Comments (10)
Like searching on env_broad_scale of "Terrestrial biome" may not retrieve "subalpine biome" samples
I suggest making an ENVO issue
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These challenges appear to hold for both the soil samples and the surface and benthic water samples
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For now, we are leaning towards using a static env_broad_scale
annotation of "Terrestrial biome" and a static env_medium
annotation of soil
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For env_local_scale
I would like to use the terms that EnvO considers equivalent to the NLCD terms asserted by NEON.
There are all "area of..." terms. I understand that means getting into shadow classes, but I don't think there are consistent axioms from the areas to something else. I will double check.
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The missing terms and inconsistent axioms may mean that users searching though the NMDC data portal may not retrieve all Biosamples that have the qualities the expect.
Like searching on env_broad_scale
of "Terrestrial biome" may not retrieve "subalpine biome" samples
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![Screen Shot 2023-06-12 at 1 07 28 PM](https://private-user-images.githubusercontent.com/25185273/245216510-69b49384-0466-4214-bd00-0b90632c102c.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.if5zL6rTA9NJtJ4iqwXj_6wTxTptzyShiq7d9etgD80)
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Add a USDA soil classification in addition to FAO
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@turbomam @cmungall There was some work over the summer with envo, did this get resolved?
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Yes, terrestrial biome and many other classes with "biome" in the label are classified as a biome by inference now.
'subalpine biome' is not classified as a 'terrestrial biome' at this point. I'm not sure whether it should be either, but I'm certainly not an expert. Do we want to say that an aquatic biome can't be a 'subalpine biome'?
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I think there's still work do do on EnvO biome modeling, but that may not all effect us
For example, a variety of classes are asserted to be subClasses of biome but should probably be inferred.
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Related Issues (20)
- Re-add OmicsProcessing typecode as a valid regex for DataGeneration HOT 1
- Update WorkflowExecution slot: `part_of` to be multi-valued HOT 1
- test if 'exhaustive' examples are really exhaustive
- What does the `see_also` of 'C01033' mean in the definition of `ChemicalConversionProcess` ?
- get `src/data/problem/valid/Database-img_mg_annotation_objects.yaml` to be clearly valid or clearly invalid, or delete it HOT 1
- the `slot_usage` of `part_of` in `classes.WorkflowExecution` should not have `multivalued: false` (berkeley schema) HOT 1
- subsets documentation pages should not reiterate descriptions
- Please replace `AFO:/process#AFP_0000112` mapping for `DissolvingProcess` in berkeley schema
- misc post-typing edits
- add `feature_category` slot to replace `type` as used by FunctionalAnnotation and GenomeFeature
- Schema contributors should run linkml linter
- Schema contributors should perform routine maintenance on their invalid example files HOT 2
- Schema contributors should ensure that there are no circular dependencies between YAML modules
- assign `feature_category` to `FunctionalAnnotation` and `GenomeFeature`
- add python test: classes should not reiterate inherited slots
- eliminate all "exhaustive biosample" examples except for one valid one
- use SPARQL construct instead of relationgraph for generating materialized visualization
- Should the schema build if a prefix is used without being specified HOT 1
- Document process of pulling changes from `nmdc-schema` into Berkeley fork HOT 5
- Prevent accidental commits of generated `project` files HOT 2
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