current land use enum with URL safe characters by turbomam · Pull Request #972 · GenomicsStandardsConsortium/mixs

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

PR Preview Action v1.8.1
🚀 View preview at https://GenomicsStandardsConsortium.github.io/mixs/pr-preview/pr-972/
Built to branch `gh-pages` at 2026-03-11 02:39 UTC. Preview will be ready when the GitHub Pages deployment is complete.

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

 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 · 2026-03-10T23:43:01Z

LinkML Linting Results

Summary

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

Copilot

Pull request overview

This PR updates the MixS LinkML schema to model current land use as a proper enumeration, aiming to use URL-safe tokens for land-use values.

Changes:

Added a new CurLandUseEnum with hierarchical is_a relationships for land-use categories.
Updated the cur_land_use slot to use range: CurLandUseEnum and removed the prior string_serialization-based enumeration description.

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

src/mixs/schema/mixs.yaml

Copilot · 2026-03-10T23:44:25Z

src/mixs/schema/mixs.yaml

+      cypress:
+        is_a: conifers
+      crop trees:
+      christmas trees:


PR title says the current land use enum is using URL-safe characters, but many newly added permissible values still contain spaces (e.g., "crop trees", "industrial areas", "permanent snow or ice"). If these values are intended to be URL-safe identifiers, consider normalizing them (e.g., kebab/snake case) and using aliases/title for human-readable labels; otherwise the PR title/intent should be updated to match the actual change (only removing /).

The PR scope is specifically replacing / characters with - for URL safety — the spaces in other permissible values are a separate concern and consistent with the existing MIxS convention for enum labels.

mines/quarries → mines-quarries and roads/railroads → roads-railroads were renamed for URL safety but the old forms need aliases so existing data remains valid.

github-actions · 2026-03-11T02:37:10Z

LinkML Linting Results

Summary

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

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

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

turbomam mentioned this pull request Jun 2, 2025

alphabetize MIxS enumerations and permissible values #975

Open

This comment was marked as outdated.

Sign in to view

turbomam added 2 commits March 10, 2026 19:40

current land use enum with URL safe characters

54c5962

no PV examples only is_as

21588f5

turbomam force-pushed the 969-cur_land_use-was-an-enum-before-linkml branch from 9b697aa to 21588f5 Compare March 10, 2026 23:41

Copilot AI review requested due to automatic review settings March 10, 2026 23:41

Copilot started reviewing on behalf of turbomam March 10, 2026 23:41 View session

Copilot AI reviewed Mar 10, 2026

View reviewed changes

turbomam mentioned this pull request Mar 10, 2026

Rebase stale open PRs onto main #1178

Open

fix: add aliases for renamed enum values in CurLandUseEnum

db3aa14

mines/quarries → mines-quarries and roads/railroads → roads-railroads were renamed for URL safety but the old forms need aliases so existing data remains valid.

Conversation

turbomam commented May 27, 2025

Uh oh!

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

Uh oh!

github-actions bot commented May 27, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Built to branch gh-pages at 2026-03-11 02:39 UTC. Preview will be ready when the GitHub Pages deployment is complete.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

lschriml commented May 27, 2025

Uh oh!

turbomam commented May 27, 2025

Uh oh!

sujaypatil96 left a comment • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

sujaypatil96 commented Jun 2, 2025

Uh oh!

turbomam commented Jun 3, 2025

Uh oh!

This comment was marked as outdated.

github-actions bot commented Mar 10, 2026

LinkML Linting Results

Summary

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull request overview

Uh oh!

Uh oh!

Copilot AI Mar 10, 2026

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

github-actions bot commented Mar 11, 2026

LinkML Linting Results

Summary

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

5 participants

github-actions bot commented May 27, 2025 •

edited

Loading

Built to branch `gh-pages` at 2026-03-11 02:39 UTC.
Preview will be ready when the GitHub Pages deployment is complete.

sujaypatil96 left a comment •

edited

Loading