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Adjust LinkML schema#5

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Adjust LinkML schema#5
maartenpaul wants to merge 4 commits into
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Propose a meta-moduleschema (module_schema.yaml)
Adjust example REMBI and ISA module schema

@maartenpaul maartenpaul requested a review from Copilot May 15, 2025 19:29

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Pull Request Overview

This PR introduces a meta-module schema and updates example metadata templates for REMBI and ISA by integrating the new module schema and reformatting annotations and slot definitions.

  • Adds a new module_schema.yaml defining the core structure for bioimage metadata modules.
  • Updates REMBI and ISA metadata templates to import and utilize the new module schema with adjusted slot values and standardized annotations.
  • Provides a corresponding JSON schema for REMBI and a detailed YAML schema for ISA high-content screening assays.

Reviewed Changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 2 comments.

File Description
module_schema.yaml Adds a new meta-module schema for structuring module-level metadata.
REMBI-BioSample/REMBI_Biosample_LightMicroscopy_CStrambio-JLacoste_v1-2-0.yaml Updates the REMBI Biosample template to import the module schema and adjusts annotation values.
REMBI-BioSample/REMBI_Biosample_LightMicroscopy_CStrambio-JLacoste_v1-2-0.json Provides a JSON representation of the REMBI Biosample metadata schema.
ISA-Assay/ISA_Assay_High-contentScreening_KatyWolstencroft_v1.0.0.yaml Updates the ISA Assay template with detailed slot definitions and annotations in accordance with the new module schema.

the characteristics of a Biosample used for Light Microscopy observation
module_template_version: v1.2.0
module_scope: Light Microscopy
module_scope_term_accession: edam:topic_3385

Copilot AI May 15, 2025

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The 'module_scope_term_accession' field is defined with a range of type 'uri' in the module schema, so providing a CURIE (e.g. 'edam:topic_3385') may lead to type inconsistencies. Consider using the full URI (e.g. 'http://edamontology.org/topic_3385') to remain consistent with the schema's expected format.

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Comment thread ISA-Assay/ISA_Assay_High-contentScreening_KatyWolstencroft_v1.0.0.yaml Outdated
@maartenpaul maartenpaul requested a review from strambc May 15, 2025 19:37
…0.0.yaml

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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2 participants