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OpenTreeOfLife / phylesystem-1

doc store for the Open Tree of Life study curation API
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clean up ^ot:curatedType #8

Open kcranston opened 8 years ago

kcranston commented 8 years ago

The nexsons include a property called ^ot:curatedType. In the UI, this is called 'Inference method'. It is currently a pulldown that provides various inference options (Bayesian inference, Maximum Likelihood, Maximum Parsimony, etc) but it used to be a free text field. As you might expect, the field is full of all sorts of free-form descriptions for trees, including software used, Figure numbers, genes used, consensus methods, etc.

If you want to see the list of values, there is a peyotl script for that:

$ python ot_phylesystem_list_property_values.py --set --tree ^ot:curatedType

It would be nice to clean up this field, moving non-standard values into another field (@description, perhaps?) and possibly renaming the field to ^ot:inferenceMethod to match both the UI and the search term for the find_trees API call. Related to the discussion on this otttreeindex issue.

jimallman commented 8 years ago

FYI, there's a stale branch (and a PR that was closed long ago) that addresses these issues, particularly in this commit: https://github.com/OpenTreeOfLife/opentree/pull/598/commits/ad7d5f705b462a0e505afe5c1a23458650460436

GitHub shows the PR as already merged, but the relevant bits are not in current master. (perhaps we merged, then backed out these changes?)