for taxa in the ingroup?

I am not sure how oti implemented this search, but the current v3 method seems to consistently return far fewer trees than the implementation here.

[snacktavish]

I lean towards the most liberal search approach - any overlap. I suppose that could get problematic as we have more trees, or with large or common taxa. People could get a lot of hits that are not what they are looking for. But I think best approach is return 'em all, and let the user decide.

[jimallman]

FWIW, we faced a similar question in the Fossil Calibrations website, and our choice was to provide multiple "cladistic search" tools for trees containing:

• any clade member of taxon A
• a specified tip taxon A
• the mrca of tip taxa A + B

[kcranston]

Coming back to this issue, I find myself often wanting to ask the question "what trees might tell me something about the monophyly of taxon X" (for example, in investigating this PR about arachnids). What I want is "trees that contain at least X descendants of this taxon". Perhaps we need more than one method, or options on the method that allows for different ways of framing this query.

[josephwb]

I don't know if this is possible, but I'd like to perform a query including all of the following:

1. Studies that include 3 or more taxa from my clade of interest (say, oh, Aves)
2. Those taxa should all be in the ingroup
3. The trees should be well-curated (including "preferred tree" annotation)

Getting a tree with only one exemplar is not useful, especially if it is in the outgroup. Having a "phylogenetically informative" search option (minimum of 3 taxa for rooted trees) seems like it would be useful.

[jar398]

Sketch of implementation: In create_otu_table.py, you modify parent_closure to maintain a counter for each ott id (from the study + all ancestors in OTT), and increment the counter at every step along the ancestor chain. So instead of returning a set, parent_closure now returns a map from OTT id to count. The caller writes an additional column to the csv file it's preparing, and this becomes an additional column of some table.