addition of taxon-neutral marker gene recovery terms by turbomam · Pull Request #974 · GenomicsStandardsConsortium/mixs

turbomam · 2025-05-28T14:09:19Z

Does not disassociate, deprecate or remove

x16s_recover
16s_recover_software

github-actions · 2025-05-28T14:10:07Z

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 · 2025-05-28T14:13:51Z

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mslarae13 · 2025-07-11T19:01:37Z

+      - marker gene
+      - taxonomy
+    slot_uri: MIXS:0001337
+    range: boolean


maybe I'm just crazy.. I thought boolean was TRUE FALSE but you have yes.. so wouldn't this need to be a yes / no enum?

Good catch, and no you're not crazy. xsd:boolean only accepts true/false/1/0 — the yes example is technically invalid against the declared range: boolean. This is inherited from x16s_recover and affects 5 of the 6 boolean-range slots in MIxS (all use yes or no examples).

The good news: linkml/linkml#3144 (merged to main 2026-03-25, not yet released) adds schema-aware boolean coercion for CSV/TSV. MIxS could add boolean_truthy/boolean_falsy annotations to accept yes/no during loading while outputting canonical true/false.

For this PR, I'll change the example to true to be correct against the current spec. The broader boolean story is tracked in #1191.

github-actions · 2026-03-10T23:34:49Z

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 extends the MIxS LinkML schema to introduce taxon-neutral “marker gene recovery” slots intended to complement existing 16S-specific recovery terms, and wires those new slots into relevant genome checklist classes.

Changes:

Add new slots marker_gene_recov and marker_gene_recov_sw to the schema.
Include the new slots in the Mimag and Misag checklist slot lists.

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turbomam · 2026-03-11T00:13:05Z

Merge order and requirements

This PR should merge before #755, which tests for digit-first slot names — a check that currently fails on x16s_recover / x16s_recover_software. Once this PR's taxon-neutral replacements (marker_gene_recov, marker_gene_recov_sw) land, #755's test should pass.

20-character structured comment name limit

The INSDC Feature Table Specification (Section 3.1) sets a 20-character maximum for qualifier names. The GSC TWG reaffirmed this constraint in issue #763 (Feb 2024, decision: option 3 — keep the limit, leave existing names as-is, apply the constraint going forward).

Both new slot names here are within the limit:

marker_gene_recov — 18 chars ✓
marker_gene_recov_sw — 20 chars ✓

Outstanding Copilot review items

Copilot raised several actionable points (duplicate slot_uri, alias ambiguity with existing x16s_recover/x16s_recover_software slots, singular vs plural title). These should be addressed before merge.

new test expects shorter term names #739 — test that enforces the 20-char limit (needs rework to use pytest, remove generated file deletion)
python test for term name length #736, write tests in python for checking constraints on term attributes like name length #735 — tracking issues for name-length tests
Updates to terms 16S recovered [MIXS:0000065] and 16S recovery software [MIXS:0000066] #801, reduce length of short name of x16s_recover_software [MIXS:0000066] #742 — the x16s naming issues this PR resolves

turbomam · 2026-03-11T02:33:58Z

ID assignment update

New MIXS IDs claimed for this PR's slots:

marker_gene_recov → MIXS:0001354
marker_gene_recov_sw → MIXS:0001355

Registered on both the MIxS new IDs and MIXS ID Space tabs. Schema updated to use these IDs (previously had a conflicting reuse of MIXS:0001338, which belongs to isotope).

See #1004 for broader discussion of ID assignment policy.

marker_gene_recov → MIXS:0001354 marker_gene_recov_sw → MIXS:0001355 Previously reused MIXS:0001337 and MIXS:0001338, which belong to prod_label_claims and isotope respectively. New IDs registered in the MIxS IDs spreadsheet.

github-actions · 2026-03-11T02:36:03Z

LinkML Linting Results

Summary

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

Mark both slots as deprecated with exact replacements pointing to the taxon-neutral marker_gene_recov (MIXS:0001354) and marker_gene_recov_sw (MIXS:0001355) from PR #974. First release cycle of the two-step deprecation process per src/docs/schema_element_deprecation_guide.md. Closes #1186. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

- Use deprecated_element_has_exact_replacement for machine-readable replacement pointers (MIXS:0001354, MIXS:0001355) - Clean up deprecated: field to be a human-readable reason string, not a redundant restatement of the replacement CURIE - Add modified_by with ORCID - Add see_also linking to both the tracking issue (#1186) and the incoming replacement terms PR (#974) Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

xsd:boolean only accepts true/false/1/0. The 'yes' example was inherited from x16s_recover but is technically invalid. Broader boolean coercion support is coming via linkml#3144; tracked in #1191. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

github-actions · 2026-03-30T20:41:22Z

LinkML Linting Results

Summary

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

turbomam linked an issue May 28, 2025 that may be closed by this pull request

Updates to terms 16S recovered [MIXS:0000065] and 16S recovery software [MIXS:0000066] #801

Closed

turbomam requested review from cmungall, mslarae13 and only1chunts May 28, 2025 14:09

turbomam requested a review from Woolly-at-EBI May 28, 2025 14:12

mslarae13 reviewed Jul 11, 2025

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turbomam mentioned this pull request Mar 10, 2026

Updates to terms 16S recovered [MIXS:0000065] and 16S recovery software [MIXS:0000066] #801

Closed

addition of marker gene recovery terms

32b4a17

Copilot AI review requested due to automatic review settings March 10, 2026 23:33

turbomam force-pushed the 801-updates-to-terms-16s-recovered-mixs0000065-and-16s-recovery-software-mixs0000066 branch from 2655164 to 32b4a17 Compare March 10, 2026 23:33

Copilot started reviewing on behalf of turbomam March 10, 2026 23:33 View session

Copilot AI reviewed Mar 10, 2026

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Comment thread src/mixs/schema/mixs.yaml Outdated

Comment thread src/mixs/schema/mixs.yaml

Comment thread src/mixs/schema/mixs.yaml

Comment thread src/mixs/schema/mixs.yaml

turbomam mentioned this pull request Mar 10, 2026

Rebase stale open PRs onto main #1178

Open

This was referenced Mar 11, 2026

new test that fails on digit first or x-digit slot names #755

Open

new test expects shorter term names #739

Open

fix: assign new MIXS IDs for marker gene recovery slots

460e6cf

marker_gene_recov → MIXS:0001354 marker_gene_recov_sw → MIXS:0001355 Previously reused MIXS:0001337 and MIXS:0001338, which belong to prod_label_claims and isotope respectively. New IDs registered in the MIxS IDs spreadsheet.

turbomam requested a review from mslarae13 March 30, 2026 19:10

turbomam mentioned this pull request Mar 30, 2026

Deprecate x16s_recover and x16s_recover_software #1189

Open

turbomam mentioned this pull request Mar 30, 2026

Test boolean truthy/falsy coercion from linkml #3144 against MIxS boolean slots #1191

Open

4 tasks

mslarae13 approved these changes Mar 30, 2026

View reviewed changes

turbomam merged commit c6a23f8 into main Mar 31, 2026
4 checks passed

turbomam deleted the 801-updates-to-terms-16s-recovered-mixs0000065-and-16s-recovery-software-mixs0000066 branch March 31, 2026 02:01

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turbomam commented Mar 11, 2026

Merge order and requirements

20-character structured comment name limit

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turbomam commented Mar 11, 2026

ID assignment update

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turbomam commented May 28, 2025 •

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