Draft: add MISIP-MIMS #1002

mslarae13 · 2025-06-23T19:22:10Z

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github-actions · 2025-06-23T19:26:27Z

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mslarae13 · 2025-06-23T19:56:26Z

@sujaypatil96 I don't understand this yamllint fail. I assume some long description isn't structured correctly for the linter.. but IDK what description or how to fix it..can you help / explain?

src/mixs/schema/mixs.yaml

…dardsConsortium/mixs into 1001-add-misip-mims

github-actions · 2025-07-29T00:59:56Z

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'

src/mixs/schema/mixs.yaml

mslarae13 · 2025-07-29T18:16:09Z

src/mixs/schema/mixs.yaml

+        recommended: true
+      internal_standard:
+        recommended: true
+    #class_uri: 


how do I get this?

src/mixs/schema/mixs.yaml

github-actions · 2025-08-15T00:12:53Z

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'

add isotope slot

3b7a986

mslarae13 linked an issue Jun 23, 2025 that may be closed by this pull request

Add MISIP-MIMS #1001

Open

mslarae13 self-assigned this Jun 23, 2025

mslarae13 added this to TWG Activity Track Jun 23, 2025

mslarae13 moved this to In Progress in TWG Activity Track Jun 23, 2025

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mslarae13 added 2 commits June 23, 2025 12:36

add isotopolog & iso label

21eee14

add gradient

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string, not text!

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add gradient pos density

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mslarae13 linked an issue Jun 23, 2025 that may be closed by this pull request

MISIP-MIMS & MISIP-MIMARKS checklist addition #575

Open

19 tasks

mslarae13 changed the title ~~Daft: add MISIP-MIMS~~ Draft: add MISIP-MIMS Jul 1, 2025

mslarae13 commented Jul 1, 2025

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yaml linting errors

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mslarae13 added 3 commits July 28, 2025 17:57

add remaining slots and class

2592a7f

Merge branch '1001-add-misip-mims' of https://github.com/GenomicsStan…

09a0817

…dardsConsortium/mixs into 1001-add-misip-mims

update class

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lint error?

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mslarae13 commented Jul 29, 2025

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mslarae13 commented Jul 29, 2025

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mslarae13 commented Jul 29, 2025

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mslarae13 commented Jul 29, 2025

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question

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mslarae13 commented Jul 29, 2025

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remove excess space

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mslarae13 commented Jul 29, 2025

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mslarae13 commented Jul 29, 2025

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mslarae13 commented Jul 29, 2025

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move requirements to slot and off slot usage

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mslarae13 added 2 commits July 29, 2025 16:12

update misip name

7865c9a

clarify multivalued slots

9878d25

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dd MimsMisip + extension combinations

429273f

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add mims example

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comment lint error

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sierra-moxon added 2 commits August 14, 2025 17:10

fix indentation

5f3bc2b

fix comment spaces

a4d4ea9

Draft: add MISIP-MIMS #1002

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Draft: add MISIP-MIMS #1002

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mslarae13 commented Jun 23, 2025

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mslarae13 commented Jun 23, 2025

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github-actions bot commented Jul 29, 2025

LinkML Linting Results

Summary

Problems per Schema

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

Errors

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github-actions bot commented Aug 15, 2025

LinkML Linting Results

Summary

Problems per Schema

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

Errors

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github-actions bot commented Jun 23, 2025 •

edited

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