current land use enum with URL safe characters #972

turbomam · 2025-05-27T13:56:45Z

No description provided.

github-actions · 2025-05-27T13:57:31Z

LinkML Linting Results

Summary

	Count
Schemas Checked	1
Schemas with Error	1
Schemas with Warning	0
Total Errors	15
Total Warnings	0

Problems per Schema

/home/runner/work/mixs/mixs/src/mixs/schema/mixs.yaml

Errors

recommended: Slot 'soil_pH' does not have recommended slot 'description'
recommended: Slot 'water_pH' does not have recommended slot 'description'
recommended: Subset 'combination_classes' does not have recommended slot 'description'
recommended: Subset 'sequencing' does not have recommended slot 'description'
recommended: Subset 'environment' does not have recommended slot 'description'
recommended: Subset 'nucleic acid sequence source' does not have recommended slot 'description'
recommended: Subset 'investigation' does not have recommended slot 'description'
standard_naming: Slot has name 'HACCP_term'
standard_naming: Slot has name 'IFSAC_category'
standard_naming: Slot has name 'air_PM_concen'
standard_naming: Slot has name 'ferm_pH'
standard_naming: Slot has name 'microb_start_taxID'
standard_naming: Slot has name 'soil_pH'
standard_naming: Slot has name 'spikein_AMR'
standard_naming: Slot has name 'water_pH'

github-actions · 2025-05-27T14:01:09Z

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turbomam · 2025-05-27T14:16:15Z

src/mixs/schema/mixs.yaml

+      cities:
+      conifers:
+        examples:
+          - value: cypress


probably want to keep "conifers: pine"

TIL the practice of adding examples on PV's! ✅

I don't think PVs should ever have examples

Will switch all examples to PVs of their own and assert is_a between them (hemlock) and their super-classes (conifer)

lschriml · 2025-05-27T14:20:13Z

As discussed we need to enumerate these longer lists as option values:
e.g. conifer
conifer:pine

Instead of having them listed as 'examples' in LinkML.

turbomam · 2025-05-27T15:10:13Z

As discussed we need to enumerate these longer lists as option values: e.g. conifer conifer:pine

Instead of having them listed as 'examples' in LinkML.

Thanks @lschriml

Could you please look though these observed values

cur_land_use was an enum before LinkML #969 (comment)
And this gap analysis
cur_land_use was an enum before LinkML #969 (comment)

I would like to analyze how much of the hierarchy should be captured in MIxS per se

cur_land_use was an enum before LinkML #969 (comment)

And reach out to the original contributors of this term to see what kinds of revisions they are comfortable with vs what really needs to be left as is

sujaypatil96

Awesome job turning the string_serialization on cur_land_use to a enumeration. I added a few comments on if/how we can possibly further enrich the CurLandUseEnum (by adding meanings)?

sujaypatil96 · 2025-05-29T14:04:18Z

src/mixs/schema/mixs.yaml

+      cities:
+      conifers:
+        examples:
+          - value: cypress


TIL the practice of adding examples on PV's! ✅

sujaypatil96 · 2025-05-29T14:09:58Z

src/mixs/schema/mixs.yaml

@@ -25,6 +25,99 @@ subsets:
  nucleic acid sequence source:
  investigation:
 enums:
+  CurLandUseEnum:
+    permissible_values:
+      badlands:


Can we add meanings to some of these PV's?

For example, is this an appropriate meaning for the badlands PV? http://purl.obolibrary.org/obo/ENVO_00000127

This is a really good idea @sujaypatil96

@cmungall and I discussed it today. Chris suggested focusing our PV meaning efforts on

enums where virtually all of the PVs would have a mapping to a well-maintained ontology

slots that are already being frequently used in INSDC Biosamples

I don't think 2 is true here, and I think 1 might be very difficult to accomplish because the current land use PVs are a mixture of land uses (which might be in EnvO) and organisms that might be found on land being used in some way. The organism names are a mixture of singular and plural, and may have many to many mappings within NCBI taxonomy

So I am going to skip PV meaning sin the PR

sujaypatil96 · 2025-05-29T14:10:32Z

src/mixs/schema/mixs.yaml

+  CurLandUseEnum:
+    permissible_values:
+      badlands:
+      cities:


Similarly, meaning for cities – http://purl.obolibrary.org/obo/ENVO_00000856

sujaypatil96 · 2025-06-02T20:56:57Z

Looks like there's a merge conflict that needs resolution on this PR @turbomam?

turbomam · 2025-06-03T15:33:42Z

ncbi_metadata.biosamples_attributes.cur_land_use.csv

github-actions · 2025-06-06T20:45:43Z

LinkML Linting Results

Summary

	Count
Schemas Checked	1
Schemas with Error	1
Schemas with Warning	0
Total Errors	13
Total Warnings	0

Problems per Schema

/home/runner/work/mixs/mixs/src/mixs/schema/mixs.yaml

Errors

recommended: Subset 'combination_classes' does not have recommended slot 'description'
recommended: Subset 'sequencing' does not have recommended slot 'description'
recommended: Subset 'environment' does not have recommended slot 'description'
recommended: Subset 'nucleic acid sequence source' does not have recommended slot 'description'
recommended: Subset 'investigation' does not have recommended slot 'description'
standard_naming: Slot has name 'HACCP_term'
standard_naming: Slot has name 'IFSAC_category'
standard_naming: Slot has name 'air_PM_concen'
standard_naming: Slot has name 'ferm_pH'
standard_naming: Slot has name 'microb_start_taxID'
standard_naming: Slot has name 'soil_pH'
standard_naming: Slot has name 'spikein_AMR'
standard_naming: Slot has name 'water_pH'

current land use enum with URL safe characters

06928b3

turbomam requested a review from mslarae13 May 27, 2025 13:56

turbomam linked an issue May 27, 2025 that may be closed by this pull request

cur_land_use was an enum before LinkML #969

Open

turbomam commented May 27, 2025

View reviewed changes

sujaypatil96 reviewed May 29, 2025

View reviewed changes

no PV examples only is_as

fc973dc

turbomam requested review from sujaypatil96 and cmungall June 2, 2025 20:12

turbomam mentioned this pull request Jun 2, 2025

alphabetize MIxS enumerations and permissible values #975

Open

Merge branch 'main' into 969-cur_land_use-was-an-enum-before-linkml

9b697aa

current land use enum with URL safe characters #972

Are you sure you want to change the base?

current land use enum with URL safe characters #972

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turbomam commented May 27, 2025

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github-actions bot commented May 27, 2025

LinkML Linting Results

Summary

Problems per Schema

/home/runner/work/mixs/mixs/src/mixs/schema/mixs.yaml

Errors

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lschriml commented May 27, 2025

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turbomam commented May 27, 2025

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sujaypatil96 commented Jun 2, 2025

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turbomam commented Jun 3, 2025

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github-actions bot commented Jun 6, 2025

LinkML Linting Results

Summary

Problems per Schema

/home/runner/work/mixs/mixs/src/mixs/schema/mixs.yaml

Errors

Uh oh!

Uh oh!

github-actions bot commented May 27, 2025 •

edited

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Built to branch `gh-pages` at 2025-06-06 20:49 UTC.
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sujaypatil96 left a comment •

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