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microbiomedata / sample-annotator

NMDC Sample Annotator
https://microbiomedata.github.io/sample-annotator/static/intro.html
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plug in @StantonMartin's code for ORNL soil type layer #17

Closed ssarrafan closed 2 years ago

ssarrafan commented 3 years ago

Part of larger issue: https://github.com/microbiomedata/nmdc-metadata/issues/330

ssarrafan commented 3 years ago

Met with @wdduncan today and he said to assign to Stan and Bill but that Stan will be training a student to work on this and so it may not be done for a couple of months. I'm leaving in the backlog for prioritization and timing to determine appropriate sprint.

@emileyfadrosh @cmungall

wdduncan commented 3 years ago

moving this to the sample-annotator repo

cmungall commented 2 years ago

We have made good progress with this. @StantonMartin did a first pass here: 86440a2d1d6e7c2946ee4a74dc679f8655e3fb13

Currently this returns values from the source ORNL DAAC vocabulary

These need to be mapped to the mixs fao_class_enum. Added a test for this #23 -- @StantonMartin will get this working

We are also working on tidying the code, see #24

wdduncan commented 2 years ago

Here is a link to the fao soil types in the mixs linkml.

wdduncan commented 2 years ago

See also nmdc-metadata issue https://github.com/microbiomedata/nmdc-metadata/issues/66

wdduncan commented 2 years ago

Adding link to text file with Zobler soil types: https://github.com/StantonMartin/Identify/blob/master/ZOBLERSOILDERIVED_540/ZOBLERSOILDERIVED_540/comp/zsoiltype_key.txt

wdduncan commented 2 years ago

@StantonMartin @cmungall Can we close this ticket?

StantonMartin commented 2 years ago

I think so. Closing.